VictorJuiz/thesis huggingface dataset:
Cyber supply chain risks in cloud computing - the effect of transparency on the risk assessment of SaaS applications

While the cloud model has many economic and functional advantages, the increased external interactions of cloud applications have expanded the complexity of its architectures and reshaped its supply chain. Due to the variety of parties involved in cloud service delivery and the high degree of supplier autonomy, assessing cloud risks has become a challenge. Also, the widespread application of traditional frameworks to cloud risk assessment has several shortcomings, including the subjectivity of risk evaluation and inability to measure cyber risk in complex systems.
Recognising that recent work on cloud risk assessment has focussed on cloud consumer risks, we sought to address the cloud service provider (CSP) risk assessment challenge. This research began with an in-depth assessment of the literature in cloud risk assessment and supply chain transparency. We conducted surveys and semi-structured interviews to validate the transparency gap and establish its link with qualitative risk assessment methods. The results of the studies substantiated the need for more rigour in cloud risk assessments and provided evidence on how this can be improved with supply chain transparency.
To address this gap, we proposed the Cyber Supply Chain Cloud Risk Assessment (CSCCRA) model; a quantitative and supply chain-inclusive model targeted at Software-as-a-Service (SaaS) CSPs. The model is made up of three main components, two of which are novel inclusions to cloud risk assessment, i.e. supply chain mapping and supplier security assessment. The CSCCRA model reflects the systems thinking approach, enabling CSPs to visualise information flow through the supply chain, assess supplier security posture, document assumptions regarding the risk factors, and appraise security controls.
In evaluating the CSCCRA model, a three-step approach was adopted. First, the developed model was evaluated by the author and members of the academic community to ensure that it met our initial criteria. Second, the model was face-validated by cloud and risk experts within the industry. Third, we conducted three real-world case studies, using the model to assess the risks of SaaS providers. The result of these evaluations confirmed the usefulness and applicability of the model for assessing cloud provider risks. Also, the case study results and subsequent development of the CSCCRA web application showed that a structured and systematic application of the proposed model within a SaaS organisation was capable of yielding objective and defensible results. The model demonstrated its utility by assisting stakeholders to quantify cloud risks, while also promoting cost-effective risk mitigation and optimal risk prioritisation.
Overall, these results advance knowledge both for research and in practice, taking us one step further into improving cloud risk assessment.

Keywords: Supplier Assessment
risk assessment
Quantitative risk assessment
systems thinking
Monte Carlo
cloud computing
Delphi
Advisor: New, S
Martin, A
The coarse geometry of group splittings

This thesis addresses Gromov’s program of studying the geometry of finitely generated groups up to quasi-isometry. In particular, we investigate when we can characterise group splittings geometrically, and how this can be used to determine whether groups are quasi-isometric.
In Chapters 2 and 3 we develop several coarse topological techniques, building on work of Kapovich–Kleiner [KK05], that we expect to be of interest in their own right. We use these techniques to show that if G is a group of type FPn+1 that is coarsely 3-separated by an essentially embedded coarse PDn space W, then G splits over a subgroup H that is at finite Hausdorff distance from W. This can used to deduce that splittings of the form G = A *H B, where G is of type FPn+1 and H is a coarse PDn group such that both |CommA(H) : H| and |CommB(H) : H| are greater than two, are invariant under quasi-isometry. These results are contained in [Mar18b].
In Chapter 4 we extend the methods of Chapter 3 to understand the 2-separating case. Building on work of Scott–Swarup [SS03], we describe a regular neighbourhood of essentially embedded coarse PDn spaces.
In Chapter 5 we show that the JSJ tree of cylinders over abelian subgroups of a RAAG is a quasi-isometry invariant. This provides a necessary condition for two RAAGs to be quasi-isometric. We then restrict to the class of RAAGs whose JSJ trees of cylinders over infinite cyclic subgroups have abelian rigid vertex stabilizers. We show that two such RAAGs are quasi-isometric if and only if they have equivalent JSJ trees of cylinders. The latter result is a special case of results we prove in [Mar18a].

