VictorJuiz/thesis huggingface dataset:
Impact of tissue microstructure on a model of cardiac electromechanics based on MRI data

Cardiac motion is a highly complex and integrated process of vital importance as it sustains the primary function of the heart, that is pumping blood. Cardiac tissue microstructure, in particular the alignment of myocytes (also referred to as fibre direction) and their lateral organisation into laminae (or sheets), has been shown by both experimental and computational research to play an important role in the determination of cardiac motion patterns. However, current models of cardiac electromechanics, although already embedding structural information in the models equations, are not yet able to fully reproduce the connection between structural dynamics and cardiac deformation. The aim of this thesis was to develop an electromechanical modelling framework to investigate the impact of tissue structure on cardiac motion, focussing on left ventricular contraction in rat. The computational studies carried out were complemented with a preliminary validation study based on experimental data of tissue structure rearrangement during contraction from diffusion tensor MRI.

Keywords: cardiac electromechanics
tissue microstructure
cardiac imaging
cardiac modelling
Advisor: Grau, V
Burrage, K
Bordas, R
Pathmanathan, P
An anthropology of engineering

This dissertation considers the place in anthropology of ‘production’ generally, and ‘engineering’ specifically, by asking the simple question: How do people make things?
Scholars of material culture have until recently focused on issues of consumption, especially the consumption of commodities (Miller), and considered production only in the abstract. Other theoretical approaches are therefore drawn upon to act as a framework for the thesis, including network theory (Law and Latour), and environmental relationism (Ingold).
A methodology of ‘parallel fieldwork’ was developed (from Bourdieu), to situate myself as an experienced engineer carrying out anthropological fieldwork. Work in a ‘familiar’ environment (the Didcot Railway Centre, UK) was used to provoke thoughts about engineering in my primary fieldsite (the Kelabit highlands, Borneo). Data from the UK thus helped frame my analysis of Kelabit engineering, presented here in four parts.
First, using the construction of two bridges as a case study, I suggest that a design can be seen as the revelation of a potential future, rather than a complete plan, as is suggested by design researchers such as Lawson and Norman. Then, by looking at changing traditions of house-building, I demonstrate the intimate relationship between materials and environment, even as the environment becomes more industrialised (Tsing), and consider this example in the light of debates about materiality (Miller; Ingold).
Personal involvement in the conception and building of a new suspension bridge allowed me to investigate in some depth the act of construction. As a communal project, this incorporated aspects of individual skill, in the way that Ingold has described, but also the organization of people, tools and materials, akin to Law’s ‘heterogenous engineering’. This leads me to conclude that a theory of engineering might come from due consideration of both these approaches to relational thinking.
Finally, I describe an abandoned longhouse and trace its deconstruction, suggesting that this is an example of creative destruction (Colloredo-Mansfeld), and re-materialization (Gregson). The dissipation of the material parts of the building shows that engineered objects should be seen as an ongoing process of material creation and disposal, and not a unified whole.
In conclusion, my hope is that this dissertation contributes to ideas about the place and nature of material culture, and advocates a more prominent place for ‘production’ within anthropology.

Keywords: production
construction
anthropology
engineering
material culture
deconstruction
Advisor: Gosden, C
Daniels, I
Model Theory of Holomorphic Functions

