VictorJuiz/thesis huggingface dataset:
Efficient computation and maintenance of datalog materialisations

Datalog is a prominent knowledge representation language whose popularity is mainly due to its ability to express recursive definitions. Datalog applications typically require efficient reasoning over datalog programs and facts. To support this, datalog systems often materialise all consequences of a datalog program so that all queries can later be evaluated directly over the materialisation. This style of reasoning is usually complemented with an incremental maintenance algorithm that updates the materialisation whenever the input facts change. Existing solutions to the incremental maintenance problem either handle only nonrecursive rules or contain steps that evaluate rules “backwards” by matching their heads to a fact and evaluating the partially instantiated rule bodies as queries. We show that this can be a considerable source of overhead even on very small updates, and we present two hybrid approaches that reduce or even eliminate “backwards” rule evaluation while still handling arbitrary datalog programs. Moreover, we observe that for both materialisation and incremental maintenance, certain (combinations of) rules can be handled much more efficiently using custom algorithms. To integrate such algorithms into a general reasoning approach that can handle arbitrary rules, we propose a modular framework for computing and maintaining a materialisation. We split a datalog program into modules that can be handled using specialised algorithms, and we handle the remaining rules using the seminaïve evaluation strategy as in most existing solutions. We also present two algorithms for computing the transitive and the symmetric–transitive closure of a relation that can be used within our framework. Finally, we show empirically that the proposed solutions are usually significantly faster than existing approaches, sometimes by orders of magnitude.

Advisor: Motik, B
Horrocks, I
Rethinking resistance

This thesis is a collection of four discrete essays on the topic of political resistance. While the contents of the individual essays are disparate, they are nonetheless connected by substantive and methodological themes. I discuss these issues, and the broader framing of the thesis, in the Introduction.
The first essay, Clarifying Our Duties to Resist, examines a prominent argument according to which the moral principles that ground individuals’ duties to comply in just conditions also ground their duties to resist injustice in unjust conditions. I argue that this argument does not apply to conditions where injustice is entrenched and normalised.
The second essay, Differentiating Disobedients, considers the question of the ways in which morally motivated individuals should differentiate themselves from criminals when they engage in political resistance or disobedience. I argue that the category of morally motivated disobedients is potentially more inclusive than has been commonly assumed.
The third essay, The Legitimate Targets of Political Disobedience, address the question of what individuals can legitimately target during their acts of political disobedience. I defend a novel principle that allows us to make fine-grained differentiation between legitimate and illegitimate targets.
The fourth essay, Vandalising Tainted Commemorations, adjudicates a contemporary disagreement about what we should do about commemorations of people or events implicated in injustice. I offer a qualified defence of vandalising tainted commemorations, as a strategy that adjudicates the demands of the two dominant yet opposing views on the issue.
In a final note, In Lieu of A Conclusion, I review the work that has been done, and identify several areas for future work.

Keywords: Defensive ethics
Resistance
Political resistance
Commemoration
Conscience
Political duties
Conviction
Civil disobedience
Vandalism
Advisor: Wolff, J
Fabre, C
Brownlee, K
Visible light-mediated cyclizations of cyclic enones

The work outlined in this thesis covers the development of visible light-mediated cyclizations of cyclic enones. Chapter one provides an overview of photochemical cyclizations, focusing on visible light-mediated cyclizations using triplet energy transfer from a suitable sensitizer, as well as an overview of the photochemical cyclizations of cyclic enones. Chapter two discusses the development of a visible light-mediated intramolecular arylation of cyclic 2-arylheteroenones to generate a wide range of cis-fused heterocycles.
Chapter three details efforts into the photochemical synthesis of spirocyclic compounds via intramolecular hydrogen atom abstraction using a cyclic enone chromophore. Chapter four discusses the development of a visible light-mediated spirocyclization of cyclic 2-amidoenones. After initial optimization, the scope and scalability of the reaction was explored, and derivatization of the products investigated. Subsequent mechanistic experiments provided insight into the high diastereoselectivity of the reaction.
Chapter five looks at applications of the previously developed reactions to acyclic chromophore systems, and the challenges present in this modification

Keywords: Triplet Energy Transfer
Visible Light
Advisor: Smith, M
Drug-device development: cancer immunotherapy with therapeutic, ultrasound-mediated delivery