Keywords: Geometric group theory
Quasi-isometric rigidity
Splittings
Right-angled Artin groups
Advisor: Papazoglou, P
Atom probe tomography analysis of near surface, low concentration impurities in single crystal silicon

Advances in semiconductor device manufacture have led to modern nanoelectronic devices incorporating features with dimensions less than ten nanometres, fabricated within tens of nanometres of silicon substrate surfaces. To refine materials processing and optimise the correlation between fabricated nanostructures and device performance, high resolution characterisation techniques, such as atom probe tomography (APT), are required. In this thesis, surface sensitive specimen preparation methodologies for APT, utilising focused ion beam techniques using metal capping layers and low energy milling, were developed. This resulted in a reproducible method of precisely placing a metal/silicon interface at the apex of an APT nanoscale tip. This approach was utilised to characterise the surface regions of two silicon material systems with technological applications.
Low concentration, low energy phosphorus ion implantation is currently being investigated for fabrication of qubit arrays for large scale quantum computers. APT was used to investigate phosphorus implantation depth accuracy. 14 kV phosphorus ions with predicted peak concentrations between 0.1 and 0.2 at.% and peak depths of ~ 22 nm were implanted into planar substrates and pre-fabricated silicon posts. Measured profiles matched well with simulation but showed a reduced peak concentration and an extended tail region, likely from ion channelling.
Phosphorus diffusion is used to getter transition metals, particularly iron, to the surfaces of silicon solar cell material, however, the exact physical mechanism underpinning this is not well understood. Secondary ion mass spectrometry depth profiles were previously used to propose the interaction of oxide particles formed near the surface. In this study, single crystal silicon substrates were contaminated with pure iron and subjected to an industrially-relevant phosphorus diffusion process. APT analyses showed oxygen-rich regions in direct contact with silicon phosphide precipitates, confirming a heterogeneous distribution of oxygen in the surface regions. This can be used to inform processing conditions for modern silicon photovoltaics.

Advisor: Moody, M
Bagot, P
Computerising diagnosis: minds, medicine, and machines in twentieth-century America

In the mid-twentieth century, physicians, engineers, mathematicians, philosophers, and others started to think about the ways in which a new technology might be applied to an old problem. These interdisciplinary teams designed computer programmes that aimed to automate one of the most fundamental tasks of medicine—diagnosis. This dissertation offers a history of computerising diagnosis through the prism of three such efforts: the Medical Data Screen, a computerised method of capturing the health of ‘the total patient’; HEME, a computer programme created to aid in the diagnosis of haematologic diseases; and MYCIN, an early expert system developed to assist in the diagnosis and treatment of microbial infections. Drawing on these case studies, this project examines early efforts to computerise medical diagnosis and decision making. It explores how these efforts built upon, interacted with, and produced certain professional tensions, disease constructions, personal identities, cultural ideals, economic interests, and material practices.
This dissertation supports a number of conclusions. First, it demonstrates that efforts to computerise medical diagnosis and decision making raised philosophical and moral questions that lie at the heart of medical practice. As physicians and engineers worked to computerise diagnosis, they were forced to reckon with fundamental epistemological and ontological questions—questions about the nature of clinical reasoning and the definitions of disease. In creating computerised diagnostic systems, early developers articulated new ideas about how physicians think and how disease categories are defined. Second, this dissertation argues that the introduction of computers into medical diagnosis was both the cause and the effect of new ways of collecting, storing, and using medical information. Third, this dissertation highlights the complexities inherent to medicine and medical diagnosis. Repeatedly early developers of computerised diagnostic systems ran up against unanticipated epistemological, social, and moral challenges.

