VictorJuiz/thesis huggingface dataset:
Hemispatial neglect: An evaluation of novel assessment methods and rehabilitation

Hemispatial neglect, is a major cause of post-stroke disability and poor functional recovery. Hence, identifying sensitive methods to assess and rehabilitate neglect is important.
Chapters 3 and 4 focused on development of novel assessment techniques for representational neglect. The ‘Shopping Mall’ and ‘Clock Cueing’ tasks improved upon previous tests and were useful in identifying dissociations in representational neglect based on type of stimuli (topological, non-topological) and time of assessment (pre-stroke, post-stroke) in chronic stroke patients.
Chapters 5 and 6 investigated the efficacy of offline inhibitory repetitive Transcranial Magnetic Stimulation (rTMS) in producing short (&LT;1 month) and long term (>6 months) changes in visual neglect behaviour. Overall, the findings from these chapters were limited due to lack of sufficient power. After controlling for the effect of baseline performance, the Intervention group’s Activities of Daily Living scores significantly improved in the short-term post rTMS, as compared to the Control group. The fMRI task attempted to recruit attention-based top down modulation of sensory activity. It revealed relative hypoactivation of the right occipital lobe in the four left neglect patients tested, both pre and post rTMS, when compared to elderly controls.
Chapter 7 explored cognitive predictors of spatial and object neglect in the sub-acute stage after controlling for demographic and stroke related factors, using multivariate blocked logistic regressions. Cognitive performance indicative of spatial attention and selective attention to local features predicted both spatial and object neglect. In addition, coding of spatial relations between features also predicted spatial neglect. Suggestions for combining neglect rehabilitation techniques to target these cognitive processes are discussed.
Overall, this thesis provides novel methods to improve representational neglect assessment and highlights the importance of ancillary cognitive domains in contributing to both representational and visual neglect. The rTMS research provides study design-related insights to incorporate in future studies with larger patient samples.

Keywords: Neuroplasticity
Transcranial magnetic stimulation
Visual neglect
rTMS
Cognitive testing
Spatial attention
Spatial neglect
Rehabilitation
Representational neglect
Object neglect
Advisor: Husain, M
Chechlacz, M
Optimal decision agents? Biases during voluntary information sampling using eye-tracking

This thesis aims to understand the policy by which humans sample information, and how this policy influences perceptual decision-making. We will address this question using a variety of methods, including behavioural measures, computational modelling, and eye tracking. First, we will highlight the importance of considering an explicit information sampling policy as an integral component of the decision-making process. Secondly, we will focus on the determinants of this information sampling policy. Finally, we will address potential methodological concerns and provide a novel analysis approach to combat these concerns.

Advisor: Summerfield, C
Role of carbonic anhydrase catalysis and gap junctional coupling in regulating ph in pancreatic ductal adenocarcinoma (PDAC)

