VictorJuiz/thesis huggingface dataset:
Automated rewriting for higher categories and applications to quantum theory

The contribution of this thesis is a novel framework for rewriting in higher categories. Its theoretical foundation is the theory of quasistrict higher categories and the practical realisation is a proof assistant Globular. The framework introduces the notions of diagrams and signatures as new mutually-recursive structures that give the algebraic basis for the approach. These structures are related the notion of an n-polygraph, but allow reasoning about quasistrict higher categorical structures in a way amenable to computer implementation. Building on this, we propose a new definition of a quasistrict 4-category, and prove a result that in a quasistrict 4-category, an adjunction of 1-morphisms gives rise to a coherent adjunction satisfying the butterfly equations.

Advisor: Coecke, B
Abramsky, S
The role of PARPs and APLF in DNA interstrand crosslink repair

Over the duration of every organism’s life its cells continuously face insults to their DNA. The accumulation of lesions results in cell death, inflammation and, following the activation of oncogenes or inactivating mutations of DNA repair factors, cancer formation. One particularly deleterious form of DNA damage are DNA interstrand crosslinks (ICLs), which prevent DNA strand seperation, therefore interfering with replication and transcription. Here we uncover a novel function for PARPs and the DNA repair protein APLF in the tolerance of human cells to DNA ICLs. Consistent with a role of PARPs in ICL repair, we observe ADP-ribosylation in response to the ICL inducing agent cis-platin. Furthermore, the inhibition of PARPs by Olaparib sensitizes human cells to ICLs. We identify the importance of PARP1 and PARP2 in these events and uncover that they are epistatic. We propose that PARP1 and PARP2 participate in ICL removal and that this is independent of the Fanconi Anemia pathway. The NHEJ repair factor APLF is recruited to chromatin in response to DNA ICLs and localizes to sites of laser induced damage in combination with the photreactive ICL inducing drug 4,5',8-trimethylpsoralen. Disruption of APLF sensitizes cells to ICLs. Additionally, the ADP-ribose binding tandem PBZ domain of APLF is essential for the restoration of MMC tolerance in aplfΔ cells. We suggest that APLF is an early responder to ICL formation. Together these data identify a novel role for PARP1, PARP2 and APLF in the tolerance of human cells to ICLs.

Advisor: Lakin, N
Foreign direct investment in the Russian agricultural sector

This thesis investigates the experiences of foreign direct investment (FDI) in the agricultural sector of the Russian Federation. The focus is on the form of FDI, and how each investor responds, and adapts, to the Russian operational environment. This is achieved through extensive qualitative, and multiple methods research on three manifestations of FDI: corporate, privately-funded investment; corporate, publically-funded investment; and smaller, individual private investment. Of interest are the Russia-specific constraints that may be largely underprepared for by foreign investors, and unexpected events that occur in the Russian space that hamper the efforts of investors. This thesis, thus, informs the reader of the variable nature of the Russian agricultural sphere, and the problems that exist within its boundaries, and presents the stories of some of the foreign investors that have tried to penetrate its market, mostly since the collapse of the Soviet Union in 1991.
The thesis consists of four papers that have either been published, or submitted for publication, in academic journals, and utilises fieldwork that was conducted between 2013 and 2014.
This thesis finds that all of the foreign investors studied have experienced – in certain aspects – failure on the Russian frontier, though there have also been certain successes. It seems that financial success is dictated by the business model of each investor; those who are afforded longer time horizons, more time to adapt on the frontier, and a source of funds that does not place short-term pressure on the business, are more likely to succeed. The Russian operating environment is unique, peculiar, and unpredictable, with a tendency to produce substantial obstacles that, for investors, are difficult to overcome; for agricultural FDI to avoid these struggles, these environmental conditions need to be anticipated and prepared for, with clear strategies painstakingly thought through before any venture physically begins on Russian soil.

