VictorJuiz/thesis huggingface dataset:
A historical geography of the Judean and Samarian Hill Country, 539 BCE–70 CE

This thesis is a historical geography of the Judean and Samarian Hill Country between the 6th century BCE and 1st century CE. The Hill Country is a small region of Palestine bordered by the Jordan Valley in the east, the Shephelah and the Coastal Plains in the west, the Negev in the south, the Jezreel Valley in the north, and the Carmel Range in the northwest. Across six chapters, I explore the ways the environment shaped (and was shaped by) the society, economy and culture of the local population, drawing on a selection of literary, epigraphic and material evidence, and arguing for the coherence and value of this fascinating historical unit.

Keywords: Historical geography
Palestine
History
Aramaic
Judaism
Hebrew
Samaritans
Israel
Numismatics
Jews
Environmental history
Ancient history
Advisor: Goodman, M
Bispham, E
Art and aristocracy in late Stuart England

Art was integral to the lives of the late Stuart aristocracy. Through case studies of the art patronage of three aristocratic couples, this interdisciplinary thesis examines their stylistic influences, the strategies and networks that underlay their patronage, and why they invested so much time, effort, and money on buildings, interiors, gardens, and moveable works of art. In doing so, it illuminates the dynamics of late Stuart aristocratic society, while simultaneously deepening our understanding of the art itself. It explores the relationship between monarchy and aristocracy in the pivotal decades around the Glorious Revolution, finding that despite the profound political consequences of the Revolution, the court continued to attract the aristocracy as the leader of artistic fashion. It emphasises that aristocrats were integrated into wider European court culture, and shows how they adopted a range of strategies to obtain fashionable and exclusive foreign artworks in order to demonstrate their proximity to the centres of fashion and differentiate themselves from their peers. They employed immigrant artists and craftsmen, adopted European designs, and some travelled to the continent, modelling their patronage on the European potentates they encountered. This thesis dethrones the lone male patron by identifying the household staff and agents, and kinship, county, associational and political networks that were integral to art patronage. It also considers the dynamics of conjugal patronage, uncovering the important contribution of married women, while recognising that it was circumscribed within legal, economic, and social strictures. Finally, it questions previous assumptions that aristocratic art, particularly in country houses, was politically motivated and directed towards instrumental purposes. Differentiating between politics and power, it demonstrates that these aristocrats principally used art to demonstrate and maintain their status through displays of magnificence; to invest in their estates on behalf of the dynasty; and to commemorate their own achievements for posterity.

Keywords: late Stuart
art
art patronage
aristocracy
nobility
Advisor: Smith, H
Barber, T
"Green are fields, not mines": the case of lithium mining and resistance in Serbia

This research is concerned with the emerging lithium extractivist frontier in Serbia. In 2004, a new mineral jadarite was discovered by the multinational mining company Rio Tinto, and it was found to be unusually rich in lithium and boron. Since then, more lithium deposits have been discovered in Serbia, with companies seeking to extract the element that is one of the essential components for batteries in electric vehicles (EVs) as well as for renewable energy storage. It is thus central to the electrification of the transport and energy systems and for the green transition more broadly. The Jadar Project, led by Rio Tinto, was set to become the biggest lithium mine in Europe, with the planned start of construction in early 2022. Nevertheless, the project drew widespread resistance from locals, with escalating protests and thousands of people blocking roads towards the end of 2021, ultimately leading to the official cancellation of the lithium mining project in January 2022. Through ethnographic fieldwork and in-depth interviews, this research examines the attitudes of locals and activists to lithium mining in Serbia. With a particular focus on the materiality of lithium as a “green” element, the spatiality of Serbia as a European periphery and the temporality of the Anthropocene as a state of emergency, this research seeks to address the largely neglected forms of harm that the global demand for lithium holds. The lithium mining initiatives in Serbia thus become key sites of contestation of what a sustainable future holds and present a fundamental challenge to the hegemonic view on sustainability that is based on mining and extractivism.

Keywords: activism
electric vehicles
extractivism
Serbia
environmental justice
Balkans
sustainability
lithium
Advisor: Lora-Wainwright, A
McCormack, D
Modular Calabi-Yau manifolds, attractor points, and flux vacua

