VictorJuiz/thesis huggingface dataset:
Comparing two cohomological obstructions for contextuality, and a generalised construction of quantum advantage with shallow circuits

We present two results on the subject of quantum contextuality and cohomology, and non-locality and quantum advantage with shallow circuits. Abramsky et al. showed that a range of examples of quantum contextuality is detected by a cohomological invariant based on Čech cohomology. However, the approach does not give a complete cohomological characterisation of contextuality. A different cohomological approach to contextuality was introduced by Okay et al. Their approach exploits the algebraic structure of the Pauli operators and their qudit generalisations known as Weyl operators. We give an abstract account of this structure, then generalise their approach to any example of contextuality with this structure. We prove at this general level that the approach does not give a more complete characterisation of contextuality than the Čech cohomology approach. Bravyi, Gosset, and König (BGK) gave the first unconditional proof that a restricted class of quantum circuits is more powerful than its classical analogue. The result, for the class of circuits of bounded depth and fan-in (shallow circuits), exploits a particular family of examples of contextuality. BGK's quantum circuit and computational problem are derived from a family of non-local games related to the well-known GHZ non-local game. We present a generalised version of their construction. A systematic way of taking examples of contextuality and producing unconditional quantum advantage results with shallow circuits.
Kotahi te moana, only one ocean: Pacific environmentalism, 1970–1995


“Pacific environmentalism” emerged as a regional ethic connecting Oceania and protecting Pacific peoples’ ways of thinking and relating to the natural world. It combined a customary body of knowledge about Pacific ecologies shaped over centuries, with decolonial politics, international science, and regional principles. This thesis considers the place of Pacific environmentalism within Pacific societies and the global environmental movement from 1970–1995. It argues that Pacific people consolidated knowledge about their ocean and islands, specifically that they are interconnected, indigenous, and inviolable, and used this to further self-determination—first as part of a regional movement, and then to make global interventions.
To account for Oceania’s vast geographical distance and thematic diversity, while demonstrating the operation of a new environmental regionalism, the thesis is structured episodically around the origins and early work of the Secretariat of the Pacific Regional Environment Programme (SPREP), an intergovernmental regional organisation. After locating SPREP in Pacific responses to nuclear colonialism, insular laboratories, and preservationist national parks in the mid-1970s, the thesis shows how Pacific scientists, diplomats, community leaders and allies retooled environmental management for regional socio-ecologies. Research conducted regionally maintained Pacific people were an indivisible part of island systems, connected by the ocean into a shared, interdependent environment. Environmental regionalism through SPREP proceeded collectively, effectively mediating technocratic metropolitan influence by emphasising traditional knowledge and community-based management, while counteracting extractive mining, fishing and forestry. Advocacy on the issues of nuclear waste dumping and climate change turned self-determination into sovereignty, using United Nations forums to challenge neo-colonialism and dependency, establishing Pacific regimes of ocean governance and interregional associations of like-minded island regions. Pacific environmentalism prevented further ecological imperialism and the region’s integration into globalised environmental management; its elaboration contributes an environmental dimension to Pacific histories of political regionalism and a regional critique of “global”-yet-Western histories of environmentalism.

Keywords: Pacific
Ocean Governance
Regionalism
Conservation
Climate Change
Anti-nuclearism
Environmental History
Indigenous Knowledge
Advisor: Belich, J
Why have suicide attacks not been adopted by a wider variety of actors?

In October 1983, Hezbollah drove two suicide trucks into the U.S. and French Marine barracks in Beirut. The first bomb killed 241 people, inflicting the largest single day loss of life in the U.S. Marine Corps since the battle of Iwo Jima in 1945. Soon after, the second truck crashed into the French barracks in West Beirut, killing another 58 soldiers. The attack was credited with influencing the U.S. to withdraw its troops from Lebanon the next year. Since Hezbollah demonstrated suicide attacks’ potential merit, the tactic has crossed ideological and cultural boundaries only on rare occasions. Considering the tactical and strategic benefits identified in the existing literature as unique to the tactic, its narrow appeal is a puzzle. Why have suicide attacks not been adopted by a wider variety of revolutionary actors? This thesis argues that cross-country, cross-ideological spread should be considered analytically distinct from instances of domestic spread, like what occurred in Lebanon in the 1980’s, or ideologically homogenous spread, as observed among Salafi-jihadis. Domestically, the high similarity between groups means that the use by one actor generates relevant information on audience costs that other groups in the same environment can use in cost-benefit analyses. Within an ideological frame, the tactic comes pre-justified and with expectations about status gains. Actors outside of these categories – the first movers in their respective social contexts and ideological frames – have little information to base their decision to adopt. Existing explanations posit that norms are an inhibiting factor for groups to use suicide attacks in these cases. I critically examine this contention and find that suicide attacks have never been normatively acceptable prior to adoption by a first mover. Based on fashion theory, I suggest that suicide attacks have spread to new social contexts based on the reputation and prestige of the group associated with the tactic, not its expected tactical and strategic benefits or conformity to local norms. The limited spread can therefore be tied to the limited prestige of the tactic’s reference group.

