VictorJuiz/thesis huggingface dataset:
Teaching mobile robots to use spatial words

The meaning of spatial words can only be evaluated by establishing a reference to the properties of the environment in which the word is used. For example, in order to evaluate what is to the left of something or how fast is fast in a given context, we need to evaluate properties such as the position of objects in the scene, their typical function and behaviour, the size of the scene and the perspective from which the scene is viewed.
Rather than encoding the semantic rules that define spatial expressions by hand, we developed a system where such rules are learned from descriptions produced by human commentators and information that a mobile robot has about itself and its environment. We concentrate on two scenarios and words that are used in them. In the first scenario, the robot is moving in an enclosed space and the descriptions refer to its motion (“You’re going forward slowly” and “Now you’re turning right”). In the second scenario, the robot is static in an enclosed space which contains real-size objects such as desks, chairs and walls. Here we are primarily interested in prepositional phrases that describe relationships between objects (“The chair is to the left of you” and “The table is further away than the chair”). The perspective can be varied by changing the location of the robot. Following the learning stage, which is performed offline, the system is able to use this domain specific knowledge to generate new descriptions in new environments or to “understand” these expressions by providing feedback to the user, either linguistically or by performing motion actions.
If a robot can be taught to “understand” and use such expressions in a manner that would seem natural to a human observer, then we can be reasonably sure that we have captured at least something important about their semantics. Two kinds of evaluation were performed. First, the performance of machine learning classifiers was evaluated on independent test sets using 10-fold cross-validation. A comparison of classifier performance (in regard to their accuracy, the Kappa coefficient (κ), ROC and Precision-Recall graphs) is made between (a) the machine learning algorithms used to build them, (b) conditions under which the learning datasets were created and (c) the method by which data was structured into examples or instances for learning. Second, with some additional knowledge required to build a simple dialogue interface, the classifiers were tested live against human evaluators in a new environment. The results show that the system is able to learn semantics of spatial expressions from low level robotic data. For example, a group of human evaluators judged that the live system generated a correct description of motion in 93.47% of cases (the figure is averaged over four categories) and that it generated the correct description of object relation in 59.28% of cases.

Keywords: language and perception
situated interaction
spatial descriptions
perceptual grounding
dialogue
natural language semantics
Advisor: Pulman, S
Perceptions of risks to elite secondary school education in South Africa

This study engages with the most important risks facing quality education in elite secondary schools in South Africa. It adopts a critical realist perspective that emphasises the importance of perceptions, as they shape the decisions and actions of those faced with risks. Through the use of surveys and in-depth semi-structured interviews, perceptions of a wide range of risks were explored: ranging from classrooms, to schools and their social contexts, to national and global political and economic factors. The perceptions of risks of different participants in this research varied considerably: with risk prioritisation tending to correspond to the risks a respondent was most directly dealing with. Several key risk themes emerged, including: the Middle Class squeeze; Race, Transformation and Political Vulnerability; Competition and the Neo-Liberal Order; Innovation and Change vs Continuity; and Fragmentation, Identity, and Social Capital. Further research is needed to aid decisions by practitioners around the specific requirements of 21st century education, as well as to find solutions to re-shape the political economy of quality teacher supply.

Keywords: South Africa Education
Elite Education
Education Risks
Advisor: Childs, A
Priority-setting for malaria control and elimination in Myanmar

In Myanmar, Plasmodium falciparum malaria is important because of both the burden of disease and the emergence of parasites resistant to artemisinin-based therapies. In 2012, concomitant with the lifting of international economic sanctions, funding for malaria control and elimination in Myanmar rose significantly. The University of Oxford was asked to support priority setting by assessing the relative cost-effectiveness of insecticide- treated bed nets and community health workers, particularly with respect to planning in the Myanmar Artemisinin Resistance Containment region along the east of the country. In the context of rising artemisinin resistance and, later, the goal of regional malaria elimination by 2030, reduction in malaria transmission was an important consideration in prioritising between interventions.
A cost-effectiveness analysis was undertaken using both a static decision tree model and a dynamic disease transmission model. Supporting work towards this analysis included a systematic review of dynamic-transmission economic-evaluations and the creation of a data repository to collate governmental and non-governmental malaria case records. In addition, initially unplanned work on economic evaluation methodology was completed; identifying challenges in the application of cost utility analysis to this decision problem and proposing a framework for budget-based geographic resource allocation as an adaptation of standard methods.
The results of this work include a tripling of the number of malaria diagnostic reports available between 2012 and 2014 (71% increase in Plasmodium falciparum cases) with this data showing a decrease in Plasmodium falciparum cases over time, alongside rising testing rates. Cost utility analysis found that, in general, malaria community health workers are more costly yet more effective than insecticide treated bed nets, though in both cases cost effectiveness is very much context dependent. Geographic allocation analyses using both static and dynamic models illustrate the potential for economic evaluation to provide both more detailed and more practical policy recommendations. Parameter uncertainty was explored in both cases. Some township recommendations were robust to both parameter uncertainty and model variation (structural uncertainty). Viewed through the lens of the Reference Case for Economic Evaluation in Low and Middle Income Countries (published during the course of this DPhil), budget-based geographic resource allocation largely adheres to the healthcare economic evaluation principles and offers improvements to dealing with heterogeneity and resource constraints. This DPhil recommends that Myanmar malaria policy is tailored to reflect geographic variation in intervention cost-effectiveness, rather than focusing on universal coverage, and illustrates a framework for economic evaluation to support budget-based geographic allocation.

