VictorJuiz/thesis huggingface dataset:
Understanding and preventing surgical site infection in hand trauma surgery
Keywords: clinical trials
infection
hand surgery
plastic surgery
trauma

Hand and wrist injuries, known as hand trauma, are a common occurrence and account for a significant number of Emergency Department (ED) visits and operations in the UK each year. Surgical site infections (SSIs) in hand trauma surgery can lead to additional morbidity, prolonged hospital stays, and even amputation. Antimicrobial sutures have been found to prevent SSIs in other surgical fields, but their effectiveness in hand trauma surgery is unknown. The aim of this thesis was to estimate the risk of SSI in hand trauma surgery and to establish the feasibility of conducting interventional trials to moderate it. The thesis comprises a systematic review, meta-analysis and meta-regression of data from 315,618 patients, an innovative national cohort analysis of primary and secondary care real world data and a multi-centre, randomised, controlled, feasibility trial of antimicrobial sutures in hand trauma surgery. Through my systematic review and meta-analysis, novel summary statistics for overall SSI in hand trauma have been generated, indicating an overall risk of 5% but in the context of substantial variation in SSI reporting. National cohort analyses have added granularity to this summary statistic, demonstrating a risk of superficial SSI of 6.2% by 30 days and 14.4% at 90 days; the deep/organ space SSI risk is 1.4% by 30 days and 2.0% at 90 days. Following this, a feasibility trial of antimicrobial interventions in hand trauma surgery was designed and executed. In seven months, 116 participants were randomised across three sites, demonstrating solid recruitment, randomisation, and adherence. Difficulty was encountered in retention. Comprehensive retention strategies are necessary for future definitive trials in this population. This thesis supports the need for evidence-based prevention of SSI in hand trauma surgery, informed by clinical trials of antimicrobial interventions.
Characterising the immune response to combined skin and solid organ transplants
Keywords: organ rejection
abdominal wall transplant
sentinel skin flap
immune monitoring

Transplantation offers a life-saving solution for patients with end-stage organ failure. Despite advances in recent years, managing acute rejection episodes remains challenging. This is partly due to difficulties in recognising when acute rejection is taking place. The concept of a sentinel skin flap for monitoring of organ transplantation has recently been introduced as a potential solution for this. The advent of abdominal wall transplants for the reconstruction of large defects in patients undergoing small bowel transplantation has further highlighted the usefulness of skin for monitoring, particularly in differentiating organ rejection from infections. Sentinel skin flaps also provide a site that is easy to biopsy, and which patients can be trained to review.
There are limited data in the literature on the alloresponse to a combined skin and solid organ transplant. The aim of this thesis is to characterise in depth this immune response. In chapter 3 the systemic immune response is examined using a combination of flow cytometry and gene expression analysis to analyse blood samples. Chapters 4 and 5 investigate the local immune response in small bowel and skin samples respectively, using the multiplexed gene expression and spatial proteomic techniques. Finally in Chapter 6 a human transgenic mouse model is used to explore the role of Langerhans cell related pathways in skin transplant rejection.
This is the first study to characterise both the systemic and local immune response in a combined skin and solid organ transplant, offering unique insights into the dynamic changes in immune phenotype post-transplantation and during rejection. The data provide support for the use of a sentinel skin flap for immune monitoring in solid organ transplantation and will be used to guide future clinical trials.
Genomic analyses of the immune system
Keywords: type 1 diabetes
regulatory T Cells
long-read sequencing
interleukin-2
structural variation
human leukocyte antigens
immunoglobulins

Project 1. Genetic variation in key immune system components
Genes underpinning the diversity and plasticity of the human adaptive immune system, such as the HLA and immunoglobulins, are known for their complex structures and polymorphism. The emergence of long-read sequencing technologies has revolutionised genomics research, in particular the characterisation of segmental duplications and structural variation. Here, using long-read sequencing and additional genomics data from a healthy donor identified as HV31, I built two iterations of de novo personal genome assemblies for HV31 as a foundation to study the genetic variation of the immune system. I analysed complex structural variants found in genomic regions encoding key immune system components, and validated them against sequencing data. I also evaluated long-read sequencing accuracy and developed a tool for genomic data visualisation. Collectively, these efforts demonstrate the applications of personal genome assemblies in studying the immune system.