Advisor: Kalyvas, E
Dynamics in the regulatory genome

The way in which DNA is uniquely folded in the nucleus into specific conformations enables and/or reflects cell-type specific interactions of active cis-regulatory elements, namely promoters and enhancers, to regulate specific programs of gene expression. The cohesin protein complex is a key player in the dynamic organisation of genome folding, orchestrating chromatin looping through a process known as loop extrusion. How this process is directed in a cell-type specific manner is currently unknown. A widely accepted hypothesis is that cohesin is recruited to active cis-regulatory elements, however current methods are unable to assay the dynamic nature of cohesin loading onto the chromatin. To address this, in this thesis I have developed inducible cellular models that enable cohesin to be tracked in a dynamic manner, in an attempt to answer this question.
Initially, I investigated if a single active enhancer was capable of recruiting cohesin to a neutral region of the genome. Using a high-resolution chromosome conformation capture approach, I showed that a new 3D domain was formed following activation of the enhancer, and that cohesin was recruited to this locus. Whilst this provided convincing evidence that cohesin plays a key role in this process, perhaps via loop extrusion mediated domain formation, data from a single locus provides no way of testing where cohesin was first recruited upon the activation of the domain. In the next two chapters I developed two novel cellular models to investigate cohesin dynamics on a genome-wide scale by orthologous ‘push’ and ‘pull’ technologies. In doing so I aimed to investigate whether active cis-regulatory elements are responsible for driving the recruitment of cohesin on a genome-wide scale.

Keywords: gene regulation
genome
ChIP-seq
cohesin
dynamics
Tracking the evolution of cancer genomes

Tumour clones consist of cancerous cells with shared ancestry. The study of cancer evolution has been further advanced by the introduction of mathematical algorithms to reconstruct the phylogenetic tree within the tumour. Bulk sequencing data pro- vides not only the VAF and ploidy information that most established methods now use to infer tumour subclonal structure, but also another equally important piece of information, namely phasing information. Phasing information from sequencing reads can be used to find the most likely phylogenetic trees.
During my Ph.D, I proposed a generative model of SNVs distribution in next-gen sequencing reads, PhaDPClust, which utilises phasing information and constructs complete phylogenetic trees automatically. This method builds on the DPClust framework, and can be applied to both single sample and multiple sample analysis.
On single sample analysis, PhaDPClust outperformed other established methods in subclone reconstruction, measured by several metrics from the SMC-HET Chal- lenge. The performance of PhaDPClust was constrained by the abundance of phase information, as evidenced by results on real tumour samples.
Then, PhaDPClust was extended to multisample analysis. PhaDPClust suc- ceeded in reconstructing phylogenetic trees in similar topology automatically, but failed to split some clusters, implying some work still needs to be done in the future.

Advisor: Wedge, D
Woodcock, D
Myers, S
Exploring the role of GPR65 in driving the pathology of ankylosing spondylitis

Genome wide association studies have identified GPR65 risk loci with many immune-mediated diseases, including ankylosing spondylitis; however, its pathogenic role remains unknown. The inflamed synovial joint has a low pH signature, therefore understanding the role of this lymphocyte-expressed, proton-sensing GPCR in the context of joint inflammation is important.
With no commercial reagents available, I set out to generate monoclonal antibodies specific to human GPR65, with the aim to use them as tools in further studies. Phage display technology paired with novel antigen design, and multiple immunisation strategies proved challenging and largely unsuccessful in my hands. Despite terminal sera titres binding GPR65-expressing HEK cells, antigen-specificity was lost upon screening against primary cells.
In parallel, I have explored receptor expression on PBMC subsets and interrogated the biology of GPR65. Upon stimulation, cellular activation and pro-inflammatory cytokine release was suppressed from cells that express the highest levels GPR65 at pH6.5, compared to those at neutral pH. Due to their receptor expression profile, response to extracellular pH changes and involvement in disease, I focused on mucosal-associated invariant T (MAIT) cells. Significant partial recovery of pH-dependent IFNγ inhibition was observed, at transcriptional and protein levels, when silencing GPR65 in this cell subset; whilst at neutral pH, a pro-inflammatory role for GPR65 activity was proposed, with an increase of IL-17A production from TCR-stimulated MAIT cells detected.

