VictorJuiz/thesis huggingface dataset:
Beyond pragmatism: Iran's foreign policy in the South Caucasus

This study provides an in-depth analysis of Iran’s foreign policy in the South Caucasus after the collages of the Soviet Union. Using a non-foundationalist theoretical framework, it offers a new perspective towards the issue, deviating from the popular argument of considering Iran’s behaviour in the region pragmatic. Here, Iran's agency as a foreign policy actor is assumed to be decentred. It is continuously produced by various competing and intertwined discursive and recognitive practices. Based on this ontological premise, new conceptualizations of identity, interests, and policies are introduced that allow looking into different aspects of Iran's behaviour in the aforementioned region.
The research investigates Iran’s policies in the South Caucasus during the presidencies of Akbar Hashemi Rafsanjani (1989-1997), Mohammad Khatami (1997-2005), and Mahmoud Ahmadinejad (2005-213) as its main case studies, and each of them is discussed in corresponding three empirical chapters. The latter are based on a discourse analysis of extensive textual data from the respective periods. The result is a more complicated image that shows how dualities, hesitance, status anxiety, and routinized practices are an integral part of Iran's policies in the South Caucasus. In this way, the study puts forward a different understanding of the issue and tries to move beyond the ideology vs. pragmatism debate in the literature on Iranian foreign affairs.

Keywords: foreign policy
Iran
South Caucasus
discourse
Advisor: Herzig, E
Katouzian, H
Actin regulation in activity-dependent synaptic plasticity at the Drosophila neuromuscular junction

Synaptic plasticity is the process by which synaptic connections are continuously modified and is the molecular basis of learning and memory. These modifications require new protein synthesis and cytoskeletal rearrangements at or near the synapse. Syncrip, an mRNA-binding protein, is conserved from Drosophila to vertebrates and is found to regulate mRNAs encoding proteins required in synaptic plasticity. Many of these proteins have functions in actin-binding, actin cytoskeleton organization, or other actin-related processes, including Msp300, which was recently described in detail by the Davis lab. Here, we investigate two other targets of Syncrip, Basigin and Cofilin (Twinstar), among the most highly expressed of these genes in the Drosophila nervous system.
By studying the activity-dependent synaptic plasticity, the change in neuronal connectivity as a result of activity, in the Drosophila neuromuscular junction, we showed that the loss of Cofilin in the presynapse leads to a decrease in activity-dependent synaptic plasticity, whereas the loss of Basigin in the postsynapse promotes plasticity. Deficiency of Basigin in the presynapse causes growth of larger boutons during development, while its effect during plasticity has yet to be determined. Furthermore, activity-induced expression of Basigin transcriptional level while the regulation of Cofilin takes place at posttranscriptional level. Basigin is present around some immature boutons. These data suggest that Basigin and Cofilin are involved in activity-dependent synaptic plasticity and have distinct roles in the pre- or postsynaptic compartments. Basigin could also play a part in the maturation of boutons. Our results add to the growing number of actin regulators that are downstream of Syncrip and have a role in neuronal plasticity.

Keywords: cofilin
actin
basigin
activity-dependent
twinstar
neuromuscular junction
synaptic plasticity
Advisor: Davis, I
Raff, J
Machine learning for the improvement of patient flow

This thesis presents how machine learning can be used to improve the allocation and use of resources in hospitals, in particular with respect to patient flow. A deep learning method is proposed that predicts where in a hospital emergency patients will be admitted after being triaged in the ED. Such a prediction will allow for the preparation of bed space in the hospital for timely care and admission of the patient as well as allocation of resource to the relevant departments, including during periods of increased demand arising from seasonal peaks in infections. The problem is posed as a multi-class classi fication into seven separate ward types. A novel deep learning training strategy is created that combines learning via curriculum and a multi-armed bandit to exploit this curriculum post-initial training. We also show that there are certain signifying tests which indicate what space of the hospital a patient will use. In showing that prediction of location of admission in hospital for emergency patients is possible using information from triage in ED, a new way of training neural networks using a teaching reinforcement learning agent is also introduced. The properties and strategies of the teacher are investigated before a federated learning method is developed to allow for learning from multiple hospitals simultaneously. It is hoped that this work will be of value to healthcare institutions by allowing for the planning of resource and bed space ahead of the need for it. This in turn should speed up the provision of care for the patient and allow flow of patients out of the ED, thereby improving patient flow and the quality of care for the remaining patients within the ED.