Tumour and tumour microenvironment exploitation of immunologic checkpoints like PD-L1 can enable immune evasion. Recent advances in oncology, have brought forward antibody drugs, such as anti-PD-L1, capable of blocking and/or mediating the eradication of cells that express PD-L1. Despite promise across a wide range of indications, clinically such agents meaningfully extend survival only in a fraction of patients treated.
Immature, heterogenous blood vessels, elevated interstitial pressures, and stromal barriers severely limit the accumulation and extravasation of drugs within the tumour microenvironment. We hypothesize that the physical size of antibody therapeutics, such as anti-PD-L1, compounded by delivery barriers could be a factor limiting their efficacy.
Recently, submicron cavitation nucleation agents, sonosensitive particles (SSPs), activated by focused ultrasound have been shown to improve the delivery of large, anti-cancer therapeutics via microstreaming-mediated transport. Our aim was to pre-clinically investigate whether systemically-dosed anti-PD-L1 followed by SSPs and the application of focused ultrasound could improve the intratumoural delivery and therapeutic efficacy of anti-PD-L1.
Efficacy studies revealed that pairing anti-PD-L1 with ultrasound-mediated cavitation can significantly extend median survival time. Cavitation was also found to enhance the intratumoural accumulation of anti-PD-L1 and three other antibodies. Further, the binding intensity and distribution of anti-PD-L1 improved in cavitation-treated tumours. Immunological analysis suggests that anti-PD-L1 paired with cavitation enables the innate and adaptive immune system to leverage the modest cavitation-induced inflammation and improved anti-PD-L1 delivery to facilitate tumour attack. Taken in a broader context, this pre-clinical work suggests that ultrasound-mediated cavitation warrants further investigation as viable tool to improve drug delivery clinically.

Advisor: Hester, J
Coussios, C
Carlisle, R
Wood, K
Reactivity studies of the 2-phosphaethynolate anion: a pathway to phosphinecarboxamides

This thesis summarises the research carried out during my PhD on the phosphinecarboxamide family. Inspired by Wöhler’s seminal synthesis of urea, the phosphinecarboxamides are obtained by the reaction of the 2-phosphaethynolate anion, PCO–, a heavier congener of the cyanate anion, with ammonium salts. These species are phosphorus-containing analogues of urea, RHPC(O)NHR’. These compounds are prime examples of primary phosphines that exhibit remarkably air- and moisture stability. Several examples of these compounds were obtained by the reaction of the 2-phosphaethynolate anion with a variety of amines such as amino acids, leading to N-functionalised chiral products and bidentate amines. The reactivity of these compounds was explored by promoting deprotonation of the molecules, which allowed post functionalisation, affording new P-functionalised species. These phosphinecarboxamides were also shown to be able to act as Lewis bases, as they were able to use the phosphorus lone-pair to coordinate to transition metals centres. Finally, this thesis underlines the reactivity of the PCO– anion with amines bearing a ferrocenyl group as well the reactivity of the resulting products.

Advisor: Goicoechea, JM
Conservative and Labour research departments, economic thought, and party policy, 1970-79

This thesis considers the influence of professional policy experts on the ideologies of the Conservative and Labour parties in 1970-9. By focusing on the Conservative Research Department and the Labour Party Research Department, the thesis seeks to connect intellectual and political practice during a decade often seen as a turning point in post-war British historiography. To do so, the thesis examines three policy areas that defined the high politics of the decade: economic governance, industrial relations, and European integration. By tracing the research departments' adoption or rejection of policies, the thesis constructs a systematic account of the departments’ ideological leanings, intellectual impact, and positions in the parties’ ideological traditions. The thesis argues that economic thought was a primary battleground, laying the basis for the parties’ approaches to other questions. In this sphere, the Conservative Research Department contributed to the party’s shift towards neo-liberalism, while the Labour Party Research Department promoted a programme of leftist state interventionism. In industrial relations, the Conservative policy unit advocated cooperative relations with trade unions, while Labour’s policy experts found their radical aspirations obstructed by party and trade union leaders. In respect of Britain’s membership in the European Economic Community, the Conservative policy unit’s enthusiastic pro-Community views stood in contrast to the Labour experts’ trenchant Euroscepticism. The thesis argues that both research departments were able to exploit their privileged organisational positions to act as intermediaries between intellectual and political practice. During the ideologically fluid 1970s, the parties’ policy experts were, for the most part, effective in promoting ideas that aligned with their intellectual preferences. The result was a radicalisation of politics, where Conservative and Labour ideas were set on diametrically opposed trajectories. The research departments contributed to this divergence, and therefore, to the transition from post-war social democracy to Thatcherite neo-liberalism.