Pancreatic ductal adenocarcinoma (PDAC) develops from the acinar cells of the exocrine pancreas. PDAC tumours are hypoxic and produce a characteristically acidic microenvironment hypothesised to favour more aggressive phenotypes. My thesis work concerned the acid-handling mechanisms in 2-D (monolayer) or 3-D (spheroid) PDAC culture, to underpin survival advantages under acid-stress. The dependence on aerobic glycolysis was assessed in PDAC cells to appreciate the metabolic lactic acid-production. Fluorescence imaging revealed variances in H+ buffering capacity between PDAC cell lines. Activity of intra- and extracellular carbonic anhydrase (CA) enzymes facilitating CO2/HCO3- buffer equilibration revealed the highest extracellular CA-activity in glycolytic Colo357 cells. Interestingly, fluorescence recovery after photobleaching (FRAP) revealed strong connexin 43 (Cx43)-mediated cell-to-cell diffusive coupling in Colo357 cells. Photolytic H+-uncaging producing local acid-disturbances at the hypoxic core of Colo357 spheroids, revealed a major Cx43-mediated acid neutralising HCO3 flux towards the core. The secondary-active HCO3- uptake was shown to take place in the spheroid rim, rather than at the core, because NBCe1 inhibition by DIDS only affected acid-handling at the core of Cx43-coupled spheroids, but not of Cx43-uncoupled spheroids. Normoxic cells in the spheroid rim thereby demonstrated metabolic altruism by donating actively imported HCO3- ions to hypoxic cells via gap junctions. Cx43 channels were also shown to transmit lactate, and in Colo357 spheroids, 80% of lactate at the core was vented via Cx43 channels compared to canonical MCT transport. Moreover, Cx43-coupling confers a survival advantage to cells at the proliferating spheroid rim, as demonstrated by co-culturing wild type (Cx43 positive) cells with GFP-expressing Cx43 knockdowns. Furthermore, orthotopic MiaPaCa2 xenografts models showed increased Cx43 staining at invasive sites, indicating the enrichment of a more aggressive phenotype in Cx43-positive cells. Overall, my studies have confirmed the importance of HCO3- as a base for neutralising cancer-derived acids and demonstrated novel pathways for venting glycolytic products.

Advisor: Swietach, P
Vaughan-Jones, R
Consumer theory

This thesis consists of three self-contained chapters covering topics in consumer theory. The first chapter presents an estimator for a Marshallian demand function which not only obeys all of the standard assumptions of consumer theory but will also converge to any true demand function which also obeys these standard assumptions. The second chapter explores Giffen behavior in the context of financial assets. The chapter finds that an agent with Maxmin preferences almost always displays Giffen behavior in some financial environments. Giffen behavior is also characterized for other classes of preferences. The last chapter, coauthored with one of my supervisors: John K.-H. Quah, develops a revealed preference test for weakly separable preferences in the spirit of Sydney Afriat. Unlike previous tests, ours does not impose concavity and applies to nonlinear budgets.

Keywords: Consumer Theory
Advisor: Quah, J
Crawford, I
The view from the fountain head: the rise and fall of John Gwenogvryn Evans

John Gwenogvryn Evans was an important figure in late nineteenth and early twentieth century Welsh Celtic Studies, because he published accurate diplomatic editions of medieval manuscripts that are still used today. He also compiled an important and detailed Report on Welsh Manuscripts for the Historic Manuscripts Commission that was of significant utility to scholars of his day, and still has uses for its detailed description of manuscripts.
His extraordinary talent for accuracy in the reproduction of medieval script came to the attention of John Rhŷs, then Professor of Celtic at Jesus College, Oxford. Through Rhŷs he was exposed to the best scholarship of his day, and with the assistance of scholars such as Egerton Phillimore and John Morris Jones, he was enabled to produce work of enduring value. Due to his limited training in Welsh linguistics, and in research methodology, there were, from the start, serious flaws in his interpretation of early Welsh. Later, on losing contact with academic influences due to unwise actions, he fell into a pseudoscientific mentality more common earlier in the 19th century, seeking to find historical fact in poetry of legend and prophecy. Major errors arose from his later inclination to consider the date of a manuscript and the date of the content to be identical, and the ridicule that resulted from his 'amendments and translations' to early poetry so undermined his credibility that he never completed the full range of his intended series of texts.
This study traces the origins, manifestations, and consequences of his dual nature through seven chapters. It considers the value of his solid earlier work, and balances it against the follies of his later translations, and seeks to give a fairer view of the value of his work to his own generation, and to those that followed on from him.