Keywords: immunology
antibody discovery
Advisor: Bowness, P
Al-Mossawi, M
Chen, L
Lawson, A
To redistribute or not to redistribute? The effects of inequality, development, absolute and relative income, and party polarisation on preferences for redistribution

When do people want redistribution? Income inequality has been on the rise in recent decades, especially in advanced democracies. Since redistribution is the main tool that governments have at their disposal to ameliorate income disparities, and government policies are (at least partly) influenced by public opinion, abating income inequality will largely depend on whether people want redistribution. Therefore, this has brought renewed importance to understanding the determinants of support for redistribution.
Redistributive preferences are commonly viewed as being driven by self-interest, implying that support for redistribution is monotonically determined by how much a person can expect to gain or lose from it. However, empirical evidence has not always been consistent with this framework, and findings have varied due to data availability as well as differences in methodology and the operationalisation of key variables.
This dissertation consists of three papers that make use of the World Values Survey and the European Values Study to analyse the determinants of respondents’ support for redistribution. The first paper focuses on the effects of inequality and development on public support for and division over redistribution. The results show that support is higher in countries that are rich and unequal, and division is lower in countries that are poor and equal. The second paper focuses on how people perceive the utility of redistribution in absolute or relative terms depending on whether they can expect to gain or lose from it. The results show that people below the mean income base their preferences on their absolute distance from the mean, whereas for people above the mean it is based on their relative distance from the mean. The third paper focuses on the role that political parties play in (de-)activating self-interest, using the Comparative Manifesto Project to measure party polarisation on economic issues. The results show that people, particularly the poor, are more self-interested when parties are more polarised in their economic positions.
Overall, the findings indicate that inequality drives support for redistribution more in rich countries because the poor have more to gain, and the rich are willing to pay more to ameliorate disparities. This suggests that public opinion in advanced democracies is unlikely to tolerate protracted rises in inequality.

Keywords: inequality
income
polarization
redistribution
development
Advisor: Evans, G
Defining the dynamic relationship between interferon-gamma and CD8+T cell dysfunction in melanoma

CD8+ T cells or cytotoxic T lymphocytes (CTLs) are crucial to anti-tumour responses, as they kill cancer cells. However, CD8+ T cells are becoming dysfunctional over time in tumours leading to tumour escape. The concept of T cell exhaustion linking the CTL dysfunction with the upregulation of inhibitory molecules known as immune checkpoints only partly explains their dysfunction, as immunotherapies targeting immune checkpoints showed very limited success. This underlines that there is a critical need to decipher other mechanisms involved in CTL dysfunction in cancer. CTL efficacy notably relies on their interferon-gamma (IFNγ) production for cytotoxic cytokine release. IFNγ is a major immune mediator with strong anti-tumour functions but also concomitant pro-tumour effects. Because IFNγ is inherently linked to tumour immunity efficacy, it is critical to fully understand how it can also simultaneously impede it. CTLs are the main IFNγ producers in tumours but how the chronic IFNγ presence affects their anti-tumour function has not been properly assessed yet. To address whether IFNγ sensing is directly involved in CTL dysfunction we used a mouse model where the interferon-gamma receptor (IFNγR) is specifically ablated in CD8+ T cells (CD8-IFNγR1KO) rendering them unable to sense the cytokine. Depleting the IFNγR1 in CD8+ T cells is sufficient to restore immunity towards B16F10 melanoma with better tumour control, although it does not substantially enhance CTL functions. The characterisation of intra-tumoral CD8+ T cells revealed that IFNγ preferentially affects a particular CD8+ T cell subset of precursor cells: the stem-like T cells. Indeed, stem-like T cells that do not sense IFNγ originate a greater T cell expansion through greater CD8+ T cell proliferation in tumours, reducing the exhaustion level of IFNγR1KO CD8+ T cells. Mechanistically, IFNγ restricts their active maintenance, preventing the steady generation of early-exhausted CD8+ T cells in tumours. Besides, while control CD8+ T cells are excluded from the tumour core, IFNγR1KO CD8+ T cells infiltrate better the tumour core. Altogether, our data show that IFNγ drives a negative feedback loop whereby IFNγ depletes stem-like T cells in the tumour restricting the CTL anti-tumour potential. Targeting this pathway might offer an alternative strategy to enhance the efficacy and longevity of adoptive T cell therapies.