Keywords: Europe
Industrial relations
Conservative Party
Economic thought
Labour Party
Research department
Advisor: Jackson, B
The pulpit and the brush: preaching and painting in seventeenth-century Spain

The Council of Trent re-examined the traditions of the Catholic Church regarding the role of the visual arts in worship. Equipped with a humanistic mindset steeped in Greco-Roman rhetoric, the leading clergy came to value paintings, first and foremost, for their ability to stir the viewers’ emotions, giving rise to a new understanding of religious images. Such a stance, common in early modern Spain, encouraged the employment of images and words as different but compatible instruments that converged to achieve a common goal, making an emotionally arresting impression on the viewer or listener. The Church regarded this strategy as the most effective way of engaging with the laity.
Contemporary printed sermons show how Spanish churchmen developed new styles of preaching based on their understanding of classical rhetoric, which helped them elicit the desired emotional reactions in the context of Catholic liturgy. One such technique, inspired by medieval meditation literature, involved using word painting to summon vivid, emotive images in the mind of the listener. Preachers couched in similar language their references to inner visions and to physical images (chiefly altarpiece paintings but also portable canvases produced from the pulpit unexpectedly), which highlights their perceived equivalence. Such practices became common and shaped the public’s visual culture.
The experience of hearing sermons played a decisive role in the development of religious art. Preachers circulated ideas to which only a small educated elite had access, and did so from a position of authority. As part of a congregation, artists and art patrons absorbed this knowledge, which informed their making and dissemination of new iconographies. A comparison of artistic and oratorical examples as well as theoretical literature from the period reveals that painters and preachers employed similar criteria in judging what type of details and ornamentation were pertinent to a specific painting or sermon.

Keywords: Catholic Church
Preaching
17-Century Spain
Rhetoric
Painting
Religious Art
Advisor: Thacker, J
Reaction-bonded silicon carbide for nuclear fusion blanket applications

Reaction-bonded silicon carbide has properties which make it useful for certain components of a nuclear fusion reactor, but its response to irradiation has not been studied since early work suggested its unsuitability. Modern commercially available samples of RB-SiC, along with some novel samples prepared in-house were investigated to identify links between microstructure and radiation and mechanical performance.
2.5 displacements per atom (dpa)and 0.25 dpa of radiation damage were introduced using ion implantation at 300 °C and 750 °C. The radiation-induced changes to mechanical properties were investigated using nanoindentation, chemical defects by Raman spectroscopy, and structural defects by electron backscatter diffraction.
Residual stresses were found to strongly influence the micromechanical properties of reaction-bonded SiC. Radiation changes these stresses leading to the degradation of macroscopic mechanical properties. Further investigation of these residual stresses found they are caused by radiation swelling of silicon carbide. This swelling is constrained by the unirradiated layer in ion irradiation experiments, creating a lateral stress which increases the apparent toughness and hardness, as assessed by nanoindentation. This constrained swelling effect appears to significantly influence the mechanical properties measured by nanoindentation of ion implanted layers.
Ion irradiation appears unable to recreate defects created by neutron irradiation. The lateral swelling stress prevents chemical bonds reaching their equilibrium length, possibly hindering their evolution. The choice of implanted ion also appears to influence defects in SiC; self-ions change the local chemistry and defect structures.

Keywords: Raman spectroscopy
radiation damage
residual stress
micromechanics
nuclear fusion
Silicon carbide
Advisor: Armstrong, D
Todd, R
An LFG account of empty pronouns in Mandarin Chinese

This thesis incorporates a study of the syntactic distribution and pragmatic properties of empty pronouns in Mandarin Chinese (Chinese in short) from the point of view of Lexical-Functional Grammar (LFG). With reference to various accounts of Chinese empty pronouns by previous researchers (e.g., J. Huang 1984; Y. Huang 1995; Pan and Hu 2000) and the problems with their analyses, we offer a conjunctive approach to capture how Chinese zero anaphora is constrained at the level of syntax and the level of pragmatics. A series of syntactic rules are proposed and every occurrence of Chinese empty pronouns must strictly obey these absolute, inviolable syntactic constraints. Intersententially, discourse-dependent pragmatic conditions based on Lambrecht’s (1994) information-structure theory form the second part of our two-way characterization of Chinese empty pronouns. Lastly, we present a comparison between the case study of empty pronouns in Japanese by Kameyama (1985) and our current study of empty pronouns in Chinese, and demonstrate two distinctive pro-drop phenomena.
Chapter 1 is an introduction to the notion of pro-drop, types of empty pronouns identified in Chinese, and the theoretical frameworks assumed in this study. Chapter 2 reviews three different previous analyses of Chinese empty pronouns, discusses the problems each account suffers, and promotes an integrating account which takes both syntax and pragmatics into consideration. Chapter 3 investigates the syntactic distribution of Chinese zero anaphora, whilst Chapter 4 provides a contrasting pragmatic characterization, followed by an examination of our proposal by testing it in naturalistic data and then a comparative study of Chinese and Japanese empty pronouns in Chapter 5. Finally, Chapter 6 summarizes the previous chapters, points out relevant issues that are not covered in this thesis but which could be research topics for future investigation, and reiterates how LFG is useful in this present work.
An investigation of the role of ASPP2 in HIF signaling and cancer