Keywords: Geography
Food Production
Russia
Foreign Investment
Financialisation
Agriculture
Advisor: Pallot, J
'They shall know that I am Yahweh': The Vindication of Yahweh in Ezekiel's Oracles against the Nations

This study examines the theological purpose of the oracles against the nations in the book of Ezekiel (Ezek. 25-32). Through detailed exegesis, this thesis contends that the recognition formula, 'they shall know that I am Yahweh', is the vehicle for this theological purpose since it is fundamentally a statement of the vindication of Yahweh. Having specified in chapter 1 that the primary thesis is supported by two further theses, 'the recognition formula illuminates Yahweh's wrath and his mercy', and 'the recognition formula invites a human response', the work begins with a review of recent Ezekiel research in general that includes a background sketch delineating the context and authorship of the book. Possible original settings of oracles against nations are discussed, as well as a survey of topical scholarly output. A review of work undertaken on the recognition formula continues the preliminary discussion. In chapter 2, the basic form of the saying is defined and this allows the phrases that have expansions or are related by close resemblance to be categorised. The study proceeds with a consideration of the formula found elsewhere in the Hebrew Bible. Chapter 3 examines the formula as it appears in Ezekiel outside the oracles against the nations, paying particular attention to the formula's expansions. In chapter 4, detailed exegesis begins with the oracles against Israel's Palestinian neighbours. It is suggested that Ezekiel uses language for its potential to remind the people of their own culpability and the possibility is mooted that Ezekiel is projecting the guilt and punishment of Israel onto the nations. Chapter 5 contends that Ezekiel's illustrations are aimed at alleviating the exiles' concern about the future by helping them appreciate a bifurcated reality of the unseen present, and that the purpose of the oracles against the nations may be perceived when the relationship between divine wrath and divine mercy is understood to be elucidated by the above theses concerning the recognition formula.

Advisor: Barton, J
Magnetotransport in graphene and related two-dimensional systems

This thesis describes studies on two-dimensional electron gases (2DEG) in graphene and related 2D systems. Magnetotransport investigations specifically in graphene and its bilayer system are demonstrated in detail, while the experimental techniques presented in this thesis are widely applicable to a large variety of other 2D materials.
Chapter 1 gives an introduction and motivation for the principal topic presented in this thesis, with a general introduction to carbon nano-materials and an overview of the current state of graphene-related research and technological development (RTD). Chapter 2 establishes a basic theoretical framework which is essential for interpreting the results presented in this thesis, starting with the crystal and electronic band structures of graphene and its bilayer, followed by high magnetic fields effects on transport properties in these 2D systems. Chapter 3 details the experimental methods directly related to the presented work.
The next three chapters report experimental results of three specific magnetotransport studies. Chapter 4 reports the disorder effects on epitaxial graphene in the vicinity of the Dirac point. Quadratic increases of carrier densities with temperature are found to be due to intrinsic thermal excitation combined with electron-hole puddles induced by charged impurities. It is also shown that the minimum conductivity increases with increasing disorder strength, in good agreement with quantum-mechanical numerical calculations. Chapter 5 reports measurements of the quantum Hall effect in epitaxial graphene showing the widest quantum Hall plateau observed to date extending over 50 T, attributed to a magnetic field dependent charge transfer process from charge reservoirs with exceptionally high densities of states in close proximity to the graphene. Using a realistic framework of broadened Landau levels this process is modelled in excellent agreement with experimental results. In Chapter 6, energy relaxation of hot carriers in graphene bilayer systems is investigated from measurements on Shubnikovde Haas oscillations and weak localisation. The hot-electron energy loss rate follows the predicted T4 power-law at carrier temperatures from 1.4 up to about 100 K, due to electron-acoustic phonon interactions. Comparisons are made between graphene monolayer and bilayer systems and a much stronger carrier density dependence of the energy loss rate is found in the bilayer system.
This thesis concludes with a summary of the most important findings of the topics that have been discussed. The significance and limitations of the present research are listed. Some suggestions and outlook are given for possible improvements and interesting areas of future research and development.