Keywords: Manuscripts
Diplomatic editions
Celtic Studies
Palaeography
Advisor: Charles-Edwards, T
Ghosts and bottlenecks in elastic snap-through

Snap-through is a striking instability in which an elastic object rapidly jumps from one state to another. It is seen in the leaves of the Venus flytrap plant and umbrellas flipping on a windy day among many other examples. Similar structures that snap-through are used to generate fast motions in soft robotics, switches in micro-scale electronics and artificial heart valves. Despite the ubiquity of snap-through in nature and engineering, its dynamics is usually only understood qualitatively. In this thesis we develop analytical understanding of this dynamics, focussing on how the mathematical structure underlying the snap-through transition controls the timescale of instability.
We begin by considering the dynamics of 'pull-in' instabilities in microelectromechanical systems (MEMS) - a type of snap-through caused by electrostatic forces in which the motions are dominated by fluid damping. Using a lumped-parameter model, we show that the observed time delay near the pull-in transition is a type of critical slowing down - a so-called 'bottleneck' due to the 'ghost' of a saddle-node bifurcation. We obtain a scaling law describing this slowing down, and, in the process, unify a large range of experiments and simulations that exhibit delay phenomena during pull-in.
We also investigate the pull-in dynamics of MEMS microbeams, extending the lumped-parameter approach to incorporate the details of the beam geometry. This provides a model system in which to understand snap-through of a continuous elastic structure due to external loading. We develop a perturbation method that systematically exploits the proximity to pull-in to reduce the governing equations to a simpler evolution equation, with a structure that highlights the saddle-node bifurcation. This allows us to analyse the bottleneck dynamics in detail, which we compare with previous experimental and numerical data.
The remainder of the thesis is concerned with the dynamics of snap-through in macroscopic systems. In particular, we explore the extent to which dissipation is required to explain anomalously slow snap-through. Considering an elastic arch as an archetype of a snapping system, we use the perturbation method developed earlier to show that two bottleneck regimes are possible, depending delicately on the relative importance of external damping. In particular, we show that critical slowing down occurs even in the absence of damping, leading to a new scaling law for the snap-through time that is confirmed by elastica simulations and experiments.
In many real systems material viscoelasticity is present to some degree. Finally, we examine how this influences the snap-through dynamics of a simple truss-like structure. We present a regime diagram that characterises when the timescale of snap-through is controlled by viscous, elastic or viscoelastic effects.

Keywords: Creep
Critical slowing down
Viscoelasticity
Elastic arch
Instability
Microbeam
Buckling
Dynamics
Snap-through
Electrostatic pull-in
Saddle-node ghost
Elasticity
Bistability
MEMS
Advisor: Moulton, D
Vella, D
Synthesis and reactivity of alkaline earth and aluminium gallyl complexes

This Thesis describes the synthesis and characterisation of new alkaline earth metal and aluminium gallyl complexes. Experimental studies were performed to investigate their structure. The reactivity of these species was also studied.
Chapter 1 introduces metal-metal bonded complexes containing alkaline earth metals and aluminium and the use of gallium(I) analogues of N-heterocyclic carbenes in the synthesis of heterobimetallic complexes of gallium.
Chapter 2 describes the synthesis and reactivity of alkaline earth gallyl complexes supported by beta-diketiminate ligands.
Chapter 3 presents the synthesis and reactivity of alkaline earth gallyl complexes supported by the carbazolide ligand CzOx.
Chapter 4 describes synthesis of aluminium-gallium bonded complexes supported by amidinate and b-diketiminate ligands and the attempted study of their reactivity.
Chapter 5 presents full experimental procedures and characterising data for the new complexes reported.

Keywords: magnesium
insertion reactions
calcium
metal-metal bonding
gallium
Advisor: Mountford, P
Alkaline earth hydroborate complexes for the ring-opening polymerisation of cyclic esters