Keywords: patient flow
meta learning
reinforcement learning
machine learning
healthcare
Advisor: Zhu, T
Clifton, D
Structural studies on oligosaccharide transport and sugar scavenging in bacteria

This thesis reports on the structural and functional studies performed using x-ray crystallography on two proteins involved in bacterial sugar metabolism. The first protein, the inner membrane oligosaccharide scramblase Wzx, is central to capsule and lipopolysaccharide export in pathogens and is thus a potential drug target. The crystal structure was determined at 2.3 Å using sulfur phasing at the long wavelength beamline I23 at Diamond Light Source. This required us to obtain high quality crystals using lipidic cubic phase, exogenous lipids, and a nanobody. The crystal structure reveals a positively charged patch at both openings to a central cavity. The structure will guide future site directed mutagenesis and mechanistic studies. Other nanobodies were identified and these could help trap other conformational states.
The second protein studied was the sialic acid oxidoreductase RgNanOx. This protein used in sialic acid metabolism by the gut bacterium Ruminococcus gnavus, which converts sialic acid (Neu5Ac) into the bicyclic form (2,7-anhydro-Neu5Ac). This involves an unusual chemical mechanism where the substrate is both oxidised and reduced. The crystal structure of RgNanOx was first determined at 1.7 Å. The structure suggested a mechanism for this unusual chemical transformation which was tested by site directed mutagenesis. The enzyme was shown to be active against the sialidase inhibitor 2,3-dehydro-2-deoxy-Neu5Ac (DANA). Co-crystallisation with DANA produced an α-Neu5Ac complex. A mutant was used to obtain a 2,7-anhydro-Neu5Ac complex. These complexes allow the mechanism to be clarified and the key catalytic residues identified. It is an unresolved question whether the true substrate is the α or β form of the sialic acid. NMR data suggest that α-Neu5Ac is consumed, which would indicate the enzyme proceeds by an unusual syn- elimination. The work opens opportunities to definitively assign the mechanism, and shed light on the role of the enzyme in the gut environment.

Keywords: Wzx
RgNanOx
Advisor: Naismith, J
Higgins, M
Ice crystal icing in gas turbine engines

Numerous turbofan power loss events have occurred in high altitude locations in the presence of ice crystals. Ice crystals enter the engine core, partially melt in the compressor and then accrete onto components that are initially warmer than freezing. The ice accretion causes blockage of the flow path, and if it later sheds can damage downstream components and potentially cause flame-out alongside other issues.
Numerical models are currently required for the design and certification of next-generation engines to fly within ice crystal icing conditions. They have successfully predicted ice growth on simplistic geometries, but are often fine-tuned to a single condition or geometry due to the high level of empiricism.
In this thesis a review of the current literature is presented, areas of missing research are indicated, some of which form the basis of the PhD. First, a new method for spatially resolving the three-dimensional ice accretion profile was developed and tested in an ice crystal icing wind tunnel. Historical measurement techniques were either two dimensional or could only be applied after the accretion had formed. This new technique provides transient, three-dimensional, non-intrusive measurement of the accretion during the ice exposure. Such measurements are deemed essential for the development of complex three-dimensional ice accretion models.
The second set of work was the development of the ice crystal icing numerical model, ICICLE. The most notable development was the inclusion of the ability to update the flowfield based on the numerically predicted accretion profile. This change in geometry alters the potential field, leading to changes in the predicted particle trajectories and resultant accretion. The new capabilities of the code were tested using two test pieces: a single compressor stator, and a triple NACA airfoil linear cascade. The results showed that certain conditions require the update of the flowfield for accurate estimation of both the shape and volume of the accretion.

Keywords: stereo vision
CFD
ice crystal icing
icing
ice
Advisor: McGilvray, M
Gillespie, D
Establishment and assessment of pancreas preservation using oxygenated hypothermic machine perfusion