Keywords: Geographic targetting
Cost-effectiveness
Economic evaluation
Malaria
Advisor: Lubell, Y
White, L
Smithuis, F
Day, N
Syndicalism, work and science in Simone Weil’s philosophy of modernity

Simone Weil (1909-1943) was a political philosopher and revolutionary-syndicalist militant who put her own body on the line as a factory worker in 1935; mobilised herself in an anarchist militia in northern Spain in 1936 and engaged as a résistante in France and then in London in de Gaulle’s Forces Françaises Libres during the Occupation. Despite the extent of her political, social and militant engagement, and the significant size of her political corpus, accounts of Weil’s life and thought tend to emphasise her idiosyncratic distance from the philosophical mainstream and her saintly detachment from the here-and-now. Her mentor, Alain, referred to her as a ‘Martian’; Gabriel Marcel called her a ‘témoin de l’absolu’. T.S. Eliot went even further, describing her ‘as a potential Saint’. Georges Bataille saw her in more fanciful terms, as a ‘Don Quichotte […] que l’impossible attirait’. Such accounts, despite their differences, led Raymond Aron to comment in 1983 that Weil had become ‘un object de culte’. It is perhaps because these views became so entrenched that Weil scholarship, whether theological or political, has tended to resist seeing her thought as engaged in a deliberate dialogue with philosophical discourses of her own time and about her own time.
By exploring in turn Weil’s philosophy work and science, this thesis seeks to redress this balance, showing how from revolutionary syndicalism to anti-Bolshevik communism; from Husserlian phenomenology to Heideggerian ontology; from Gaston Bachelard’s historical epistemology to Freudian sublimation; from Walter Benjamin’s modern shock experience to Bergson’s experience of time as duration, Weil was deeply and deliberately engaged in a shared reflection on the challenges and dangers of the modern world.

Advisor: Howells, C
The ‘low pay penalty’ associated with part-time employment and its gendered implications

Rather than looking across the earnings distribution as a whole (the ‘average worker model’), this thesis investigates the implications of working part time for men and women at the lower end of the distribution. Focusing on the UK, the thesis is comprised of four stand-alone papers, each of which explores a different aspect of the relationship between part-time employment and low pay. The results show that men and women who work part time are considerably more likely to be low paid, and less likely to progress out of low pay, than their full-time counterparts. Few previous studies of part-time employment include men in the analysis, or consider how the implications of working part time may differ according to gender. This thesis shows that the part-time ‘low pay penalty’ is, in fact, more pronounced for men than for women. However, women are disproportionately affected in the sense that they work part time in greater numbers. The analysis shows that part-time work has historically played, and continues to play, a crucial role in shaping gender inequality in low pay. However, there has been a sustained decline in the importance of part-time employment as a contributing factor to the gender gap in low pay for UK employees. The thesis provides robust estimates of the relationship between part-time employment and low pay across a range of European countries for the first time. Far from being a quirk of the UK labour market, the part-time ‘low pay penalty’ is observed in most, if not all, European countries. However, there is considerable variation in the extent to which part-time workers face a higher risk of low pay compared to full-time workers. This variation appears to be more closely related to the incidence of low pay than to cross-national differences in working time practices.