This Thesis describes the activity and mechanism of alkaline earth organohydroborate, tetrahydroborate and alkoxide catalysts for the ring-opening polymerisation (ROP) of cyclic esters including rac-, L-, D- and meso-lactide (LA), and rac-β-butyrolactone (rac-BBL).
Chapter One introduces cyclic esters and general mechanisms for their ROP to give polyesters. Living and immortal ROP, an overview of stereocontrolled ROP, and determination of polylactide (PLA) stereosequences are given. Various techniques for polymer characterisations are also described.
Chapter Two describes the activity and mechanism of heavy alkaline earth organohydroborate complexes for the ROP of LA. The synthesis and characterisation of alkaline earth alkoxide complexes serving as model species are also described, together with their activities for the ROP of LA.
Chapter Three describes the activity and mechanism of a cyclic organohydroborate calcium complex for the ROP of LA. The role of borinic esters as chain transfer agents in the ROP of rac-LA is also discussed.
Chapter Four describes the activity and mechanism of heavy alkaline earth tetrahydroborate complexes for the ROP of LA. The immortal ROP of rac-LA using heavy alkaline earth alkoxide complexes and borate esters as chain transfer agents is discussed.
Chapter Five describes the activity and mechanism of alkaline earth organohydroborate, tetrahydroborate and alkoxide complexes for the ROP of rac-BBL.
Chapter Six presents experimental procedures and characterising data for new complexes reported.

Keywords: Alkaline earth metal complexes
Cyclic esters
Ring-opening polymerisation
Hydroborate complexes
Advisor: Mountford, P
Software security investment modelling for decision-support

While it is widely agreed that contemporary computer security is insufficient to meet the challenges faced, the remedies for its failures are far less obvious. Vast resources have been placed into technical solutions to little effect, prompting some to employ the constructs of economics to frame this problem as one to be 'managed', rather than 'solved'. However, to date economically-inspired decision support approaches have focused disproportionately on post-deployment security investment. With the preponderance of security issues stemming from the introduction of vulnerabilities during design and development, models that span the system development lifecycle are essential to efficiently address the root of many security issues. In addition, the need to impact system security at a fundamental level requires integration with existing security-development processes and standards.
This dissertation presents an approach to secure software development that is derived from an economically-inspired understanding of security. After demonstrating how existing security guidance can give rise to inefficient decisions, models for security investment are developed that incorporate investments made in software security during system inception and development relative to those made during deployment and operations. By employing these models, conditions are identified whereby software security improves the return on (security) investment, and provide theoretical and empirical evidence to support the adoption of software security. This is followed by an exploration of how economic considerations can drive existing secure software engineering processes, culminating in a case study that illustrates the application of these principles to an ongoing system development effort.

Advisor: Simpson, A
Interactions between memory and attention orienting across development

The influence of our past experiences in shaping our expectations and preparing us for future perceptual processing is now well documented, but many questions regarding how our long-term memories influence where we direct our attention remain unanswered. This thesis explores three of them. First, how do memories
interact
with other sources of attention orienting? In Chapter 2, we examine how memories influence attention when novel, transient visual events occur within scenes with learned associations. In Chapter 3, we extend this work by investigating how changing the time-course at which the transient visual event occurs affects the degree to which people use memories to orient attention. Second, when multiple sources of orienting are present, how does the degree to which each influences attention change across development? In Chapter 2, we examine how the degree to which concurrently presented memory cues and transient visual events influence attention differs between school-aged children and adults. In Chapter 4, we describe the results of a key control experiment in which we examine memory-guided attention in isolation across these two age groups. Finally, we address the question of how memory- guided attention influences subsequent recognition memory. Chapter 5 details three experiments exploring how previous experiences influence encoding of novel information.
With regards to the first two questions, we found that the onset of transient visual events interferes with memory-guided attention to a greater degree in adults than in children. However, with longer durations between the onset of a salient visual event and a target stimulus, adults also demonstrate an influence of memory on attention. Our follow-up control experiment suggests the developmental differences we observed may be due to children’s greater use of memories to guide attention at short time-courses in the absence of other competing sources of orienting. With respect to the third question, we did not find any evidence for an effect of memory-guided orienting on subsequent encoding. Together, these largely unexpected findings suggest that memories may be a particularly important influence on attention early in life, though their influence on future memory formation remains uncertain. Future experiments should a) further probe the development of memory-guided attention, with a focus on how its time-course may shift from childhood to adulthood, and b) continue to examine whether the spatial attention biases that emerge from experience interfere with or support subsequent recognition memory.