Keywords: artificial intelligence
diagnosis
health informatics
epistemology
disease
biomedical computing
history of medicine
computing
bias
Advisor: Harrison, M
An edition of Oxford, Trinity College, MS 29

Oxford, Trinity College, MS 29 is a late 15th-century manuscript which contains a large number of excerpts from diverse religious and secular medieval texts like the Vulgate, Caxton’s print of the Polychronicon, de Worde’s print Information for pilgrims unto the Holy Land, Chaucer’s Canterbury Tales, Peter of Poitiers’s Compendium historiae in genealogia Christi, Gower’s Confessio Amantis, a Holy Cross legend, Jacques Legrand’s Book of Good Manners, and Mandeville’s Travels. These texts are compiled in an idiosyncratic manner, forming a seamless prose history of the world, which starts with the creation of the world and ends incompletely with a description of Hannibal’s exploits. Written by a single compiler-scribe, the manuscript offers fascinating insights into methods of compilation employed by medieval historiographers at the close of the Middle Ages. Two other manuscripts in the same hand are extant – San Marino, Huntington Library, MS HM 144 and London, Lambeth Palace Library, MS 84 – which show similarities in design and compilatory technique.
To date, MS 29 has received only little critical attention. This thesis presents for the first time a full edition and comprehensive study of the text. The thesis consists of two volumes, the first of which contains an analysis of the edited text, including a complete description, investigation of sources, linguistic analysis, discussion of genre, context, and audience, as well as a commentary. The second volume contains the edited text as an appendix (excluded from the word count, according to the regulations for DPhil theses).
The way in which the compiler of MS 29 interacts with and selects from his source texts provides a better understanding of medieval habits of reading and writing and of the cultural climate predominant at the time of the manuscript’s production. This extensive analysis thus serves as a detailed case study, which is relevant to a wide range of late medieval texts.

Keywords: medieval studies
medieval english
compilation
historiography
fifteenth century
middle english
edition
Advisor: Wakelin, D
Rapid synthesis of the Taxol core

This thesis describes the combination of prochiral/racemic electrophiles and non-stabilised nucleophiles in transition metal catalysed asymmetric transformations.
The first part of the thesis focuses on the synthetic approach towards the Taxol core, Taxadiene. The key steps involve a Cu-catalysed asymmetric conjugate addition (ACA) of alkylzirconocenes to enones and cyclisations. Three different routes towards the synthesis of Taxadiene were explored and investigations into the Cu-catalysed ACA led to the discovery of a novel domino hydrozirconation/conjugate addition/enolate trapping reaction.
The second part of this thesis builds on the Rh-catalysed asymmetric coupling of boronic acids (vinyls, benzenes and heteroaromatics) and cyclic allyl chlorides, developed in the Fletcher group. Here, the main point is to couple a similar library of boronic acids to a more challenging electrophile, a racemic tetrahydropyridine (or N-heterocyclic piperidene) chloride, in order to access new chiral building blocks that can be found in a variety of natural products and their derivatives. The utility of this method is demonstrated by the total and formal asymmetric synthesis of the antipsychotic drug (-)-Preclamol.
The last chapter builds on the Cu-catalysed asymmetric allylic alkylation of alkylzirconocenes to cyclic allyl chlorides, also developed in our group. The main goal of this work is once again to apply this methodology to the racemic N-heterocyclic piperidene chloride. Investigations led to the discovery of a kinetic resolution process which afforded novel 3-alkyl substituted tetrahydropyridines and enantioenriched 3-chloro-1,2,3,6-tetrahydropyridines in high enantioselectivities.

Keywords: 1,4-conjugate addition
Organocatalysis
Asymmetric allylic alkylation
Suzuki-Miyaura coupling
Kinetic resolution
Tetrahydropyridines
Taxol
Advisor: Stephen, F
Mechanisms of co-stimulatory and inhibitory receptors in human cancer-specific cytotoxic T cells