Advisor: Bukodi, E
Bennett, F
Structures and mechanisms for synthetic DNA motors

DNA provides an ideal substrate for nanoscale construction and programmable dynamic mechanisms. DNA mechanisms can be used to produce DNA motors which do mechanical work, e.g. transportation of a substrate along a track.
I explore a method for control of a DNA mechanism ubiquitous in DNA motor designs, toehold-mediated strand displacement, by which one strand in a duplex can be swapped for another. My method uses a mismatch between a pair of nucleotides in the duplex, which is repaired by displacement. I find that displacement rate can be fine-tuned by adjusting the position of the mismatch in the duplex, enabling the design of complex kinetic behaviours.
A bipedal motor [1, 2] is designed to walk along a single-stranded DNA track. Previously the motor has only taken a single step, due to a lack of designs to extend the single-stranded track. I present a novel design for track held under tension using a 3D DNA origami tightrope, and verify its assembly. The bipedal motor design is adapted and a method to specifically place motors on tightropes is demonstrated. Motor operation is investigated on truncated tracks and tightrope tracks by electrophoresis and spectrofluorometry. The motor does not accumulate appreciably at the track end; this is tentatively attributed to rearrangement of the motor between track sites without interaction with fuel.
Tightrope origami can hold single-stranded DNA under pN tension. I use tightropes to study hybridization kinetics under tension and find dramatic, non-monotonic changes in hybridization rate constants and dissociation constants with tension in the range &Tilde;0-15 pN. Extended tracks for a 'burnt-bridges' motor which destroys its track as it moves [3] are created on the inside of DNA nanotubes, which can be polymerised to create tracks up to a few mm in length, and on tiles which I attempt to join in a specific order. Crossing of the motor between tubes is verified, and microscopy experiments provide some evidence that track is being cleaved by the motor, a requirement for movement along the track. Tile based tracks are imaged by super-resolution DNA PAINT [4], providing proof-of-principle for track observation to infer motor movement.

Keywords: Kinetics
Nanotechnology
DNA origami
DNA
Toehold-mediated strand displacement
DNA tension
DNA motors
Molecular motors
Strand displacement
Mismatches
Self assembly
Advisor: Turberfield, A
The dynamics of wild woodland rodents

This thesis investigates the variation of life history traits within species, how they underpin population dynamics in woodland rodent populations and how they are effected by interactions between species. We ask how do life history traits differ between populations of the same species in similar habitats? We then go on to ask how two different species living in sympatry differ and the possible effects of interactions. We used data collected against three populations of Columbian ground squirrels (Urocitellus columbianus) in Canada and two species of woodland rodents from a site in the UK. Integral Projection Models or IPMs were used to compare the three populations of Columbain ground squirrels and identify differences between them. By using a form of perturbation analysis on the IPMs it was possible to identify the driving demographic and trait transition functions for the differences between the three populations. We then looked at interactions between wood mice (Apodemus sylvaticus) and the bank vole (Myodes glareolus) in the UK, and the possible effect on trapping bias. As data was limited for the two UK species, we could not construct a full IPM, but instead looked at the differences in growth rates of both species to determine what was the most important factors.
Comparing the population level estimates from the IPMs for the Columbian ground squirrels, revealed significant differences between the populations. In particular the populations differed in growth rate (λ), generation length and R0. Perturbation analysis of the three IPMs revealed the adult survival function to be the major contributor to the differences between the three population. The inheritance function also had a large impact on the offspring estimates.
For the two UK rodent species we found a large impact on the trapping bias due to interactions between the two species. With a significant increase in the chance of the same species being caught within a trap as previously caught. When analysing growth rates, we found that environmental factors only impacted growth for some groups, and we suggest that this may be due to the mitigation by the woodland of impacts of the environmental conditions. We did find that the density of a third species, the yellow necked mouse (Apodemus flavicollis), did have a large negative impact on growth rates on the other two species.
In summary species population dynamics can very considerably between populations, even when the populations exist in potentially similar habitats. It is also possible for species living in sympatry to also have an impact on each other’s population dynamics. Extreme care should then be taken when making comparisons between species based solely on single population data.

Advisor: Coulson, T
Mathematical modelling and optimisation of Venturi-enhanced hydropower

In this thesis we study a novel type of hydropower generation which uses a Venturi contraction to amplify the pressure drop across a turbine, allow- ing for cost-effective hydropower generation in situations where the head drop is small, such as in rivers and weirs. The efficiency is sensitive to how the secondary flow, which passes through the turbine, mixes with the accelerated primary flow, which is diverted around the turbine, within the confines of a closed geometry. In particular, it is important to understand the behaviour of the turbulent shear layers between the primary and sec- ondary flows, which grow downstream, mixing the flows together. The behaviour of the shear layers in the expanding part of the Venturi con- traction is strongly dependent on the shape of the channel. An important consequence of the channel shape, and hence the flow behaviour, is the degree of pressure amplification across the turbine, which determines the amount of generated power.
We focus on mathematically modelling the mixing of the flows in turbu- lent shear layers, and we investigate two different ways to increase pres- sure amplification: optimising the shape of the channel, and using swirl to enhance mixing. The channel shape optimisation reveals an interest- ing balance between the effects of mixing and wall drag. Wide channel expansion tends to accentuate non-uniform flow, causing poor pressure amplification, whilst shallow expansion creates enhanced wall drag, which is also detrimental to pressure amplification. We show how the maximum power is generated with a channel shape that strikes a balance between these two effects. We find that swirl enhances mixing by increasing shear layer growth rates, but it produces large pressure losses in doing so, and for large amounts of swirl a slowly recirculating region can form along the channel centreline. Whilst swirl does not improve efficiency, there may be some inevitable swirl present in the flow, and we show how this affects the optimum channel shape. We also establish the criteria for the existence of such a recirculation region so that it may be avoided.