The overarching theme of this thesis is the relation of physics - specifically string theory compactifications - to Calabi-Yau modularity, which is a phenomenon where it is possible to associate a modular form to a Calabi-Yau manifold. The coefficients of this modular form can be related to the number of points on the manifold defined over finite fields.
We begin by studying the geometry of a five-parameter family of Calabi-Yau manifolds first studied in connection with modularity by Hulek and Verrill, focusing on aspects related to mirror symmetry. These Hulek-Verrill manifolds have an S6 symmetry group, which makes the seemingly daunting task of finding periods and computing instanton numbers and monodromies significantly easier.
Using the geometric results, we investigate the modular properties of these manifolds. Extending the existing computational methods to cover multiparameter families, we are able to compute the zeta function on various one-parameter subfamilies of Hulek-Verrill manifolds. We observe that along the locus of S5 symmetric manifolds, the zeta function numerator factorises, revealing that this locus consists of weight-two modular manifolds. This is related to existence of supersymmetric flux vacua in type IIB string theory compactified on these manifolds. We introduce a method of constructing families of such modular supersymmetric flux vacua by utilising the Z2 symmetry of the compactification manifold. As expected by modularity conjectures, the zeta function of the manifold can be related, in numerous examples we study, to elliptic, Hilbert, or Bianchi modular forms, depending on the number field the manifold is defined over. It is an interesting question whether these modular forms and their coefficients have a natural geometric of physical interpretation. We take steps towards answering this question by developing an iterative procedure for solving attractor equations in one-parameter compactifications. In some important special cases we find closed-form series solutions, which can be used to compute the entropy of associated black holes in terms of Gromov-Witten invariants of the compactification manifold. The entropy formula takes on a form very reminiscent of modular form asymptotics and can be shown to satisfy some properties expected of the asymptotic form of a modular form counting black hole microstates.

Keywords: zeta function
number theory and physics
flux vacua
black holes
modularity
mirror symmetry
Calabi-Yau manifolds
attractors
Advisor: Candelas, P
De La Ossa, X
Mixed convective flows for future operation of power generation turbines

There has been a fast uptake of renewable sources in power generation in the recent years to mitigate the climate change. However, steam and gas turbines are expected to be in use to provide load levelling capacity when the demand cannot be met by the renewables due to their intermittent nature. This intermittency with renewables pose a grand challenge to the conventional power generation systems which are designed to provide a base load but now must adapt to the presence of renewables with frequent start-ups and shut-downs. Therefore, the focus in turbine design is shifting away from overall efficiency towards more operational flexibility.
The fundamental change in turbine design philosophy necessitates a thorough understanding of mixed convective flows during shut-down regimes which are responsible for non-uniform cooling leading to thermal stresses and compromise clearances which directly limit the operational flexibility. Numerical methods are needed to investigate these flows since the direct measurements are often not possible. A novel experimental facility that operates at engine realistic conditions has been designed and commissioned to simulate the mixed convective flows inside turbine casings. A number of experimental campaigns for various mixed convection scenarios have been performed and unique data sets have been generated, which have served as validation cases for the numerical methods. Subsequently, wall resolved large eddy simulations have been performed to gain a deeper insight into the flow field and heat transfer characteristics. A new universal RANS based model which incorporates and blends Reynolds stress and turbulent heat flux treatments has been developed and found to improve flow field and heat transfer predictions in buoyancy influenced flows.
Since the buoyant flows which cause non-uniform flow field and cooling are undesirable, the experimental facility has been modified with a blockage plate to create a local jet effect to suppress large thermal boundary layer development. The results have suggested that a simple modification to turbine casings could remarkably reduce flow field non-uniformity by suppressing the buoyant flows.
Additionally, the influence of cast surface roughness which are commonly encountered in turbomachinery industry on heat transfer, flow field and aerodynamics has been investigated with scale resolving simulations of multiple scaled-up roughness heights. It has been concluded that these rough surfaces have a significant impact on heat transfer, and cause similar velocity and temperature deficit which would potentially be simulated by a single low-order turbulence model.

Keywords: buoyancy suppression
scale resolving simulations
turbine flexible operations
flow control
buoyant flows
new RANS treatment
NNR
power generation turbines
mixed convection
turbine cooling
casting roughness
facility development
Advisor: Rosic, B
Novel approaches to targeting ATM-deficient tumours

Ataxia-telangiectasia mutated (ATM) is an apical kinase involved in the response to DNA damage through the coordination of DNA repair with temporary cell cycle arrest. Germline mutations in ATM give rise to ataxia-telangiectasia (A-T), a genome instability syndrome characterised by progressive neurodegeneration, profound radiosensitivity and susceptibility to cancer.
The role of ATM in the DNA damage response (DDR) to irradiation and irinotecan treatment was evaluated using both ATM-deficient cell lines and mice, and by using pharmacological inhibition of ATM.
This study revealed the frequent loss of ATM protein expression in human tumours, with the greatest extent reported in pancreatic cancers. Through a pharmacological kinase screen, compounds that can preferentially target ATM-deficient cells were identified including insulin-like growth factor 1 receptor (IGF1R) inhibitors. Studies in ATM-deficient cells revealed potentially complex compensatory mechanisms for DDR signalling following irinotecan treatment. The characterisation of the DDR in vivo clearly demonstrated ATM-dependent S phase DNA damage signalling in normal tissues as a consequence of irinotecan treatment, with the surprising observation of an S phase-independent DDR in regions of the heart and lung.
Whilst the concept of targeting ATM loss in tumours remains promising, the complexities surrounding compensatory DDR signalling and the inconsistency of synthetic lethality in combination with topoisomerase I inhibition are confounding and will require further study to better understand the potential of irinotecan in the treatment of ATM-deficient tumours. Alternative targets, such as those identified in the compound screen, warrant further investigation.