Keywords: Energy Loss Rate
Hot Carriers
Dirac Point
Magnetotransport
Quantum Hall Effect
Graphene
2D Materials
Advisor: Nicholas, R
The role of surgery in early osteoarthritis of the knee

Early knee osteoarthritis (EKOA) is common, hard to treat and can be debilitating for symptomatic individuals. Whilst end-stage osteoarthritis is treated reliably with knee replacement surgery, such surgery is not routinely offered to those with less severe OA as it is associated with a poorer outcome. These patients are said to be in a 'treatment gap' and they are the primary focus of this thesis.
A series of large epidemiological studies were designed to clarify the natural history of symptomatic EKOA. A prospective cohort study including 1,634 symptomatic knees with EKOA found that malalignment was the most potent risk factor for structural progression. A subsequent study, which included a detailed assessment of lower limb alignment, established that this structural progression was driven by the alignment of the proximal tibia. Using semi-quantitive MRI analysis it was found that the increased structural progression seen in subjects with proximal tibia vara, was due to more full thickness cartilage loss in the central medial tibia. These are novel observations which have implications for future research as the alignment of the proximal tibia can be corrected with surgery.
Following this epidemiological description of EKOA, attention was turned to intervention and treatment. A systematic review of the literature identified moderate to very low quality evidence to support the role of surgery in treating symptomatic EKOA. A single-centre prospective cohort study for patients undergoing a novel neutralising high tibial osteotomy was established and excellent early (1yr) and mid-term (3-5 years) clinical outcomes are reported. A retrospective study was designed to investigate whether full thickness cartilage loss on magnetic resonance imaging, but not on plain film radiographs, is sufficient to warrant proceeding to unicompartmental knee arthroplasty (UKA). Outcomes for this cohort of patients were excellent, highlighting the usefulness of MR for the early identification of patients suitable for UKA.
In summary, this thesis has reported the natural history of symptomatic EKOA and identified proximal tibia vara as a potent risk factor for structural progression. The paucity of trials investigating subjects with this disease has been highlighted and surgical interventions which are safe and clinically effective have been identified. The direction of future research in this area has been proposed.

Keywords: Osteoarthritis
Advisor: Price, A
Beard, D
Javaid, K
Essays on development in open economies

This thesis analyses the interaction between development and integration into global markets.
Chapter 1 studies whether international crop prices affect formal land tenure in Uganda. Higher agricultural prices induce farmers to increase their share of titled land. This effect results from the combination of an income effect, an incentive effect, and the interaction between social status and social capital. Prices have a positive impact on agricultural income and sales revenues. The effect of prices on land tenure is stronger when farmers have undertaken investment on the land, for the prices of export crops, and when farmers fear expropriation and land grabbing. In areas with lower social capital, land insecurity is higher. Elite groups in low-social-capital communities respond more to an increase in prices, whereas disadvantaged groups are better-off where social capital is higher.
Chapter 2 evaluates the adjustment cost to the DR-CAFTA free trade agreement in Honduras. The agreement produces a reduction in household income in Honduran regions more intensely exposed to trade. The result is driven by local labour market effects: workers are not able to relocate across locations or sectors, and a generalised reduction in wages pushes many out of the labour force or into less lucrative, informal-sector activities.
Chapter 3 investigates the relationship between migrant remittances and financial development across Italian provinces in the late Nineteenth-early Twentieth centuries. Remittances have a positive impact on the growth of bank deposits. Higher remittances are associated with increased GDP and a higher number of active bank branches, and therefore contribute to enhancing financial inclusion.
Chapter 4 is an empirical application of theoretical models of trade with product variety and firm heterogeneity, and measures the gains from trade predicted by these models for Italy between 1870 and 2000. The analysis accounts for gains from variety, firm selection effects, and technology spillovers, and allows the trade elasticity to vary over time, reflecting the main economic and political phases of Italian history.