Clinical studies have shown that the upregulation of immunocheckpoints such as PD-1 on tumor-infiltrating T lymphocytes (TILs) can impair the clinical outcome of cancer patients. However, current immunocheckpoints-targeting immunotherapies have failed to improve response in some patients and cancer types. This is likely due to the heterogeneity of the tumor immune composition, the overall complex TILs immunophenotype and the influence of the immunosuppressive tumor microenvironment. It is therefore important to assess the characteristics and mechanisms of TILs, especially cancer-specific cytotoxic CD8+ T cells (CTLs), in order to develop more effective T cell immunotherapy strategies.
In this study, comprehensive assessment using paired tumor, paratumor and peripheral blood from cancer patients demonstrated concomitant upregulation of both inhibitory CD94/NKG2a receptor and its HLA-E ligand in tumor. Although their engagement has been described on NK cells, it remains unclear whether this interaction could constitute an additional immunocheckpoint of cancer-specific CTLs in cancer. We demonstrated that the engagement of NKG2a and HLA-E resulted in impaired anti-tumor cytotoxicity, cytokine production and proliferation of CTLs, which recovered following antibody-blockade treatment. In contrast, the antagonistic NKG2a and CD103 expression on TILs suggest a distinct anti-tumor role of CD103. The CD103+ cancer-specific CTLs were found to self-produce TGF-β to sustain own CD103 expression, have improved TCR antigen sensitivity, faster cancer killing and elevated energy potential. However, they are more susceptible to apoptosis after prolonged cancer exposure. In addition, we demonstrated that a sizeable portion of cancer-specific CTLs lacks IFNγ expresssion and production, and discovered that this is contributed by CpG hypermethylation of its IFNγ promoter.
In summary, this study carried out in-depth investigation into the impacts of the inhibitory receptor NKG2a, costimulatory receptor CD103, and epigenetic DNA methylation, on anti-tumor T cell responses. The thorough understanding of these key factors in affecting cancer-specific CTL functions and their restoration potential, could be important for future designs of more effective cancer immunotherapy strategies.

Keywords: Co-stimulatory receptor
Inhibitory receptor
CD103+ T cells
Advisor: Dong, T
Peng, Y
Vanadium and zinc isotope ratios in lunar basalts

Measurements of isotopic ratios have been useful in understanding the formation and evolution of planetary bodies in our Solar System. However, studies have typically been limited in sample overlap, thereby limiting possible interpretation. This study presents the first highprecision vanadium isotope data, zinc isotope data (via double-spiking), and trace-element data for a suite of lunar basalts. Companion analyses of chlorine and sulphur isotope ratios were obtained at University of New Mexico and University of Maryland.
Vanadium isotope ratios span a larger range (~2.5‰) within this suite of lunar basalts than found in all igneous terrestrial rocks (~2.3‰). Lunar isotopic ratios are almost uniformly lighter than those from the bulk silicate Earth (BSE). Unlike on Earth, variation in vanadium isotope ratios is mainly due to cosmogenic effects, where bombardment of lunar samples by energetic particles (from solar and galactic cosmic rays) alters primary isotopic compositions. Modelling of cross-sections shows that iron is likely the most important target element in lunar samples. Correcting for cosmogenic effects shows lunar basalts to have uniform vanadium isotope ratios within error of recent estimates for the BSE. Where published meteorite data is available, accounting for cosmogenic exposure shows no resolvable difference between the BSE, Mars, Moon, and chondrites, in contrast to earlier studies.
Zinc displays a large isotopic range (~10‰) even amongst samples of the same lithological subtype, likely reflecting the volatile behaviour of zinc. Chlorine isotope ratios for the water-soluble fractions of the basalts in this suite (and for published data) correlate negatively with zinc isotope ratios, indicating a mixing trend between a heavy-Zn, light-Cl endmember, and a light-Zn, heavy-Cl endmember. Mobilisation of volatiles enriched in the lunar crust during magmatic ascent or eruption is the most plausible explanation for this trend.

Keywords: Lunar rocks
Vanadium
Moon
isotope ratios
vanadium isotopes
Zinc
Isotopes
Advisor: Barling, J
Halliday, A
Larner, F
Prytulak, J
Russell, S
Clinical delineation and immunopathogenesis of autoimmune encephalitis