Background: Pancreatic transplantation is the treatment of choice for a selected group of patients with the most severe complications of diabetes. The two main causes of early failure in this transplant are pancreatitis and venous graft thrombosis. Due to its anatomy and physiology, the pancreas is an organ that is particularly sensitive to ischaemia reperfusion injury. The current standard technique for preserving transplants after removal and before transplantation remains static cold storage (SCS). Changes in donor characteristics (older, with more co-morbidities) have led transplant teams to consider for transplant increasingly high-risk pancreases, which are even more susceptible to ischaemia reperfusion injury.
Aim: The objective of this study was to establish the modalities of an innovative technique for the preservation of pancreatic transplants on a pulsatile hypothermic perfusion machine (HMP) and to compare SCS, HMP and Hypothermic Oxygenated Pulsatile Perfusion (HMPO2) preservation methods for pancreas in a Donation after Circulatory Death (DCD) porcine model.
Methods: Pancreases were retrieved after cold preservation solution flush from Sus scrofa domesticus pigs sourced at an abattoir, in a DCD model. Pancreases were cold preserved with Static Cold Storage (n=5), Hypothermic Machine Perfusion (Waves machine) (n=4), or with Hypothermic Oxygenated Pulsatile Perfusion (n=4) (medical air 300ml/min). General injury markers (lactate; lactate dehydrogenase) and exocrine markers (amylase, lipase) were assessed in the perfusate (or preservation solution for SCS) during preservation. Pancreatic resistance index, pressure and flow were also analysed. Biopsies were collected to assess pancreas oedema (wet to dry weight ratios before and after preservation).
Results: SCS resulted in an oedema scale assessment score of 0 when compared with both HMP groups (score 1), however wet-to-dry weight ratio percentage difference was highest for SCS indicating the presence of oedema. Flow and resistance index were shown to be reciprocal, with the highest flow being achieved in the HMPO2 group. No statistically significant difference was found between HMPO2 and HMP groups for oxygen pressure in the perfusate over time. LDH levels were significantly higher in the SCS group, as well as lactate levels. Amylase and lipase levels were found to be significantly greater in the HMPO2 group. Glucose levels were highest in the HMPO2 group, whilst pH was greatest in the SCS group despite being stable across all three groups HMP, HMPO2 and SCS.
Conclusions: HMPO2 appears to be a promising alternative method to SCS preservation, despite research in the pancreas proving more challenging than in other organs. The flow was higher in the HMPO2 group, while the degree of oedema appeared to be lower alongside lower levels of general tissue injury markers, making HMPO2 a potentially suitable alternative to preservation by static cold storage.

Advisor: Friend, P
Branchereau, J
Identification of pre-clinical cardiovascular imaging phenotypes related to blood pressure in young adults

Hypertension prevalence in young adults is rising and is associated with an increased risk of stroke and cardiovascular disease in later life. However, hypertension management guidelines for patients below the age of 40 years remain conservative as their absolute risk of imminent vascular events is low. Additionally, due to the relatively short duration of exposure to hypertension, traditional measures of target organ damage such as left ventricular hypertrophy are often normal. In this thesis, I sought to identify pre-clinical cardiovascular phenotypes associated with blood pressure elevation in young adults, which might be of value for monitoring disease progression in young people.
A cohort of young participants aged 18 to 40 years with a range of blood pressure measures were recruited through clinical studies conducted at the Cardiovascular Clinical Research Facility for multi-dimensional assessment of cardiovascular health. Detailed cardiac structure and function assessment was performed using a range of imaging modalities including resting and stress echocardiography imaging. First, I established that participants with suboptimal blood pressure (≥120/80 mmHg) have novel changes in cardiovascular remodelling identifiable with echocardiography. Specifically, I identified a reduction in left ventricular systolic function during physical exercise, which was associated with altered left atrial pump function at rest. Then, I studied whether it was possible to combine multiple echocardiographic measures using a contrastive trajectory inference machine learning model to describe the progression of cardiovascular remodelling in young adults with hypertension, and place participants on a pseudo-temporal trajectory of disease, with a corresponding score, from health (zero) to disease (one). I demonstrated feasibility of this approach and the practicality of summarising this disease progression as a single score. Finally, I demonstrated that longer duration of treatment was associated with higher score and was consistent with an established modifiable cardiovascular risk score and fitness levels. Therefore, I have demonstrated that there are progressive changes in cardiac structure and function, identifiable with echocardiography, in young adults with suboptimal blood pressure. Further work is now needed to determine whether these measures could be used clinically to better manage blood pressure in younger patients.

Keywords: artificial intelligence
young adults
machine learning
cardiac remodelling
hypertension
Advisor: Leeson, P
Lewandowski, A
Lapidaire, W
Combining gospels in early Christianity: the one, the many, and the fourfold