The ability to sense and respond to hypoxia is essential for the survival of living organisms and is frequently co-opted by tumor cells to adapt to hypoxic microenvironment. As the pivotal transcription factor for hypoxic responses, the hypoxia inducible factors (HIFs) transactivate a wide repertoire of genes that can mediate divergent functional outcomes. The regulation of HIF target gene selectivity is complex, involving the canonical regulation by oxygen sensors prolyl hydroxylases and factor inhibiting HIF (FIH) and the regulated recruitment of transcriptional cofactors, such as p300. However, how HIF target gene selectivity is regulated in cancers has yet to be fully understood.
Apoptosis stimulating protein of p53 2 (ASPP2) belongs to the ASPP protein family whose members are established regulators of p53-family proteins. Recently, it was found that ASPP2 is one of the alternative substrates of FIH and may be a potential competitor of HIFalpha for FIH activity. However, whether ASPP2 plays a role in the regulation of HIF activity in cancer remains unclear.
In this work we showed that ASPP2 regulates the expression of a subset of HIF target genes irrespective of FIH status. Using HIF target gene EGLN3 for further investigation, we further found that ASPP2 does not affect either the protein expression, subcellular localization, or the level of DNA-binding of HIFs to the HRE-containing EGLN3 loci.
To explore whether ASPP2 modulates the expression of EGLN3 and potentially other ASPP2-sensitive HIF targets through regulating another signaling pathway that crosstalks with HIFs at the transcriptional level, we constructed a bioinformatics pipeline that combines gene coexpression analysis and gene set enrichment analysis to successfully identify both known and hitherto unknown ASPP2-coexpressed pathways at a pan-cancer level.
Among these ASPP2-coexpressed pathways, we focused on the hippo pathway in which transcriptional coactivator YAP has previously been reported to act as a transcriptional cofactor of HIF1alpha. We found that the loss of ASPP2 reduces the nuclear localization of YAP under hypoxia. It also attenuates the nuclear interaction between YAP and HIF1alpha, as well as the level of DNA-binding of YAP at HRE-containing loci of EGLN3.
Overall, this study demonstrates for the first time that ASPP2 modulates a subset of HIF target gene expression, potentially by regulating the interaction between YAP and HIF1alpha. Our work also identifies novel pan-cancer ASPP2-associated pathways that would assist in unlocking hypothesis to expand the functions of ASPP2 in human cancers and beyond.

Keywords: cell biology
transcriptomics
interactomics
CRISPR-Cas9
phosphoproteomics
ASPP2
cancer
hypoxia
molecular biology
cell signaling
gene co-expression
bioinformatics
Advisor: Lu, X
Ratcliffe, P
Entanglement between nodes of a quantum network

Quantum devices are rapidly gaining momentum as a technology that will induce a paradigm shift in computing, communication and cryptography. Trapped ion qubits are one of the leading candidates for implementing a quantum computer, having previously demonstrated all of the required criteria. Local gate fidelities between ions exceed those for all other platforms, but the total number of ions in a trap is limited by unavoidable issues – one possibility for scaling the ion trap quantum processor is to create entanglement between ions in separate traps via single photons. The work in this thesis demonstrates the generation of remote entanglement between ions at high fidelity and rate, paving the way towards protocols using multiple entangled pairs for computations.
We describe the construction from scratch of a twin-trap apparatus designed to entangle separated ions. We demonstrate the entanglement of strontium ions in traps separated by ∼ 2 m by swapping entanglement from single photons emitted by the 88Sr+ ions. A novel photon collection geometry is used, maximising the entanglement between the ion and photon without impeding optical access for standard ion trap laser beam geometries. The Bell state fidelity of the ion-photon state, which is itself a valuable entanglement resource for blind computation, is at least 97.70(12) % in either trap, with entangled pairs detected at a rate of at least 3.98 × 103 s−1. The remote ion-ion Bell state fidelity is 94.0(5) %, and is generated at a rate of 182 s−1, representing the highest fidelity remote entanglement reported in ions by a large margin, at a rate more than an order of magnitude faster than previous experiments.
The two identical trap systems are designed with capabilities beyond those demonstrated here. We can co-trap 88Sr+ and 43Ca+ in a microfabricated trap suitable for local ion transport operations, opening up the possibility of performing distillation of remote entanglement in the same apparatus. Entanglement distillation can be used to make remote entanglement with similar fidelity to local operations, and would represent a significant step towards a fully scalable ion trap quantum computer architecture.

Keywords: Quantum networking
Trapped ions
Advisor: Lucas, D