Neuroglial surface antibody (NSAb)-mediated diseases are autoimmune brain diseases including autoimmune encephalitis (AE). Early immunotherapy improves outcome making prompt diagnosis crucial. In N-methyl D-aspartate receptor antibody encephalitis (NMDAR-AbE), improved description of the associated movement disorder (MD) should aid early recognition. Similarly, clarifying the purported association between NMDAR-antibodies and systemic lupus erythematosus (SLE) would help clinicians. Finally, the underlying immunology in patients with AE secondary to leucinerich glioma inactivated protein-1 (LGI1) and contactin-associated protein-like 2 (CASPR2) antibodies remains unexplored and a likely source of novel, targeted immunotherapies.
To improve recognition, MD experts rated 76 videos of 34 patients with NMDAR-AbE. The associated MD was described as a characteristic triad of dystonia, chorea and stereotypy, distributed across the body and variable over time. Patients with NMDARAbE are defined by the presence of conformationally-sensitive autoantibodies, these were not found in patients with neuropsychiatric SLE. In fact, existing linear protein assay techniques demonstrated high artefact rates. This suggested a lack of autoantibodies with pathogenic potential in NPSLE.
In a different form of AE, a novel class II HLA association was demonstrated in 48% of CASPR2-antibody patients (HLA-DRB1*11:01, n=31) and a known association was confirmed in 91% of LGI1-antibody patients (HLA-DRB1*07:01, n=68). This suggested an important role for T helper cells and, experimentally, evidence was found of antigenspecific T cells in these patients. Individuals with CASPR2-antibodies and HLADRB1* 11:01 had higher autoantibody titres and less clinical improvement with immunotherapy. Lymphocytes from these patients, when cultured, produced CASPR2- antibody matching serum CASPR2-antibody subclass and epitope-specificity. However, a marker of germinal centre activity, serum CASPR2-IgM, was seen only rarely. CASPR2- antibody patients carrying HLA-DRB1*11:01 produced more autoantibody in culture and to a wider range of CASPR2-epitopes in culture and serum. This may explain the poorer response to immunotherapy seen in these patients, highlighting the B-T cell interface as a key therapeutic target.

Advisor: Irani, S
Waters, P
A political ecology of smallholder oil palm production and forest conservation in the Peruvian Amazon frontier: towards a balanced approach to development

Through its meteoric rise to the top of the vegetable oils sector, palm oil has become one of the most contentious commodities on the planet. In recent years, the sector is increasingly spreading into new ‘frontiers’ in Latin America and Africa. There is concern about the prospect of oil palm projects being implemented in contexts where the socio-political and environmental dynamics of land and resource use are not adequately understood. This thesis presents a historical political ecology of oil palm in the Peruvian Amazon frontier region of Ucayali. The three pillars of the sustainable development agenda (social, environmental and economic) are used as a heuristic to facilitate the wider communication of the researching findings, with a focus on forests, livelihoods and society. The central premise of the thesis is that socio-environmental questions related to sustainable development are fundamentally political questions. The research deepens understanding about the scantily articulated dynamics and interaction between international commodity markets, land and resource access and use, and a poorly understood smallholder reality in the Amazon. A multi-methods approach including 450 surveys, 350 stakeholder interviews, visual remote sensing of 2,447 hectares of smallholder land and 14 months of participant observation is employed to critically explore social, environmental and economic aspects of smallholder oil palm production on the Ucayali forest/farm landscape.
Empirical findings reveal that oil palm is having a profound, but not always negative socioenvironmental and economic impact in the study site, and that outcomes were highly dependent on specific modes of production, as well as international, national and regional policy that is not always directly related to oil palm. Political dynamics such as political regimes, unequal power dynamics, poorly planned and implemented decentralization of government power and vertical and horizontal multi-level governance contexts including trade and development agreements are important underlying drivers of environmental and social change in the region. However, common misconceptions about particular resource users (small and large holders) and crop types (e.g. oil palm) are other important political factors influencing socio-environmental change and acting as barriers to effective forest conservation and sustainable use in the region. Rural smallholders are highlighted as skilled resource managers that lack not in capacity, but rather in opportunity to engage with a sustainable development agenda. Many constraints to opportunity are policy and politics centred. Findings reveal opportunities for forest conservation and regeneration that can include these poorly understood smallholding groups without significantly altering or compromising their production strategies, crop choices, access to resources or cultural integrity.

Advisor: Malhi, Y
Dermott, C