How and why did the gospels according to Matthew, Mark, Luke, and John begin to keep exclusive company with one another as the authoritative collection of Jesus books? The present study seeks to answer this question by investigating gospel combinations of the second century. I focus on the textual identities, mode, integrity, interactions, and authority of gospels as they are combined by second-century Christian authors and readers. I examine gospel combinations in interpretive rewriting (the Gospel of Thomas and the Epistula Apostolorum), gospel orchestration (the Diatessaron), pericope interpolation (the Longer Ending of Mark), second-order Christian discourse about gospel books, and artifactual juxtapositions (e.g. P45). My first major conclusion is that the four proto-canonical gospels were keeping congenial company as early as Papias, and consistently throughout the second century. This is seen in the way that the Gospel of Thomas synthesizes material from Matthew and Luke. It is demonstrated in the gospel epitome of the Epistula Apostolorum, which integrates material from all four proto-canonical gospels and situates them in a Johannine-Synoptic sequence. Tatian’s Diatessaron showcases a tapestry of all four proto-canonical gospels, intricately sequenced. The Longer Ending of Mark does the same on a smaller scale. Papias is the first explicitly to mention gospel authors, and throughout the rest of the second century, gospel authors become the literary symbols by which Christians describe the pluriform nature of the one gospel. Multi-gospel codices of the second and third centuries CE corroborate these patterns, combining proto-canonical gospels in ways that manifest their intertextual connectedness. My second major conclusion is that noncanonical traditions were also valued for their contribution to the collective memory of Jesus, but they functioned mainly as ancillary to the fourfold gospel core. Thus, while it may be anachronistic to speak of a fourfold gospel “canon” before Irenaeus, it is certainly accurate to speak of a fourfold gospel “center of gravity” in the first half of the second century.

Keywords: New Testament Papyri
second-century Christianity
Diatessaron
Four-Gospel Canon
Epistula Apostolorum
gospels
gospel of Thomas
noncanonical gospels
Advisor: Bockmuehl, M
Machine learning methods for next generation sequencing data: applications to MLL-AF4 leukemia and demographic inference

As next generation sequencing technologies continue to mature and find applications across genomics, it has become clear that the scale and scope of generated data far exceeds our ability for manual interpretation. Machine learning has shown remarkable success in finding patterns in this data and generating biologically testable hypotheses. In this thesis, I develop and apply machine learning methods which use NGS data to answer outstanding questions in population and functional genomics.
An understanding of the genetic history of global populations has been hindered by a lack of methods capable of inferring directional migration over time. I use a sequential Monte Carlo approach (a particle filter) to sample from the posterior distribution of ancestral recombination graphs and infer likely population size and migration histories from whole genome sequencing data. I apply this particle filter to global sequencing biobanks and uncover an abundance of migration from the ancestors of non-Africans into Africa between 40 and 70 thousand years ago. I show that latent directional migration has broader implications for the inference of population size in gold-standard approaches and explore this migration in the context of African pre-history.
On a cellular rather than population scale, I apply latent Dirichlet allocation to NGS-based chromatin accessibility assays in order to model shared and distinct regulatory pathways between different cell types. I demonstrate the method's utility by recovering known regulatory biology in erythroblast development. I apply this topic modelling approach to understand cis-regulatory element usage in a treatment-resistant leukemia caused by the MLL-AF4 oncoprotein. The results highlight a previously uncharacterized class of enhancer elements depleted in DOT1L-deposited H3 lysine 79 methylation and enriched for PAF1c binding.
In this thesis, I have developed and applied machine learning approaches to identify patterns in large genomics databases and answer biological questions on both population and cellular levels.

Keywords: sequential monte carlo
ATAC-seq
upper paleolithic
topic modelling
directional migration
machine learning
MLL-AF4 leukemia
functional genomics
enhancer biology
latent Dirichlet Allocation
demographic inference
Advisor: Milne, T
Lunter, G
Philosophical foundations of norms of legal method

Legal method is about identifying and applying the law in a particular legal system. Norms of legal method regulate that activity. They are about, among other things, sources of law, legal interpretation and conflicts of law. The thesis asks questions regarding their philosophical foundations, that is questions that are not limited to any particular legal system but concern law in general. The questions are, firstly, about the norms themselves: What do they do? How many norms can there be? Are any of them necessary? Of what kind are they? What is their normative character? What is their function? Then the thesis addresses questions about the norms’ significance for some central issues in jurisprudence, namely legal validity and legal systems. It is claimed that understanding norms of legal method together philosophically is important to elucidate them as well as some questions or problems in jurisprudence.
What are the answers? Very briefly speaking, the norms have diverse roles and can be categorised accordingly. Norms of recognition and change address the issue of existence. Norms of interpretation address the issue of content. Norms of applicability address the issue of applicability. Norms of subsumption address the issue of application and norms of institutional decision-making address issues of institutional considerations and powers. The norms are united by sharing the overall role of identifying and applying the law. While there can be many (ultimate) norms in each category in a legal system, there must be at least one norm of recognition. Some of the norms are legal norms but others are so-called interpretive norms. While some norms are duty-imposing, permission-granting and power-conferring, others are so-called qualifying norms. The norms partly constitute the law. The norms are also important for legal validity and the structure and foundations of a legal system.

Keywords: secondary norms
legal norms
legal validity
legal systems
legal method
Advisor: Green, L
Adams, T