VictorJuiz/thesis huggingface dataset:
Infra-red laser applications in the reproductive sciences: improving safety for assisted reproductive technology and developing novel research tools

Assisted reproductive technology (ART) has been rapidly expanding since the birth of Louise Brown, the first test tube baby, in 1978. Although an increasingly complex array of laboratory skills and procedures have been developed for infertility treatments, the success rate of ART remains low. In an attempt to make ART safer and more efficient, international medical practice is trending towards single embryo transfers and the use of innovative, sophisticated technologies to identify promising gametes and embryos with the highest potential to generate a pregnancy. Laser technology is increasingly being used to accomplish these aims. The application of lasers for ART has been successfully employed in clinical practice for some time now and is continually the subject of investigative research in order to generate new methods to improve operations. Moreover, lasers serve as a powerful tool at the forefront of investigative research in the reproductive sciences, assisting in broadening our understanding of reproductive and developmental biology. Nevertheless, there is a paucity of literature pertaining to the safe standardisation of such laser procedures with evidence at the molecular level. The primary aim of this thesis was to optimise applications of laser technology for clinical ART and research applications in the reproductive sciences. This thesis utilised the mouse embryo model to investigate potential deleterious effects of different laser treatment applications, both by the operator and hardware manufacturer. Safe and unsafe laser operator parameters were elucidated by assessing deleterious effects to the plasma membrane integrity, blastocyst survival rate, DNA fragmentation levels, and changes in gene expression of key developmental genes. The effect of altering the laser hardware to lower the power output was evaluated and it was determined that if a lower power laser is used to deliver a set amount of energy over a longer period of time, a smaller amount of damage is incurred. Work in this thesis also established a new method in which laser technology can be used as a research tool for the reproductive sciences, by creating a novel stimuli-responsive laser-activated nanoparticle delivery system with spatial control and increased efficiency in a mammalian cell model. The field of reproductive science continues to benefit greatly from laser application clinically to improve infertility treatments, and in research, to elucidate mechanisms underlying infertility, with a hope of increasing our understanding and eventually developing new treatment options.

Keywords: Assisted reproductive technology
Preimplantation embryo
Infertility
Infra-red laser
Mouse embryo
Mesoporous silica nanoparticle
Advisor: Coward, K
Quantum electrodynamics of semiconducting nanomaterials in optical microcavities

Semiconducting nanocrystals in open-access microcavities are promising systems in which enhanced light-matter interactions lead to quantum effects such as the modulation of the spontaneous emission process and exciton-polariton formation. In this thesis I present improvements of the open cavity platform which serves to confine the electromagnetic field with mode volumes down to the λ3 regime and demonstrate results in both the weak and strong coupling regimes of cavity quantum electrodynamics with a range of different low-dimensional materials. I report cavity fabrication details allowing a peak finesse of 5 × 104 and advanced photonic structures such as coupled cavities in the open cavity geometry.
By incorporating two-dimensional materials and nanoplatelets in the cavity I demonstrate the strong coupling regime of light-matter interaction with the formation of exciton-polaritons, quasi-particles composed of both photon and exciton, at room temperature. In the perturbative weak coupling regime I show pronounced modulation of the single-photon emission from CdSe/ZnS quantum dots and the two-dimensional material WSe2 and demonstrate Purcell enhancement of the spontaneous emission rate by factors of 2 at room temperature and 8 at low temperature. The findings presented in this thesis pave the way to establish open microcavities as a platform for a wide range of applications in nanophotonics and quantum information technologies.

Keywords: Optical microcavities
Two-dimensional materials
Nanomaterials
Advisor: Smith, J
Sir Thomas Tresham (1543-1605) and early modern Catholic culture and identity, 1580-1610

What did it mean to be a Catholic elite in Protestant England? The relationship between the Protestant crown and its Catholic subjects may be examined fruitfully through a study of an individual and his world. This thesis examines this relationship through the example of Sir Thomas Tresham, who has often been seen as the archetypal Catholic loyalist. It is argued that the notion of Catholic loyalism must be reconfigured to account for the complexities inherent in the relationship between Catholics and the government. The duty to honour the monarch's authority was bound up with social and national sentiment, but it often accompanied criticisms of the practice of that authority, and the ways in which it encroached on personal experience. Intractable tensions lay behind expressions of loyalty, and this thesis travels in these undercurrents of cultural, social, religious, and political conflict to investigate the nuanced relationship between English Catholics and English society.
Political resistance as classically understood — actions which directly opposed and undermined government policy — risks the exclusion of culture and identity, through which resistance was redefined. It is argued that Tresham’s participation in elite activities became vehicles for resistance in the Catholic context. Book-collecting, reading, and the donation of books to an institutional library are framed as forms of resistance which countered the spirit of government legislation, and provided for the continuation of a robust tradition of Catholic scholarship on English soil. Through artistic and architectural projects, Tresham found ways to participate in elite culture which were not closed off to him, and in which Catholicism and gentility could sit side by side. These activities were also avenues for resistance, whereby the erection of stone testaments to Tresham's faith defied the government's attempts to redefine Englishness and gentility in Protestant terms, to the devastation of Catholicism. These artistic works combined piety, gentility, and resistance, and, together with Tresham’s two Catholic libraries, they were to be his legacy.