This thesis is concerned with a conjecture of Zilber: that the complex field expanded with the exponential function should be quasi-minimal′;t
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i
s,allitsdef∈ab≤⊂sshod̲becountab≤orhavecountab≤comp≤ment.Ourpurposeis→studythe≥ometryofthisstructureandotherexpansionsbyholomorϕcfunctionsofthecomp≤xfieldwithouthav∈gfirst→se≤anyνmber-theoreticprob≤ms,bytreat∈gallcountab≤setsonanequalf∞t∈g.Wepresentaξoms,model≤donthoseforaZariski≥ometry,def∈∈ganon-first-orderclassof`quasi-Zariski'' structures endowed with a dimension theory and a topology in which all countable sets are of dimension zero. We derive a quantifier elimination theorem, implying that members of the class are quasi-minimal. We look for analytic structures in this class. To an expansion of the complex field by entire holomorphic functions R we associate a sheaf OR of analytic germs which is closed under application of the implicit function theorem. We prove that OR is also closed under partial differentiation and that it admits Weierstrass preparation. The sheaf defines a subclass of the analytic sets which we call R-analytic. We develop analytic geometry for this class proving a Nullstellensatz and other classical properties. We isolate a condition on the asymptotes of the varieties of certain functions in R. If this condition is satisfied then the R-analytic sets induce a quasi-Zariski structure under countable union. In the motivating case of the complex exponential we prove a low-dimensional case of the condition, towards the original conjecture.
The impact of preeclampsia on the cardiovascular phenotype of offspring in early life.

In recent times the potential impact of preeclampsia on the cardiovascular health of offspring has been identified. This thesis explores the relationship between preeclampsia and offspring cardiovascular phenotype during the first three decades of life. A systematic review and meta-analysis provided evidence that there was increased blood pressure and BMI in the offspring of preeclamptic pregnancies (n = 45,249). There was however limited data on metabolic features and inadequate characterisation of the degree of prematurity or growth restriction in existing literature. I therefore studied data on two birth cohorts with up to 28 years of detailed prospective follow up (n = 2868 and n = 926). Those born very preterm to preeclamptic pregnancies had transient perinatal reductions in insulin and cholesterol, although extreme prematurity was the only determinant of variation in cardiovascular risk in later life, with changes in both metabolism and blood pressure. In those born closer to, or at term, gestation was no longer relevant and an independent impact of preeclampsia on blood pressure was evident, so that by age 20, those born at term to preeclamptic pregnancies were four and a half times more likely to demonstrate clinically-apparent hypertension. I then investigated whether there were changes in other features of cardiovascular phenotype, independent of blood pressure, in preterm neonates born following preeclampsia (n = 46). At 3 months of age preterm infants born to hypertensive pregnancies had subclinical alterations in cardiac strain, independent of gestation or birth weight but not differences in blood pressure, or microvascular structure. These findings highlight preeclampsia and prematurity as key, independent perinatal factors, important in determining cardiovascular phenotype and risk during early life. Preeclampsia is associated with a specific lean, hypertensive phenotype, associated with cardiac functional alterations; these findings begin to define a distinct at risk population who may require targeted preventative interventions.

Keywords: diabetes
cardiac strain
obesity
early life
children
cardiovascular risk
microvascular function
hypertension
young adults
infants
preeclampsia
offspring
Advisor: Leeson, P
Program analysis with interpolants

This dissertation discusses novel techniques for interpolation-based software model checking, an approximate method which uses Craig interpolation to compute invariants of programs. Our work addresses two aspects of program analyses based on model checking: verification (the construction of correctness proofs for programs) and falsification (the detection of counterexamples that violate the specification). In Hoare's calculus, a proof of correctness comprises assertions which establish that a program adheres to its specification. The principal challenge is to derive appropriate assertions and loop invariants. Contemporary software verification tools use Craig interpolation (as opposed to traditional predicate transformers such as the weakest precondition) to derive approximate assertions. The performance of the model checker is contingent on the Craig interpolants computed. We present novel interpolation techniques which provide the following advantages over existing methods. Firstly, the resulting interpolants are sound with respect to the bit-level semantics of programs, which is an improvement over interpolation systems that use linear arithmetic over the reals to approximate bit-vector arithmetic and/or do not support bit-level operations. Secondly, our interpolation systems afford us a choice of interpolants and enable us to fine-tune their logical strength and structure. In contrast, existing procedures are limited to a single ad-hoc choice of an interpolant. Interpolation-based verification tools are typically forced to refine an initial approximation repeatedly in order to achieve the accuracy required to establish or refute the correctness of a program. The detection of a counterexample containing a repetitive construct may necessitate one refinement step (involving the computation of additional interpolants) for each iteration of the loop. We present a heuristic that aims to avoid the repeated and computationally expensive construction of interpolants, thus enabling the detection of deeply buried defects such as buffer overflows. Finally, we present an implementation of our techniques and evaluate them on a set of standardised device driver and buffer overflow benchmarks.