Project 2. Effects of low-dose IL-2 immunotherapy in T and NK cells
Low-dose interleukin-2 (IL-2) immunotherapy is a promising treatment for type 1 diabetes (T1D). IL-2 supresses autoimmune reactions by increasing the number of regulatory T cells (Tregs). To better understand the mechanism of action of low- dose IL-2 immunotherapy, I analysed single-cell multiomics data of T and NK cells collected from T1D patients before and after low-dose IL-2 treatment. I confirmed that low-dose IL-2 selectively expanded thymic-derived FOXP3+ HELIOS+ regulatory T cells and CD56br NK cells, and showed that the treatment reduced the frequency of IL-21-producing CD4+ T cells. In addition, I identified a long-lived gene expression signature induced by IL-2, which featured the upregulation of CISH and downregulation of AREG. Notably, I found that the signature remained detectable one month after the treatment. Further analyses of publicly available COVID-19 cohort data revealed that SARS-CoV-2 infection induced opposite changes that persisted for several months after recovery. These findings suggested potential mechanisms of long COVID and longer-term benefits of IL-2 immunotherapy.
Is the UK tax system effective in supporting disabled people?
Keywords: tax disability

In 2020-21, some 22% of people in the UK reported a disability. The impacts of different impairments are hugely variable but for many disabled people – and their families – they may be profound, including limitations on the ability to work; and the need to meet considerable additional costs.
The UK benefits system is the most substantial source of public financial support for disabled people and their carers - alongside a range of public services. Separately, UK tax legislation contains nearly 40 reliefs spanning multiple taxes for eligible disabled taxpayers. The rationales for these reliefs vary: for example, some mitigate tax costs to assist with meeting ‘costs of disability’; others seek to eliminate discrimination; or facilitate an intended ‘after-tax’ result from a compensation claim or benefit payment.
Against this backcloth, this thesis seeks to answer the question ‘Is the UK tax system effective in supporting disabled people?’. In answering this question, the thesis does not seek to evaluate the nature and extent of general redistribution to disabled people: its focus is on the effectiveness of the existing range of tax reliefs, together with ease of tax compliance and administration for disabled people and those who support them. It draws upon comparative analysis with four other countries to identify areas where alternative – or additional reliefs – may be effective in achieving policy intent.
This thesis finds that the position is variable: many tax reliefs work smoothly and deliver meaningful results; others have limited effects, suffer from implementation issues, or are overly-complex. Whilst taxing authorities have made considerable progress in improving system access and compliance for disabled people, it seems that more can be done. The thesis makes a number of recommendations for modifications, further research, or the consideration of alternative reliefs to achieve overall policy intents.
Sport in Greek and Roman epic: an affective-narratological approach
Keywords: pity
ship race
Valerius Flaccus Argonautica 4
affective narratology
boxing
Silius Italicus 16
Virgil Aeneid 5
Homer Iliad 23
epic sport
chariot racing
suspense
Statius Thebaid 6
Apollonius Rhodes 2

Despite scholarly interest in the affective power of epic sport, its emotional potential has never been examined in detail. In exploring this subject, the present thesis pursues two goals: first, to offer detailed interpretations of a selection of epic sports narratives by a text-centred reading of their potential to create emotive effects, and secondly, to develop these readings by means of diachronic comparison. The prolegomena of the thesis first set the parameters of the investigation, establishing the material of the study, the reader model to be used, and the emotive effects it targets. In the chapters that follow, two of these effects, suspense and pity, are selected for an in-depth theoretical discussion, resulting in narratological categories of analysis.
The main section of the thesis comprises six case studies which fall into two groups. The first is occupied with racing in the context of funeral games and examines three chariot races (Homer, Statius, and Silius Italicus) and a naval contest (Virgil). Based on models delineating the conditions under which a narrative might plausibly elicit an effect, these studies provide new readings of the contests, illuminating, for example, how narrators create suspense as to the victor’s identity and pity for the defeated, but also elicit surprise when a pursuit ends contrary to expectations. With the progression of these investigations, the comparative approach intensifies. One result is the emergence of a pattern showing different tendencies of effects in the four races; another is the increasing importance of allusion in influencing affective engagement. The second group of case studies illustrates ‘challenge contests’ and covers two versions of the boxing match from the Argonautica saga (Apollonius Rhodes and Valerius Flaccus). These chapters reveal, among other things, how the two narrators use allusion to establish the protagonist and the antagonist and build emotional engagement with the contestants ahead of the fight and towards its outcome, but also how the Flavian account aims for a stronger impact; the chapters moreover consider how the rich embedding of these contests into the plot of the epic in different ways influences their affective power. The concluding discussion is devoted to a review of the main results; it closes by indicating some areas of interest for future research into emotive effects, sport, and epic.
Structural and electronic properties of Si:TiO2 interfaces from first principles