Keywords: History of the Book
Religious History
Cultural History
Early Modern Catholicism
Gentry
Identity
Library History
Advisor: Brigden, S
Gajda, A
Ethical issues surrounding access to care for BRCA mutations

Harmful BRCA (breast cancer susceptibility genes 1 and 2) mutations greatly increase women's risks of breast and/or ovarian cancer but are found in less than 1 per cent of the general population. Thus, care is targeted at women with strong family histories of breast and/or ovarian cancer. Genetic testing can determine if these high-risk women carry harmful mutations; if so, they may pursue care that facilitates cancer prevention, detection, and/or treatment.
In this thesis, I examine in which cases it is problematic that some British and American women do not access this potentially life-saving care. In recognition of the difficulty in measuring access, a view informed by preliminary interviews and a literature review, I use three complementary approaches to illustrate different aspects of access. First, a critical review surveys how British and American clinical guidelines, laws, policies, and legal rulings govern service availability. Second, a scoping study describes the US and UK literature on barriers and facilitators to access. Third, an empirical study involving focus groups with UK and US genetics professionals and support group members details how women provide and pursue care.
Using Beauchamp and Childress's 'four principles' framework, I analyse how these approaches inform four elements of access: availability of services, barriers to care, relevance and effectiveness of services, and equity of access. I distinguish between cases in which women do not want and/or need care and cases in which women are denied care they want and need, and I propose strategies to redress current inequities in access. I further suggest that offering Ashkenazi Jewish population screening alongside family history-based screening may be appropriate. I conclude that whilst most problematic cases are country-neutral, only US women are problematically constrained by insurance and legal loopholes, and only UK women are problematically constrained by regional variations in health authority funding.

Keywords: Breast cancer
Ethics
Ovarian cancer
Genetics
Access to care
BRCA
HBOC
Advisor: Parker, M
Lucassen, A
Indifference to past human rights violations in Chile

The purpose of this thesis is to explain how and why a sector of the Chilean population is indifferent to past human rights violations committed during the dictatorship of General Augusto Pinochet (1973-90), and also what the consequences of that indifference are in Chile today. An explanatory sequential and non-nested mixed methods design has been applied: the quantitative analysis is based on the 2013 National Bicentennial Survey (N=2,004), and the qualitative analysis is carried out from fifty-three in-depth and semi-structured interviews to indifferent and non-indifferent individuals. It is argued that indifference to past human rights violations is the result of various processes of socialization that influence the individual, being relevant life experiences and social interactions related to political issues. According to the survey, 16.02 percent of the sample is indifferent to past atrocities. Regarding the causes of indifference, binomial logistic regression highlights four variables: political orientation, socio-economic status, generational cohort, and perception of social conflict. The analysis of in-depth interviews shows that the three most common sets of variables that explain indifference to past human rights violations are: the predominant emphasis on search for family and personal well-being, discomfort with politics, and fear of a recurrence of the pre-coup d'état crisis and post-coup authoritarian experiences. Qualitative analysis shows that indifference is dynamic and visible. There are also different intensities in the spectrum of indifference. As the indifferent are a heterogeneous group, distinctions between disillusioned, submissive, depoliticized, and resigned indifferent are presented. It is also argued that the indifferent cynics are a problematic group for transitional justice, democratic consolidation, and the rule of law. Regarding the social consequences, the indifferent may actively promote social indifference in their interactions; indifference has become a socially accepted norm by other sectors, and indifference facilitates the persistence of the culture of impunity over time.