Keywords: software verification
Craig interpolation
logic
decision procedures
Advisor: Kroening, D
Imperialism, industrialisation and war: the role of ideas in China's Japan policy, 1949-1965

This thesis is a study of the People’s Republic of China’s foreign economic policy towards Japan between 1949 and 1965. In particular, the thesis explores Chinese policy-makers’ ideas about Japan in the wake of the War of Resistance against Japan (1937-1945), and considers how those ideas shaped China’s foreign economic policy towards Japan between 1949 and 1965. To do so, the thesis employs a four-part ideas framework that examines Chinese policy-makers’ background, foreground, cognitive and normative ideas about Japan, and shows how the interaction between these four different idea types shaped China’s Japan policy between 1949 and 1965. Furthermore, the thesis draws on over 200 recently declassified Chinese-language archival records from the Chinese Foreign Ministry, as well as additional Chinese, Japanese, US and British archival sources. It argues that China’s experience of Japanese imperialism, industrialisation and war during the first half of the twentieth century deeply shaped Chinese ideas about Japan after 1949, though in ways that at first seem counterintuitive. Although Japan had waged a brutal war against China, Chinese policy-makers viewed Japan as an important source of industrial goods, technology and expertise, and a symbol of a modern, industrialised nation-state. However, China’s experience of Japanese imperialism and militaristic aggression often made it difficult to justify the policy of ‘trading with the enemy’. Ultimately, the thesis argues that China sought to expand economic ties with Japan after 1949 because Chinese policy-makers believed that doing so would assist China in becoming a modern and industrialised state, one that was strong enough to withstand foreign imperialism and restore its central position in the international system. Chinese conceptions of Japan thus help to explain how Japan became China’s largest trade partner by 1965, despite the bitter legacy of the War of Resistance and the Cold War divide between the two countries after 1949.

Advisor: Foot, R
Mitter, R
The transformation of East Asian welfare states: the politics of welfare reform in South Korea

East Asian welfare states have experienced major reforms in the last two decades, raising the question as to whether these welfare reforms signify a fundamental departure from the East Asian welfare model, or merely an adaptation of the model to socioeconomic changes. Overshadowed by the state-driven policy-making model with a strong functionalist bias focusing on socio-economic drivers, the existing East Asian welfare state literature has overlooked the fundamental political change brought by the dual transition (i.e., democratisation and economic liberalisation), which have led to the emergence of pluralistic societies. In order to fill this gap in the literature, this thesis investigates the political underpinnings of welfare reforms in Korea with special attention to societal actors, (notably trade unions, employers’ associations, and political parties) whose role feature prominently in the comparative welfare state literature, are still largely neglected in East Asian welfare state research. Bringing these actors into the analysis, the thesis examines how the rise of societal actors has changed Korean welfare politics by constraining policy autonomy of the state in the domains of employment protection, unemployment protection, and work/family reconciliation policies. To this end, the thesis engages in analysing policy documents and in-depth elite interviews with senior government officials as well as high-profile representatives of employers associations, trade unions and parties.
The thesis argues that the politics of the Korean welfare state has undergone a three step transformation process in the post-transition period. The developmental alliance could no longer function as the sole driving force of welfare state development during the first civilian government (1993-1998), when organised labour exercised its newly acquired status of a veto player. Furthermore, the old driving force of social policy-making, the developmental alliance, was replaced by the new alliance between the centre-left party and organised labour during the first left government (1998-2003) Lastly, parties moved to centre stage of social policy-making during the second left government (2003-2008) and the current conservative government (2008-presnet).
Drawing on competing theories of the welfare state –in particular, the Power Resource approach, the employer-centred varieties of capitalism perspective, and the state-centred theorem, and the parties-matter thesis – the thesis contributes to developing a comprehensive political account on welfare state transformation in East Asia and to the better embedding of the East Asian welfare state literature into the comparative welfare state literature.