Keywords: photovoltaics
band alignments
infrared sprctra

A number of transition metal oxides that serve as electron/hole selective contacts in solar cells have attracted attention due to their simple and low-cost deposition methods. Among them, TiO2 has been identified as a promising electron transport layer in Si solar cells. Experiments have shown that the Si:TiO2 interface undergoes structural changes depending on how it was fabricated. However, the sensitivity of electronic properties, such as band alignments, to different structural features of the Si:TiO2 interface is not well understood. In this thesis, first-principles calculations are performed to calculate the band alignments between Si and anatase TiO2, investigating different surface orientations and terminations. By using the vacuum-level alignment method, a 2.1 eV reduction in band offsets is observed for the O-terminated Si slab compared to other terminations. However, this large reduction in band offset is not found when using the heterointerface alignment method in which band offsets are obtained with four different heterointerface models. Even though these heterointerface models contain an excess of oxygen, their offsets agree well with the vacuum-level alignments using stoichiometric or H-terminated slabs. Moreover, a 0.4 eV increase in band offset is found for the anatase (101) surface compared to the (001) surface for both alignment methods. Additionally, different exchange-correlation treatments are investigated including rSCAN, PBE+U, and post-processing GW corrections. By considering the results of calculations on a test set of 21 semiconductors, rSCAN is demonstrated to provide more accurate band offsets than PBE, but the errors are still of order 0.7 eV. Next, the infrared spectra of two Si:TiO2 interface models are calculated to assist future spectroscopy experiments in assigning observed features to particular structures. Finally, a comparison of oxygen and hydrogen-terminated surfaces is carried out for Si and C, linking the current study to previously published work on diamond-C surfaces.
Algorithmic problems for subsemigroups of infinite groups
Keywords: computational group theory
infinite groups
decidability
semigroups

This thesis is concerned with several algorithmic problems for subsemigroups of infinite groups. The main objective is to construct algorithms that decide various properties of finitely generated subsemigroups of a given infinite group G (for example, a matrix group). Such problems might not be decidable in general. In fact, they gave rise to some of the earliest undecidability results in algorithmic theory. Nevertheless, when the group G admits additional structures, many algorithmic problems become decidable for its subsemigroups. In this thesis, we study the decidability and the complexity of these algorithmic problems in the cases where G is nilpotent, metabelian, or represented as a low-dimensional matrix group.
Two of the main problems we consider are the Identity Problem and the Group Problem. Given a finite subset X of a group G, the Identity Problem asks whether the semigroup ⟨X⟩ generated by X contains the neutral element, and the Group Problem asks whether this semigroup is a group. We show that both problems are decidable in finitely generated nilpotent groups of class at most ten, and in PTIME if the input is given as unitriangular matrices. We also show the decidability of these problems in finitely generated metabelian groups, as well as their NP-completeness in the special affine group SA(2,Z).
Apart from the Identity Problem and the Group Problem, we also consider Semigroup Intersection and Orbit Intersection. Given two finite subsets X and H of the group G, Semigroup Intersection asks whether the semigroups ⟨X⟩, ⟨H⟩ generated by X and H have empty intersection, while Orbit Intersection asks whether the sets S · ⟨X⟩ and T · ⟨H⟩ intersect for given elements S, T ∈ G. We show that Semigroup Intersection is decidable in class two nilpotent groups (PTIME if the input is given as unitriangular matrices), and that Orbit Intersection is decidable in the Heisenberg group H3(Q).
We apply a large variety of mathematical tools in the study of these problems, ranging from Lie algebra, algebraic geometry and number theory, to combinatorics, graph theory and convex geometry. By adding these techniques into the toolbox, we are able to significantly advance the current state of art in the algorithmic theory of semigroups.
Droplet-on-hydrogel bilayer based assay for functional study of membrane proteins
Keywords: ATP synthase
proton-motive force
F1Fo
electrochemical potential
droplet-on-hydrogel bilayer
perfusion system
membrane proteins
functional study of membrane proteins
molecular motors
transmembrane potential

Functional study of membrane proteins, especially when a transmembrane potential is required for protein function, is notoriously difficult. In this thesis, I introduce an experimental assay that adapts the droplet-on-hydrogel technique for a high-resolution functional study of membrane proteins with independent control of the electrical and chemical transmembrane potential.
This experimental assay is the next step toward studying a membrane protein of interest embedded into an energised lipid bilayer. The bilayer is formed between a 200 nl water droplet and a supporting layer of hydrogel, granting a stable, functional, and accessible lipid bilayer. Delivery of proteins, labels, substrates, or ions to the droplet above the bilayer is achieved through a low-cost custom-built electronically controlled perfusion system. Experiments presented in this work show a stable perfusion with 26.68 ± 2.5 nl steps.
The main motivation for creating this experimental assay is a desire to observe the ATP synthase F1Fo in conditions mimicking the protein’s natural environment. This complex of two molecular motors - membrane-embedded Fo and water-soluble F1 - catalyses the synthesis of ATP molecules, the basic energy units of life. Using site-directed mutagenesis, I modified TA2.A1 F1Fo in two places, to be able to label the protein with a gold nanorod and anchor it to the agarose-streptavidin gel for a high-resolution functional study experiment. The assay may allow us to study the activation potential of the protein at different conditions, as well as to observe high-resolution single-molecule rotation steps of F1Fo at the time scale of a few microseconds.
"I just have to do this.": Native American student perceptions of the US college application process
Keywords: Native American
college application
higher education
United States