Keywords: Chile
Human Rights
Transitional Justice
Indifference
Advisor: Payne, L
Social aspects of educational inequality

Social factors have long been included in theories that aim at explaining educational inequality, for example social integration or social influence from significant others. Using social network data from the Children of Immigrants Longitudinal Survey in Four European Countries (CILS4EU), I am investigating to what extent social aspects can contribute to our understanding of ethnic and gendered patterns in educational inequality.
The first two empirical chapters focus on explaining ethnic patterns in school grades and in the aspirations to attend university. In these, I find a positive relationship between low school grades and extent of social exclusion, measured through the absence of friendships and the existence of social rejection from classmates. This helps explaining ethnic grade disadvantages of recently arrived migrants, since they are more likely to be socially excluded. Further, I use friendship network data to detect social clusters within school classes, and find that changes in cluster members’ aspirations are relatively more important for changes in individual aspirations than the corresponding changes of classmates outside of the social cluster. These chapters use an ego-centric network approach, i.e. they utilise social network data to capture characteristics of the social dimension around individuals and analyse them in regression models on the individual level.
The latter two empirical chapters investigate how social influence can stabilise gendered patterns of favourite subjects and competence beliefs. Examining why girls get discouraged from subjects in the field of Science, Technology, Engineering, and Maths (STEM), I find evidence for influence from friends on favourite subjects, as well as for the tendency of girls to be affected by the preferences of other girls in the classroom specifically when it comes to preferences for STEM subjects. Moreover, I show that there is a social influence from friends on maths competence beliefs, especially for boys, while girls tend to be more influenced by maths grades. These two chapters take a socio-centric approach, i.e. they deploy complete network analysis to detect patterns of social influence, while accounting for network structures and processes.
This thesis shows that social aspects can contribute valuable insights into the study of educational choice and attainment. In identifying concrete social mechanisms surrounding and affecting individuals, this approach can thus help us understand how differences in educational outcomes come about.

Advisor: Jonsson, J
The evolution of early-type galaxies

Early-type galaxies (ETGs) are typically thought of as `red and dead' with little to no star formation and old stellar populations. Their detailed kinematics measured locally suggest an interesting array of formation mechanisms and high-redshift observations are starting to reveal a two-phase evolutionary path for the most massive galaxies. In this thesis, I take a combined approach to studying the formation of ETGs. I look to distant quiescent galaxies in one of the densest regions of the early Universe and at the fossil record of a local galaxy to shed light on some of the unsolved mysteries of how ETGs evolved. Using the unique multiplexed instrument, the K-band Multi-Object Spectrograph (KMOS), the evolution of galaxies at both low and high redshift were studied as part of this thesis. I maximised the capabilities of this multi-integral field unit (IFU) near-infrared (NIR) instrument to study different aspects of ETG evolution. With 24 separate IFUs, many quiescent galaxies were efficiently observed in a massive high-redshift cluster as part of the KMOS Cluster Survey. Coupling KMOS spectroscopy with Hubble Space Telescope photometry, I studied the ages, kinematics, and structural properties of the galaxies. I then analysed the detailed properties of a massive local ETG with interesting kinematics, IC 1459. Coupling the NIR IFU data from KMOS with a large mosaic of optical data from the Multi-Unit Spectroscopic Explorer, I was able to study the spatially resolved kinematics, stellar populations, and initial mass function of the galaxy. The work presented in this thesis provides some interesting clues as to the formation of ETGs and possible diversity of their evolutionary paths.

Keywords: integral field unit
Galaxies
Early-Type Galaxies
kinematics
Galaxy Cluster
initial mass function
Stellar populations
Advisor: Davies, R
Why do they call it Raška when they mean Sandžak? On the synchrony and diachrony of identities in Southwest Serbia

This thesis investigates the diverse ways in which social agents construct the relationship between past, present and future through a study of historical consciousness and its role in the negotiation of identity and shifting power relations in the border region of Southwest Serbia. The focus of the research falls on ethnic relations between Serbs and Bosniaks, who predominantly inhabit the area, and the boundaries that they imagine surround the world they live in. The goal has been to trace the life of these ethnic boundaries, and with it the relationships between those who imagine them by following their transformations in history, as well as to inquire into elements of social patterns that may be discernable within a contextualized and historicized analysis of the region. In order to achieve this, I have analysed the diverse pasts and futures that coalesce in the many 'time spaces' that Southwest Serbia’s social actors inhabit in any present moment and from which they (re)construct these boundaries and their identities. The research has been situated within the wider anthropological discussion about the relation of culture (memory) and history and draws on insights made by relevant studies and ethnographies conducted on the territory of the former Yugoslavia.
The data presented demonstrates that ethnicity and nationality are not fully crystalized as concepts in Southwest Serbia, their contents are imagined in inconsistent ways in and between social groups, while ethno-national identities and histories are not on the whole felt to be crucial to one's personal sense of self, but are perceived and put to use as malleable political resources. As a result, the most dominant allegiance in Southwest Serbia is to one’s family, the only group whose 'essence' escapes political malleability and whose members share a common cross-temporal vision.