Keywords: Ataxia Telangiectasia
DNA damage response
ATM deficiency
Ataxia Telangiectasia mutated (ATM)
radiation
Irinotecan
Advisor: Ryan, A
Seymour, L
Online higher education experiences for First-Generation and/or Low-Income students during the Covid-19 pandemic: an explorative study through the lens of Self-formation

The experiences of First-generation and/or Low-income (FGLI) students in elite higher education institutions (EHEI) are important to analyze as often they are further disadvantaged due to the large discrepancies between them and peers who are not FGLI. Through the lens of the COVID pandemic this research seeks to understand what experiences FGLI students had and how it led to their outcomes. This case study focuses on Columbia University due to its location, reputation, and proximity to Covid. In thinking about their institutional experience students discussed disparities/stressors, their livelihood, and prestige. Through the impact of Covid, issues of housing, mental health, and loss were expressed. With the transition to online learning students examined academic policies, digital inequality, and the importance of interior spaces. Through these difficulties’ students brought forth concepts of Simon Marginson’s (2022) higher education as self-formation. Through independent conscious action, growth/moral responsibility, motivation/drive, and transformational change. These FGLI students had a mutually beneficial relationship with their higher education institution in which they helped create programs for students as well as improve their personal outcomes. Many participants were able to overcome these obstacles, and many spoke about coming out better in the end through self-formation. In looking at higher education as self-formation we can see how these high achieving individuals consider higher education as a means to better their lives and advance their livelihood. By examining this population, we can further understand the needs of this marginalized community, and in learning some of the difficulties these students face, institutions can be better prepared to assist current and future students.

Keywords: first-generation student
elite higher education institution
self-formation
online education
inequality
low-income-student
Covid-19
capital
Structure and uncertainty in deep learning

Designing uncertainty-aware deep learning models which are able to provide reasonable uncertainties along with their predictions has long been a goal for parts of the machine learning community. Such models are also frequently desired by practitioners. The most widespread and obvious method to provide this to this is to take existing deep architectures and attempt to apply existing Bayesian techniques to them, for instance, by treating the weights of the neural network as random variables in a Bayesian framework. This thesis attempts to answer the question: are existing neural network architectures the best way to get reasonable uncertainty? In the first part of this thesis, we present research on the uncertainty behaviour of Bayesian neural networks in an adversarial setting, which demonstrates that, while a Bayesian approach improves significantly on deterministic networks near the data distribution, the extrapolation behaviour is undesirable, as standard neural network architectures have a structural bias toward confident extrapolation. Motivated by this, we then explore two alternatives to standard deep learning architectures which attempt to address this issue. First, we describe a novel generative formulation of capsule networks, which attempt to impose structure on a learning task by making strong assumptions about the structure of scenes. We then use this generative model to examine whether these underlying assumptions are useful, arguing that they in fact have significant flaws. Second, we explore bilipschitz models, a family of architectures which address the more limited goal of ensuring prior reversion in deep neural networks. These are based on deep kernel learning, attempting to control the behaviour of neural networks out of distribution by using final classification layers which revert to a prior as the distance to a set of support vectors increases. To maintain this property while using a neural feature extractor, we describe a novel 'bilipschitz' regularisation scheme for these models, based on preventing feature collapse by imposing a constraint motivated by work on invertible networks. We describe various useful applications of these models, and analyse why this regularisation scheme still appears to be effective even when the original motivation behind it no longer holds, in particular, where the feature dimensionality is lower than the input.