Keywords: South Korea
welfare reform
East Asian welfare stattes
Advisor: Seeleib-Kaiser, M
Walker, R
A field and laboratory investigation of the compliance of fractured rock

Compressional and shear wave velocity and attenuation measurements were obtained in the laboratory from 50 mm diameter, cylindrical, limestone core samples over a confining pressure range of 5 – 60 MPa. Normal and tangential fracture compliance values, as a function of confining pressure, were calculated for a single fracture cut perpendicular to the long axis of the core. The ratio of the normal to tangential compliance was approximately 0.4 and was independent of the applied stress. Values of normal and tangential fracture compliance calculated were of the order 10-14 m/Pa, and decreased with an increase in confining pressure. Both Q-1
P and Q-1S1/Qs were shown to be small for these samples.
A borehole test site was constructed in a Carboniferous limestone quarry, at Tytherington, situated north of Bristol, UK. This quarry was chosen because the rock type was fairly homogeneous and the fractures could be mapped in the quarry walls as well as down three, 40 m vertical boreholes drilled in-line in the quarry floor. Wireline logs were obtained in all the holes and a seismic crosshole survey was carried out between the two outermost boreholes. An estimate of in-situ normal fracture compliance, ZN, was obtained from the log and crosshole data, in 4 different ways, using effective medium theories as well as the displacement discontinuity theory. An additional estimate of ZN was obtained from a separate borehole test site constructed in fractured Devonian meta-sediments at Reskajeage, Cornwall, UK. These fractures were much larger in size than those observed at Tytherington quarry. From the above field and laboratory measurements, fracture compliance was shown to increase approximately linearly with the size of the fractures. In addition, a study of crosshole seismic attenuation was performed at Tytherington quarry. Q was found to be frequency dependent. This frequency dependence was interpreted as being due to scattering rather than intrinsic attenuation.

Keywords: fractured rock
anisotropy
fractures
compliance
Advisor: Worthington, M
Judicial discourse on India's affirmative action policies: the challenge and potential of sub-classification

This thesis is primarily concerned with the distribution of quotas in higher education and public employment within identified beneficiary groups. In a system of quotas based on preferential treatment of groups, the question about which members of the group must benefit over others is a crucial one. One of the main themes in the thesis is to critically analyse the judicial understanding about the nature of these groups. The homogeneity (in backwardness) that is attached to beneficiary groups in differing degrees is challenged in the thesis using the examples of Scheduled Castes and Muslims within the Other Backward Classes category. The differences within beneficiary groups have great significance for the fairness of India’s reservation policies. By ignoring internal differences, the most marginalised groups are left behind in terms of accessing the benefits of reservations. I have argued that any attempt to address the issue of sub-classification must begin by recognising multiple axis of marginalisation within the framework of intersectionality. This lack of sufficient engagement with the issue of sub-classification highlights the failure of the Supreme Court of India to develop a normative framework within which reservations might be viewed. This lack of normative clarity informs spheres of reservations like higher education and public employment along with according homogenous treatment to beneficiary groups internally. The Supreme Court has viewed reservations in higher education and public employment as essentially performing the same function. I have argued that reservations in these spheres perform different functions and the resulting obligations on the state in terms of constitutional justifications must also differ. While the demands for sub-classification present an opportunity to make distribution of reservations fairer, it also exposes the limitation of reservations as a tool of social transformation.