Keywords: Balkan studies
Sandžak
Serbia
Identity building
Yugoslavia
Raška
Ethnic relations
Western Balkans
Advisor: Parkin, R
Immune regulatory networks in inflammation-driven cancer

The incidence of colorectal cancer (CRC) is increasing and the prognosis for patients with advanced or metastatic disease is relatively poor. Immunotherapies hold great promise, but deploying them effectively in CRC patients will require further knowledge of the complex cellular and molecular interactions that occur between intestinal tumours and the host immune system. The objective of this study is to understand the mechanisms by which lack of immune cell regulation in the gut can drive the formation of colon adenocarcinomas. In addition, this work aims to identify new mechanisms involved in progression to metastatic disease.
Using mouse model systems, we found that aberrant activity of Treg cells deficient in IL-10 can promote inflammation-driven CRC. IL-10 deficient Tregs have increased capacity to drive tumourigenesis compared to their CD4+ effector T cell counterparts. RNA sequencing revealed specific upregulation of several genes, including a newly-described cytokine, in tumour-promoting Tregs. We explored cytokine regulation and the tumour microenvironment, and show that the inflammatory cytokine IL-6 and TGFβ are necessary for tumour formation in this model. Moreover, disease is associated with a marked stromal cell signature that is induced as a consequence of Treg deficiency in IL-10 production. Gp38+ stromal cells are dominant producers of IL-6, and potent ECM modellers. Furthermore, tumours driven by IL-10 deficient Tregs express high amounts of the pro-mesenchymal transcription factor Sox4. Using combined in vitro and in vivo analyses, we confirm that Sox4 is involved in tumour growth and characterise its expression in CRC patients.
Collectively, our findings suggest that Tregs and stromal cells act together to foster a microenvironment that promotes disease progression, notably through the expression of Sox4 in tumour cells. These findings open an exciting avenue to explore the phenotype of tumour-promoting Tregs and to study Sox4 function in metastatic disease.

Keywords: tumour immunology
regulatory T cell
stromal cell
Advisor: Powrie, F
Critical analysis of Guillaume Groen van Prinsterer’s Christian-historical principle, with a comparative critical analysis of his argument of ‘history’ with that of Edmund Burke’s as used in their critique of the French revolution

This thesis provides an analytical interpretation of the critique Dutch nineteenth-century statesman-cum-historian Guillaume Groen van Prinsterer (1801-1876) articulated of French revolutionary ideology. It achieves an original reading of Groen’s thought as Protestant right-order theory. This reading achieves a clarification of the functions that Scripture, 'nature', and ‘history’ have in his thought, and connects his thinking to that of a small group of contemporary British-based political theologians, notably Oliver and Joan Lockwood O'Donovan, and their minority view on the ontological grounding of justice. Our comparison of Groen's argument of 'history' with that of Edmund Burke achieves original critical leverage on their concepts of 'history', and draws out that Burke's critique of the Revolution purposes to re-affirm English common law, while Groen’s is an apologia for Christianity.

Keywords: 'history' as polemical argument
anti-revolutionary principle
political theory
Belgian Revolt
Christian-historical principle
political theology
anthropocentric constitutional theory
unwritten constitution
right-order theory
theocentric constitutional theory
divine right of government
sphere sovereignty
Advisor: Biggar, N
Intestinal stromal cell types in health and inflammatory bowel disease uncovered by single-cell transcriptomics

Colonic stromal cells provide critical structural support but also regulate immunity, tolerance and inflammatory responses in the mucosa. Substantial variability and plasticity of mucosal stromal cells has been reported but a paucity of distinct marker genes exist to identify distinct cell states. Here single-cell RNA-sequencing is used to document heterogeneity and subtype specific markers of individual colonic stromal cells in human and mouse.
Marker-free transcriptional clustering of fibroblast-like cells derived from healthy human tissue reveals distinct populations corresponding to myofibroblasts and three transcriptionally and functionally dissimilar populations of fibroblasts. A SOX6 high fibroblast subset occupies a position adjacent to the epithelial basement membrane and expresses multiple epithelial morphogens including WNT5A and BMP2. Additional fibroblast subtypes show specific enrichment for chemokine signalling and prostaglandin E2 synthesis respectively.
In ulcerative colitis, substantial remodelling occurs with depletion of the SOX6 high population and emergence of an immune enriched population expressing genes associated with fibroblastic reticular cells including CCL19, CCL21 and IL33.
A large murine dataset comprising over 7,000 colonic mesenchymal cells from an acute colitis model and matched healthy controls reveals strong preservation of the SOX6 high and myofibroblast transcriptional signatures. Unsupervised pseudotemporal ordering is used to relate fibroblast subsets to one another producing a branched developmental hierarchy that includes a potential progenitor population with mesothelial characteristics at its origin. This work provides a molecular basis for re-classification of colonic stromal cells and identifies pathological changes in these cells underpinning inflammation in UC.

Keywords: ulcerative colitis
single cell RNA sequencing
Advisor: Simmons, A