Advisor: Rauch, F
Fenske, J
Gauge/gravity duality and non-equilibrium dynamics of strongly coupled quantum systems

This thesis explores applications of gauge/gravity duality to strongly coupled quantum field theories out of equilibrium. Within the framework of holography, it addresses both small deviations from equilibrium accessible via the effective theory of hydrodynamics, as well as far-from-equilibrium dynamics, which are studied using a first-principles approach. After an introduction into the duality and a presentation of the two approaches to out-of-equilibrium physics, we present our results on holographic fluids in the first part of the thesis. We derive new Kubo formulae for five second-order transport coefficients of relativistic non-conformal fluids and apply them to a class of non-conformal holographic field theories at infinite coupling. We find strong evidence that the Haack-Yarom identity, which is known to hold for conformal holographic fluids at infinite coupling, is universally satisfied by strongly coupled fluids regardless of conformal symmetry. We prove analytically that the identity is obeyed when taking into account leading non-conformal corrections and provide numerical evidence that the result holds beyond these leading corrections. In the second part of the thesis, we examine two proposals for the holographic dictionary for correlation functions in out-of-equilibrium states. We show that these proposals are equivalent on the level of two-point functions of operators dual to free scalar bulk fields. We then use one of the two non-equilibrium dictionaries to study the thermalisation of two-point functions of scalar operators and effective occupation numbers in a holographic model of quantum quenches. We find that both thermalise with a rate set by the lowest quasinormal mode of the final-state black hole in the gravitational dual.

Advisor: Starinets, A
Iranian-Armenian language contact in and before the 5th century CE

This study provides new insights into the historical language contact between Classical Armenian and West Middle Iranian, specifically Parthian. Next to an up-to-date account of known lexical, morphological, and phraseological Iranian loans in Armenian, the discussion focuses on one major and three minor syntactic patterns which, it is argued, are the result of pattern replication.
The major pattern, the Classical Armenian periphrastic perfect, has previously been the focus of numerous papers owing to its unusual construction: while intransitive verbs construe with nominative subjects and an optional form of the copula in subject agreement, transitive verbs exhibit genitive agents, accusative objects and an optional copula in a invariable 3.sg form. Based on a discussion of morphosyntactic alignment patterns in general, and of Armenian and West Middle Iranian in particular, it is shown that previous accounts cannot satisfactorily explain the syntax of the perfect. In a new approach, it is argued that Armenian exhibits tripartite morphosyntactic alignment as the result of 'copying' and adapting the ergative alignment pattern of the West Middle Iranian past tense. This analysis is supported both by the historical morphology of the perfect participle and by a corpus analysis of five major works of Armenian 5th-century historiography.
The minor patterns—ez&emacr;fe-like nominal relative clauses, subject resumption and switch-reference marking using the anaphoric pronoun Arm. ink'n, and the quotative use of Arm. (e)t'&emacr;—are equally linked to parallel constructions in West Middle Iranian, which may have served as syntactic models for their Armenian counterparts.
The final part of the study discusses the Armenian–Iranian relationship from a language contact point of view and, making use of historical, epigraphic, and literary sources, proposes that a superstrate shift of the Parthian-speaking ruling class of Armenia to Armenian as their primary language best explains the amount of Parthian linguistic material and patterns in Armenian.

Keywords: pattern replication
multilingualism
morphosyntactic alignment
language contact
Advisor: van Lint, T
Tucker, E
Elucidating the molecular mechanism that determines the specific localisation of gurken mRNA during Drosophila development