Keywords: CD8+ T cells
T cell dysfunction
melanoma
stem-like T cells
Advisor: Gerard, A
Midwood, K
Getting your money's worth: how fees affect students' approaches to employability and university

The last three decades have seen significant changes in the higher education (HE) sector in England. Alongside a shift towards a market-based approach to HE and the implementation—and subsequent raising of—tuition fees, there has been a growing focus on employability and getting “value for money”, together with a growing concern about the growing prevalence of the so-called “student-consumer”. Even today, university funding continues to be a shifting and divisive issue, with tuition fees at the forefront of debates around students returning to universities during the COVID-19 pandemic. By contrast, Scotland has retained a system-based approach to HE and free tuition for both Scottish nationals and EU students.
Though much research has looked at the possible impact of tuition fees on university applications, little has been done to explore what tuition fees might do to the way that students experience and approach university. This study therefore aims to fill an important gap in our knowledge about how students are reacting to the differing funding arrangements in England and Scotland. It asks, specifically: how do different university funding systems influence undergraduates’ approaches to employability and university?
To address this, the study employed a mixed methodology consisting of three phases: a scale development phase, a quantitative phase (involving surveying 700 students at six universities in England and Scotland), and a qualitative phase (involving interviews with a subset of over 30 students). Key findings showed that the relationship between university funding and how students approach university is complex and impacted by social background: while being from a lower socio-economic background was related to a higher consumer orientation, students who self-identified as working-class were shown to be more learner-oriented when paying tuition fees than not, while middle-class students were less learner-oriented when paying tuition fees than not. On the other hand, though social background did not appear to affect approach to employability, and there was no significant relationship between fee-paying and approach to employability, university country played a significant role: students in Scotland appeared to be more employability-savvy than their peers in England. These and other important findings have significant implications, both in terms of the two nations’ HE/labour market policies and the discourse around the student- as-consumer.

Keywords: tuition fees
employability
student attitudes
higher education
Advisor: Baird, J
Keep, E
Stories theology lives by: a narrative and phronetic theology of liberation

What if, far from being a centre or force of liberation, academic theology itself needs liberation? Considering this requires theological reflexivity concerning theology’s purpose and praxis and sociological reflexivity concerning how the field of theology functions as a system. Pierre Bourdieu’s method of sociological analysis is especially suited to facilitating this reflexivity. Employing a pioneering Bourdieusien analysis through a case study of the Yale School of Narrative Theology, this interdisciplinary thesis explores how in allowing a set of reductive and non-inclusive epistemic assumptions to control the mode theologising, the field of theology has perpetuated symbolic violence, namely a legitimation of the status quo of theological mode. In this analysis, those from marginalised communities suffer most, either by being forced to theologise according to the dictates of the dominant or by being disregarded in or disenfranchised from participation. However, the assumption of an abstractionist discursive mode for theological epistemology also renders it epistemically reductive: both of the modes of theological production and knowledge and of the sociological dimensions of doing theology. So, building upon our Bourdieusien analysis and synthesis of the Yale School’s theological insights, we construct a truly productive narrative and phronetic theology of liberation through love that removes symbolic violence from theology without resorting to it. Through dialogue with Gustavo Gutiérrez, Hans Urs von Balthasar, Bourdieu, Cognitive Science of Narrative, and Christian Scripture we construct a dialectic and phronetic epistemology of love in which one loves in order to know. This removes symbolic violence from academic theological epistemology by embracing creative dialectical subjectivity and objectivity in knowing through love. Inseparable from this, we uncover the fundamentally existential origins of symbolic violence and narrate an alternative to legitimation-through-power in Christ incarnate and crucified expressing a radical embodied solidarity with God and humanity in love.

Keywords: Balthasar
symbolic violence
Ricoeur
sociology
Yale School
Hauerwas
phronesis
theology
H. Richard Niebuhr
love
cognitive science
Lindbeck
Pierre Bourdieu
constructive
Frei
epistemology
liberation
narrative
Gutiérrez
biblical interpretation
Advisor: Ward, G
Understanding & incentivising innovation for a climate compatible future

Net-zero emissions are needed to stabilise mean global temperatures. This is one of the greatest challenges of our generation. Innovation will play a fundamental role in ensuring economic activity becomes “climate-compatible”. Yet, robust empirical evidence on how to best incentivise investment and innovation in low-carbon technologies is limited. This thesis explores this question using rich datasets related to energy generators, firms, and patents. It is divided into three papers which respectively seek to understand (i) the role of price and risk-mitigation policies, such as feed-in-tariffs, in bringing breakthrough clean technologies to market, (ii) the joint impact of different policies on firms’ incentives to undertake clean innovation, and (iii) patterns of learning and knowledge diffusion across clean and dirty technologies. This thesis deploys tools from modern econometrics, causal inference, and network analysis to study these questions. It finds that risk reduction policies alongside subsidies are important in bringing nascent clean technologies to market, that environmental and innovation policy, if not well-coordinated, can lead to un-intended impacts, and that, on aggregate, knowledge embedded in clean inventions is intellectually distant to that embedded in dirty inventions, despite a few areas of close proximity. Collectively, the papers demonstrate the importance of understanding innovation processes and policies for the net-zero transition.

Keywords: feed-in tariffs
solar energy
R&amp;D tax credits
knowledge spillovers
innovation policy
energy policy
risk reduction
directed technical change
environmental policy
Advisor: Hepburn, C
Pless, J