Keywords: Bayesian machine learning
deep learning
machine learning
uncertainty
machine vision
Advisor: Gal, Y
Quantitative analysis of the mode and tempo of virus molecular evolution

Estimating the rate of nucleotide and amino acid substitutions is fundamental to our understanding of how fast species evolve. It also enables us to reconstruct their natural history. The development of sophisticated statistical methods and software in molecular sequencing analysis has made it easier for biologists to test and compare various evolutionary hypotheses and infer evolutionary parameters. However, the use of these software packages as a ‘blackbox’ without paying close attention to the underlying assumptions can lead to spurious rate estimations across different timescales which often result in erroneous inferences of virus evolutionary histories. In this thesis, I develop quantitative methods to understand biological mechanisms that can alter the molecular evolutionary rate of viruses over time and investigate the implications of having a time-dependent rate of evolution for reconstructing the phylogenetic history of viruses. I also explore alternative methods to estimating the time of origin and reconstructing the evolutionary trajectory of viruses using mobility data, national vital statistics, and serology surveys. I show how three evolutionary processes of rapid within-host evolution during chronic infections, purifying selection, and site saturation can determine the changes in evolutionary rate of viruses over different timescales, from a few weeks to millions of years. I also leverage excess mortality and seroprevalence data to correct for under-reporting of COVID-19-related deaths, reconstruct early transmission dynamics of SARS-CoV-2, and estimate the start of the Iranian epidemic as well its growth rate in the absence of high-quality genome sequence and province-level epidemiological data. This work will build towards the goal of making more accurate estimations of the timescale of phylogenetic histories and the rate at which species evolve. It also further strengthens the conceptual link between phylogenetics, population genetics, and molecular evolution.

Keywords: virus evolution
pathogen dynamics
excess mortality
population genetics
molecular epidemiology
molecular evolution
Advisor: Pybus, O
J.M. Coetzee's Hispanic worlds

My dissertation seeks to bring into critical focus the connections between J.M. Coetzee’s work and Hispanophone literature and culture, 1970 to the present day, in order to demonstrate in broad terms how he has used his symbolic capital to open a Hispanic and southern perspective onto Anglophone world literature. In four chapters, I develop different but complementary readings relating to what I call four distinctive Hispanic worlds. Having first established the methodology and the scope of Coetzee’s Hispanic involvements in the Introduction, in Chapter 1 I examine the translation, publication and reception of Coetzee’s works in the Hispanosphere (1983-2022) with a view to showing the distinctiveness of the circulation of world literature in a non-Anglophone global context with significant southern elements. In Chapter 2, I analyse Coetzee’s praxis as a reviewer, critic and scholar of Hispanophone letters (1973-2017), and demonstrate that throughout this period he was influenced by Hispanic literature even as he promoted it in diverse contexts and through varied intellectual praxes. In Chapter 3, I delve into Coetzee’s engagement with Borges and discuss how he develops his personal idea of the south in dialogue with the Argentine author, and through his academic, publishing and outreach efforts in the Southern Cone more broadly (2015-19). In Chapter 4, I show how these different worlds come together in the narrative landscape of the Jesus novels and their crepuscular fictional reality (2013-19) which, I argue, establishes a southern literature of Cervantean origin and allows for a Hispanic reading of Coetzee.

Keywords: Argentine literature
English literature
Miguel de Cervantes
Jesus novels
Australian literature
South
Pablo Neruda
Chilean literature
Don Quixote
Hispanic
world literature
South African literature
world-making
J.M. Coetzee
J.L. Borges
Advisor: Boehmer, E
Kelly, M
Mathematical modelling of macrophage functioning in inflammatory bowel disease

Macrophages play a central role in host defence and the orchestration of the immune response. Macrophage functioning defects contribute to the development of inflammatory bowel disease (IBD), in particular Crohn’s disease. Mechanistic understanding of IBD is needed to improve clinical care. We combined mathematical modelling with existing and novel experimental data to drive insight in the role of macrophages in IBD.
We developed a method to extract a minimal, weighted network from cytokine interaction data using ordinary differential equations and the Akaike information criterion. By applying our method to an existing PBMC flow cytometry dataset, we extracted a network of the regulation of IL-23, a key cytokine in IBD. Our findings suggest that IL-1 is an important regulator of cytokine responses and a promising therapeutic target for IBD patient subgroups.
Genetic studies in IBD suggest that that the hyper-inflammatory phenotype in subgroups of Crohn’s disease patients could be driven by a degree of immunodeficiency causing defective antibacterial activity and subsequent inflammation. We studied this immunodeficiency component using a combination of mathematical modelling and killing and cytokine concentration assays. Our framework, complemented with literature data, suggests that, in the presence of an impairment in cytokine production capability due to genetic defects in the NOD2 pathway, elevated cytokine levels could be solely driven by an increased bacterial load during infection.
We constructed a bacterial-load structured model to study what factors drive granuloma formation and verified our model against an existing agent-based model. We parametrised our model to represent an in vitro granuloma model and found that macrophage fusion, implemented as non-local source and sink terms in our model, does not play a large role in this context.
In summary, we combined mathematical modelling with experimental data to drive insight in macrophage functioning in IBD, while focussing on cytokine signalling, anti-microbial activity, and granuloma formation.

Keywords: cytokine interaction network
network inference
macrophages
mathematical immunology
Advisor: Gaffney, E
Uhlig, H
Coles, M