The project presented here explores how Native American students perceive the process of applying to college in the United States in the twenty-first century. Little research has been done on student perceptions of the application process in general, and even less scholarship has been dedicated to the Native American experience of applying to college. Without research in this area, universities, governments, and outside organizations remain unable to provide targeted support to ease the challenges Native American college applicants face.
The dissertation combines two theories—Markus and Nurius’ (1986) possible selves lens and Cotton et al.’s (2017) resilience framework—to create a more complex analytical theory, which allows for the findings to be analyzed in chronological cross-sections, revealing the changes and continuities of participants’ experiences and perceptions over time. Informed by the theoretical framework, the data consists of ten semi-structured interviews which asked participants to recall their memories, experiences, feelings, and stories from their college application process in three stages: before applying, while applying, and after applying.
The findings reflect the participants’ overwhelmingly challenging and isolating application experiences; nine out of ten characterized their experience as wholly negative. The most striking message in the findings was that participants viewed attending college as a necessary life step; no matter how frustrating or even impossible the application seemed, the participants persevered. As one participant put it, speaking as her high school self, “I just have to do this.”
Cooperation unavowable: British government relations with communists in Britain and France, 1938 – 1945
Keywords: counter-espionage
espionage
transnational resistance
Cold War
NKVD
Karl Retzlaw
Resistance
SOE
Karl Groehl
Section D of SIS
Hugh Sinclair
KPD
Intelligence
Parti Communiste Francais (PCF)
Laurence Grand
Communism
World War 1939 - 1945

More than thirty years on from the dissolution of the USSR, British government interaction with the Soviet Union, representatives of the Communist International (Comintern) and individual communists in the period 1938 - 1945 continues to be viewed primarily through the lens of ideological disparity and mutual suspicion, of espionage and counter-espionage. Nowhere has this been truer than in accounts of the activity of Britain’s Special Operations Executive (SOE), and its predecessor Section D, in France and the United Kingdom. While the past decade has seen an interest in the role of SOE in supporting, for example, the communist resistance in Yugoslavia, relatively little research has been conducted into the dynamics of proactive engagement between representatives of the British government and communists who followed the Soviet line (as well as the many who did not) or the impact of these associations on British colonial policy. Triangulating a broad range of archival evidence against literature from the UK, Germany and France, this thesis argues that there is much to be gained from adjusting what are effectively Cold War narratives to allow stories of transnational, and trans-ideological cooperation, however mutually manipulative, to emerge. By plotting a series of projects in which British representatives not only controlled, but also supported and learnt from current and former members of the Kommunistische Partei Deutschlands (KPD), the International Brigades, and the Soviet Naródnyy komissariát vnútrennikh del (NKVD) along a continuum of cooperation spanning the years 1938 to 1945, the thesis complements recent studies around transnational anti-fascist cooperation, urging a re-assessment of the geographical, political and temporal boundaries of British government involvement in anti-Nazi resistance.
Continuous hidden Markov models and the sequential probability ratio test
Keywords: HMM
exponent
variation
Lyapunov
total
model
hidden
distance
SPRT
probability
distinguishable
ratio
equivalence
equivalent
likelihood
sequential
Markov
distinguishability
test

We consider Hidden Markov Models that emit sequences of observations which are drawn from continuous distributions. For example, such a model may emit a sequence of numbers, each of which is drawn from a uniform distribution, but the support of the uniform distribution depends on the state of the Hidden Markov Model. Such models generalise the more common version where each observation is drawn from a finite alphabet. We consider a distance measure on Hidden Markov Models called the total variation distance. When this distance is 0 we say the models are equivalent. When this distance is maximal we say the models are distinguishable. We prove that for two Hidden Markov Models with continuous observations one can decide in polynomial time whether they are equivalent and also whether they are distinguishable. We also consider the Sequential Probability Ratio Test applied to Hidden Markov Models with finite observations. Given two distinguishable Hidden Markov Models and a sequence of observations generated by one of them, the Sequential Probability Ratio Test attempts to decide which model produced the sequence. We show relationships between the execution time of such an algorithm and Lyapunov exponents of random matrix products. Further, we give complexity results about the execution time taken by the Sequential Probability Ratio Test.