Keywords: Optimisation
Fluid mechanics
Optimal control
Applied mathematics
Mathematical modelling
Advisor: Hewitt, I
Please, C
Functional evaluation of the human fat distribution HOXC13 gene locus

Gynoid fat distinguishes from android fat in developmental origin and possesses metabolically protective roles, especially in women. Growing evidence supports that epigenetic modifications could potentially explain the regional differences between fat depots. Recent progress in transcriptome analysis has revealed that long non-coding RNAs (lncRNAs) play roles in epigenetic regulation, but their potential functions in fat depot-specific transcription remain largely unexplored. HOX transcript antisense RNA (HOTAIR) is a lncRNA that is expressed exclusively in the gluteal subcutaneous adipose tissue (GSAT); it is undetectable in the abdominal subcutaneous adipose tissue (ASAT) and locates under the fat distribution - genome-wide association studies (GWAS) locus near and around the HOXC13 gene. Therefore, the aim of this project was to investigate the depot-specific functional roles of the HOTAIR gene.
GSAT HOTAIR expression was highly variable between individuals but generally expressed at lower levels in females compared with men. Detailed annotation of HOTAIR-haplotype tagging single nucleotide polymorphisms (SNPs) identified the minor allele of rs76084431 as a GSAT HOTAIR expression quantitative trait locus (eQTL) associated with increased android to gynoid fat mass ratio in females. Comparison of histone marks between abdominal and gluteal preadipocytes showed that rs76084431 is positioned in an open chromatin region and which could be considered as a HOTAIR enhancer in gluteal preadipocytes. HOTAIR stable knockdown and constitutive overexpression in human adipocytes provided further evidence that the HOTAIR gene is essential for the gluteal adipocytes, but anti-adipogenic for abdominal adipocytes. Weighted Gene Co-expression Network Analysis (WGCNA) of RNA-seq from HOTAIR knockdown cells data suggested regulation a number of regulated pathways: extracellular matrix and protocadherin genes appear to be predominant HOTAIR downstream pathways in the gluteal preadipocytes. CEBPD, PTEN and PCDH10 were shown to be epigenetically regulated by HOTAIR during adipogenic differentiation of the gluteal preadipocytes. Overall, these data suggest that HOTAIR is a novel and dynamic regulator of the adipocyte epigenome with functional importance for regional human adipose tissues.

Advisor: Karpe, F
Pinnick, K
Creative reading: using books in the vernacular context of Anglo-Norman England

This thesis responds to a lack of information regarding reading practice in literature in early Middle English. Here, reading is often used as a metaphorical or symbolic act—representing piety, devotional practice, or intellectualism—but how reading took place, how users engaged with books, is rarely figured. Other seams of evidence are therefore needed to access the reading process. The corpus of manuscripts on which I focus consists of thirty-three multilingual books containing English, Latin, and French produced in England between 1066 and c. 1300. Using this corpus, and inspired by the work of Leah Price, Juliet Fleming, Kathryn Rudy, and others, I seek to test the boundaries of what has previously been considered permissible evidence for reading, thereby adjusting and expanding current conceptions of the range of activities and practices high medieval book use entailed.
The thesis begins with a case study of some important readers: scribes. In chapter one, using the seven surviving copies of Poema Morale as a corpus I read against current critical considerations of variance in manuscript transmission as a sign of ‘scribal authorship’ in order to establish practices of scribal reading. Chapters two and three go on to demonstrate how these ‘scribal readers’ prefigured a work’s use as they copied, particularly when they chose to introduce or exclude textual apparatus in the form of titles, capitals, or paraph marks. The final part of the thesis examines the retrospective evidence of use left by readers who marked and altered their books to determine the extent to which readers conformed to the practices imagined by manuscript producers.
As a whole, then, the thesis showcases the variegated nature of reading practice—from critical analysis to nugatory scanning—and the alternative uses for books in English in this period. It shows that vernacular reading was a work of ‘embodied intellectual labour’ that benefitted from the material form of the book, and that engagement and manipulation of this form was not just tolerated, but expected, and perhaps actively encouraged.

Keywords: Materiality
Manuscript
Reading
Book History
early Middle English
Medieval
Poema Morale
Advisor: Wakelin, D