mRNA localisation is a widely used mechanism for achieving temporal-spatial restriction of protein expression and is essential during development to establish cell polarity. mRNA localisation is particularly well studied in the Drosophila egg chamber where gurken mRNA is localised to the dorsal-anterior corner of the oocyte in a Dynein-dependent process that establishes the anterior-posterior and dorsal-ventral axes of the future embryo. An RNA stem-loop called the gurken localisation signal is necessary and sufficient to drive gurken localisation through interactions with a specific complement of protein factors. However, the exact RNA sequence and structural features required to promote each stage of gurken localisation are unknown. Using a live-cell injection assay I have dissected regions of the mRNA signal that are responsible for driving gurken transport and anchoring through their association with Egalitarian, Me31B and Squid proteins. I show the structure of an AU-rich stem and a purine stack are essential for gurken transport, and demonstrate that the size of the internal loop between these stems is important. These features of the localisation signal are essential for recruitment of Egalitarian, which links the mRNA to the Dynein transport machinery. I also show that these mRNA sequence and structural elements are present in several other Dynein-transported mRNAs. The bulge at the distal end of the gurken localisation signal is important for anchoring grk at the dorsal-anterior of the oocyte, possibly through Squid binding, and the proximal third of the signal is essential for recruitment of the translation component Me31B. These studies indicate that the role of the gurken localisation signal in controlling gurken transport, anchoring and translation can be mapped to distinct regions of the signal and provide insights into how the signal carries out these numerous functions at a molecular level. Determining the molecular interactions involved in mRNA localisation improves our understanding of how specificity is generated to direct different mRNAs to distinct regions of the cell to restrict protein expression.

Advisor: Davis, I
The balancing effect between MAPK and NFkB pathways for the transcriptional regulation of Toll-like receptors

Toll-like receptors (TLR) are a family of pattern recognition receptors crucial for pathogen pattern recognition. Upon activation, TLRs induce innate immune responses such as cytokine production. However irregular TLR activities can provide fatal, hence fine tuning of the TLR induced responses are necessary.
The TLR mediated immune responses are controlled by the positive/negative regulation of TLR signalling pathways, relocation of TLR proteins and modulation of TLR transcription. Systematic analyses of the agonist-induced transcriptional changes of TLRs were shown for the first time in my thesis. In my experiments, I have shown that each agonist induced a unique pattern of TLR transcription. Following PAM stimulation, mRNA levels of the cognate TLR1/2 increased whereas mRNA levels of the cross-regulating TLR4, 7/8/9 reduced in both cell lines and splenic macrophages from different mice strains. Through investigation of the signalling pathways responsible for mediating such TLR transcriptional changes, I then discovered the balancing effect between NFκB and MAPK signalling pathways. PAM induced TLR transcriptional changes were controlled by the additive and/or antagonistic interference between MAPK signalling cascades, ERK, JNK, P38 and NFκB signalling pathways. This was the first time that signalling synergy between MAPK and NFκB pathways were shown. Furthermore, PAM induced transcription of TLR1 and TLR8 may be partially regulated by the indirect feedback mediated by protein production. Importantly, the maintenance of the basal TLR mRNA expression also required activation of both MAPK and NFκB signalling pathways.
In addition, signalling control for TLR transcription induced by different agonists (PAM vs. LPS) or in different species (chicken vs. mice) was compared. LPS induced transcriptional changes of the cross-regulating TLR1/2 and 3 but not the cognate TLR4 in RAW cells. The LPS induced TLR transcriptional changes required activation of a combination of MAPK and NFκB signalling pathways which shared both similarities and differences to the PAM induced signalling activation. In chicken, PAM induced more potent signalling activation, regulating the TLR transcriptional changes at a lower concentration than in mice. Overall, this thesis demonstrates that the transcriptional regulation of TLRs is complex, mediated by the coordination between MAPK and NFκB signalling pathways. These studies have significant implications in providing detailed insight of TLR transcriptional regulation which plays an important role in the regulation of TLR mediated innate immune responses.
Please watch the following videos that I made for:
A short introduction about TLR regulation - https://youtu.be/LTDdEZ3S97o
A short explanation about TLR signalling - https://youtu.be/51IY5XhdJR8

Keywords: Signalling pathway
Toll-like Receptor
Advisor: Smith, A
Shimeld, S