Keywords: Affirmative Action
Equality
India
Reservations
Fundamental Rights
Supreme Court of India
Social Justice
Advisor: Fredman, S
Self-referential poetics: embedded song and the performance of poetry in Greek literature

This thesis is a study of embedded song in ancient Greek narrative poetry. The introduction defines the terminology (embedded song is defined as the depiction of the performance of a poem within a larger poem, such as the songs of Demodocus in Homer’s Odyssey) and sets the study in the context of recent narratological work done by scholars of Classical literature. This section of the thesis also contains a brief discussion of embedded song in the Homeric epics, which will form the background of all later examples of the motif.
Chapter 1 deals with embedded song in the Homeric Hymns and Hesiod’s Theogony. It is argued that the occurrence of embedded song across these poems indicates that the motif is a traditional feature of early Greek hexameter poetry, while the possibility of “inter-textual” allusion between these poems is considered, but finally dismissed.
Chapter 2 focuses on Pindar, Bacchylides and Corinna, and explores how lyric poets use this motif in the various sub-genres of Greek lyric. In epinician poetry, it is argued that embedded song is used as a strategy of praise and also to boost the authority of the poet-narrator by association with the embedded performers, who can be seen to have in each case a particular source of authority distinct from that of the poet narrator.
Chapter 3 considers the Hellenistic poets Apollonius Rhodius and Theocritus, and how their interest in depicting oral poetry meshes with their identity as literate and literary poets.
Appendix I gives a list of all the examples of embedded song I have found in Greek poetry.
Appendix II gives an account of Pindar’s Hymn to Zeus, a highly fragmentary poem which almost certainly contained an embedded song, analysing this as an example of the difficulties thrown up by lyric fragments for a study of embedded narratives.

Keywords: narratology
Theocritus
Homeric Hymns
poetics
Pindar
lyric
Bacchylides
performance
Homer
Apollonius Rhodius
narrative
embedded song
epic
Advisor: Allan, W
Structure of the RNA-dependent RNA polymerase from influenza C virus

The influenza virus causes a disease that kills approximately 500,000 people worldwide each year. Influenza is a negative-sense RNA virus that encodes its own RNA-dependent RNA polymerase. This protein (FluPol) carries out both genome replication and viral transcription. Therefore, like the L-proteins of non-segmented negative-sense RNA (nsRNA) viruses, FluPol also contains mRNA capping and polyadenylation functionality. In FluPol, capping is achieved by snatching cap structures from cellular mRNAs, so requiring cap-binding and endonuclease activities. This makes FluPol a substantial machine. It is a heterotrimeric complex, composed of PB1, PB2 and PA/P3 subunits, with a total molecular weight of 255 kDa. PB1 houses the polymerase active site, whereas PB2 and PA contain, respectively, cap-binding and endonuclease domains. Currently, we only have high resolution structural information for isolated fragments of FluPol. This severely hampers our understanding of influenza replication and consequently inhibits the development of therapies against the virus.
In this DPhil project, I have determined a preliminary structure for the heterotrimeric FluPol of influenza C/Johannesburg/1/66, solved by x-ray crystallography to 3.6 Å. Overall, FluPol has an elongated structure with a conspicuous deep groove. PB1 displays the canonical right-hand-like polymerase fold. It sits at the centre of the particle, sandwiched between the two domains of P3, and with PB2 stacked against one side of this dimer. In the structure, the polymerase and endonuclease catalytic sites are both ~40 Å away from the cap-binding pocket. This pocket also faces a tunnel leading to the polymerase core. This suggests a mechanism for how capped cellular mRNAs are cleaved and then fed into the polymerase active site to prime transcription. The structure also hints at a unique trajectory for template RNA, in which the RNA exits at an angle ~180° from which it came in. This provides an explanation for how the polymerases of influenza, and other nsRNA viruses, can copy templates that are packaged into ribonucleoprotein complexes.
My work reveals the first molecular structure of any polymerase from an nsRNA virus. It uncovers the arrangement of functional domains within FluPol, illuminating the mechanisms of this and related viral polymerases. This work will help focus future experiments into FluPol biology, and should hopefully spur the development of novel antiviral drugs.

Keywords: Virology
RNA-dependent RNA Polymerase
X-ray crystallography
Structural Biology
Influenza
Advisor: Fodor, E
Grimes, J