Advisor: Scerif, G
Nobre, K
Structural characterisation of calnexin cycle components and assessment as antiviral targets

N-glycosylated proteins that traverse the endoplasmic reticulum (ER) can make use of the calnexin cycle to attain their correct fold. The calnexin cycle modifies the N-glycan structure and allows for association of the glycoprotein with the ER lectins calnexin and calreticulin, which in turn recruit further chaperones that assist folding. Most enveloped viruses encode glycoproteins, which, upon infection of a host cell, crucially depend on the calnexin cycle to aid their folding. This includes diverse families such as Flaviviridae, Retroviridae and Orthomyxoviridae. We studied the calnexin cycle components with the ultimate aim of developing broad-spectrum antivirals.
X-ray crystallography was used to structurally characterise the murine ER α-glucosidase I, which controls entry into the calnexin cycle, with a number of inhibitory antiviral iminosugars. These data reveal flexibility in the ligands’ alkyl tails and may act as a basis for the discovery of enzyme specific inhibitors.
UDP-glucose: glycoprotein glucosyltransferase (UGGT) is the quality control checkpoint of the calnexin cycle whose full-length structure from the thermophilic fungus Chaetomium thermophilum was recently determined. Presented here are a higher resolution structure in addition to SAXS studies of UGGT’s interaction with Sep15, a protein that enhances UGGT activity.
UGGT’s reaction releases into the ER lumen UDP, which is the only known small molecule inhibitor of UGGT. An ER-resident UDPase, ENTPD5, breaks down UDP into UMP. Enzymatic characterisation of ENTPD5 reveals its substrate specificities; in addition we show a paralog, ENTPD6, possesses similar activities. Presented here is work towards crystallisation of these two proteins and a test of the anti-Zika activity of ENTPD5 inhibitors.
Finally, CRISPR/Cas9 knock-out cells were generated to test, in principle, whether modulation of the activity of proteins involved in the calnexin cycle could be antiviral. The data confirm that the ER glucosidases are likely the best targets of those studied.

Keywords: Glucosidase
Iminosugar
Dengue
Calnexin cycle
UGGT
Zika
CRISPR
Advisor: Zitzmann, N
On the valued constraint satisfaction problem

The Valued Constraint Satisfaction Problem (VCSP) is a framework which captures many natural decision and optimisation problems. An instance of the VCSP consists of a set of variables, which are to be assigned labels from a finite domain, and a collection of local constraints, each specified by a weighted relation mapping labellings of the variables in the constraint's scope to values. The objective is to minimise the total value from all constraints. The VCSP is commonly parameterised by a language, i.e. a set of weighted relations that are available for use in the constraints. Languages are classified according to the computational complexity of the VCSP as tractable, for which the problem can be solved in polynomial time, and intractable, for which the problem is NP-hard. The recently proved VCSP dichotomy theorem established a classification of all languages into these two categories. Additionally, various structural restrictions can be imposed to limit the set of admissible instances further, thus potentially changing the complexity of the VCSP.
Our first contribution relates to the algebraic approach to the VCSP, which proved instrumental in recent advances in the field. We generalise the Galois connection between weighted relational clones and weighted clones so that it applies to infinite sets as well. Second, we study a structural restriction requiring that the incidence graph be planar. In this setting, we establish a complexity classification of conservative languages (i.e. languages containing all {0,1}-valued unary weighted relations) and a necessary tractability condition for Boolean languages (i.e. languages over a two-element domain). Third, we study the surjective variant of the VCSP, in which labellings are required to assign every domain element to at least one variable. We establish a complexity classification of Boolean languages, which encompasses a new tractable class of problems.

Advisor: Živný, S