VictorJuiz/thesis huggingface dataset:
Luminescent guest encapsulated metal-organic framework composites for photonic sensing technology

Luminescent metal-organic frameworks (LMOFs) are promising hybrid materials and are considered ideal for fabricating sensors and optoelectronics. A unique direction of LMOFs research is to harness MOFs as ‘hosts’ to encapsulate various luminescent ‘guest’ (LG) molecules for producing LG@MOF systems. However, feasible design ideas and in-depth mechanism analyses are scarce, compromising their practical engineering potential. This section, combined with the structure, synthesis, types, and applications of LG@MOF systems, is described in detail in Chapter 1 and 2.
In Chapter 3, 4, and 5, three new LG@MOF systems have been designed and prepared. The results demonstrated that effective wavelength-tuning (~ tens of nanometres) or turn-on (~ tenfold) type sensing materials could be readily synthesised even with common fluorescent materials (e.g., rhodamine B, tetraphenylethylene, perylene). Different polymers have been combined with the obtained LG@MOF systems to enhance stability and processability.
Detailed photophysical characterisations have been conducted to investigate the obtained LG@MOF systems. By analysing the excitation, emission, lifetime, and quantum yield, three novel sensing mechanisms have been proposed: (i) Guest aggregates of different sizes are protected differently by the MOF, thus, generating sensing behaviours. Moreover, the configuration of the guest aggregates may change under stimuli leading to further sensing performance (Chapter 3); (ii) MOF can provide a strong caging effect to aggregation-induced emission (AIE) materials resulting in turn-on type mechanochromism (Chapter 4); (iii) The lattice of MOF can influence the electron-phonon coupling of guest excimers causing distinct luminescent properties (Chapter 5).
Overall, this work helps address the pain points of LG@MOFs research and illustrates the possibility for large scale production, which may inspire more research into high-performance fluorescent sensors. These are summarised in Chapter 6, along with some specific examples of future development.

Keywords: luminescence
sensors
metal-organic frameworks
guest-host interactions
Advisor: Tan, JC
Nutrient cycling of Bornean tropical forests

The thesis addresses a novel topic of nutrient cycling of tropical forests and substantially adds to the small amount of currently available data in the area. While nutrients like nitrogen (N) and phosphorus (P) are considered to limit net primary productivity (NPP) in lowland tropical forests, direct evidence of nutrient limitation of NPP is scarce.
The thesis focuses on humid lowland tropical forests along a disturbance gradient in Malaysian Borneo and quantifies key biological processes of nutrient cycling: nutrient requirement, uptake, use efficiency, resorption and allocation. The first empirical chapter examines wood-specific nutrient concentrations and their radial and vertical allocation within a whole tree. The second and third empirical chapters examine the effects of logging disturbance and soil availability on net primary productivity and nutrient cycling. Five macronutrients of N, P, potassium (K), calcium (Ca), magnesium (Mg), and carbon (C) are considered. I developed and employed a novel approach of coupling data on nutrient stoichiometry and NPP to provide direct estimates of fluxes and allocation of nutrients within forest ecosystems.
In logged forests, the contribution of leaf resorption towards meeting nutrient requirement and the allocation of nutrients to canopy were lower, while allocation of nutrients to wood was higher than in old-growth forest. Contrary to expectation, NPP did not correlate with soil nutrient availability of any elements, suggesting soil availability is a weak predictor of NPP. Depending on the nutrient, different strategies, such as changes in resorption rates and changes in nutrient use efficiency, were adopted to compensate for low supply of that nutrient. Overall, this study demonstrates the value of coupling NPP with stochiometric data to gain insights into the nutrient cycle of intact and disturbed forests. These insights explain how limited supply of P, K and Ca is a challenge in lowland tropical forest ecosystems.
The study found higher concentrations in sapwood relative to heartwood for Dipterocarp species, which provide empirical support for wood resorption during sapwood senescence. It also showed exceptionally high nutrient concentrations in the bark, which suggest debarking during logging operations could substantially contribute to maintaining nutrients within forest ecosystems.

Keywords: net primary productivity
nutrient resorption
nutrient cycling
carbon cycling
Malaysian Borneo
SAFE Project
nutrient uptake
tropical forest
ecophysiology
Advisor: Malhi, Y
Riutta, T
Aspects of disease burden and risk factors for bacterial disease in low- and middle-income countries

Bacterial infections cause substantial morbidity and mortality, particularly in low- and middle-income countries. Strained healthcare systems, limited access to clean water, and fragmented hygiene and sanitary infrastructure increase risk of disease transmission. However, effective vaccines have been developed and can be deployed strategically to prevent disease. This thesis sets out to measure aspects of cholera and typhoid disease burden and to evaluate how natural infection and WASH affect disease risk in endemic settings. The analyses are performed on historical datasets of clinical studies of cholera and typhoid vaccines that were conducted in Bangladesh and India, respectively. Using a vaccine probe analytical approach, I assessed whether there was evidence of cholera in diarrhoeal cases that tested negative for cholera by conventional faecal culture and provided evidence that cholera cultures are highly sensitive. Secondly, I developed a clinical definition for typhoid fever that satisfied the criteria of being predictive of culture-confirmed typhoid fever and being protected against by an effective typhoid vaccine. Thirdly, I measured the degree to which natural typhoid protected against a subsequent typhoid fever episode and found little evidence for the development of natural immunity. Finally, I evaluated which components of household WASH in a typhoid endemic setting were associated with reduction of typhoid risk and asked whether WASH and vaccine interventions acted synergistically to control typhoid.

Keywords: vaccine probe
low and middle income country
recursive partitioning
clinical trial
infectious disease
Advisor: Baker, S
Turner, P
Melancholia, noise and intertextuality in Louis Andriessen’s La Commedia and portfolio of original compositions

While questions of irony and politics abound in the literature on Louis Andriessen (1939–21), a critical evaluation of intertextuality in his work does not yet exist, despite the composer’s constant drive towards a polystylistic language in music and theatre that very often incorporates multiple outside sources and a wide range of texts as compositional or narrative inspiration. La Commedia (2004–08), a ‘film opera’ by the composer with filmmaker Hal Hartley, provides a useful case study for opening this discussion as it comprises many textual, visual, and musical voices (often overlayered and semantically obscured) to express something of a deeply intertextual and sometimes impenetrable author and text: Dante and his Divine Comedy. This thesis hypothesises that the intertextuality of La Commedia is not just a postmodern and irreverent commentary on the Comedy, but that the opera’s intertext is a way of reflecting the most important narrative, historical and theological aspects of Dante’s complex epic. To interrogate this idea, this thesis proposes that two themes operating as dramatic devices throughout the work are inextricably linked to its intertextuality—and, therefore, to Dante—so must shape the analysis of its music, media, and staging: melancholia and noise. Appended to this thesis is a portfolio of five original compositions by the author: Grim's Ditch, Jacinto Chiclana, The Beginning of an Idea, Life Piles Up, and FLUX.

Keywords: Louis Andriessen
The Divine Comedy
melancholia
opera
music theatre
La Commedia
intertextuality
composition
noise
Dante
Advisor: Harry, M
Ouzounian, G
The making of first movers: a micro-level study of high-risk dissent initiators in Burma 1988-2011


In the high-risk environment of authoritarian regimes, why do some people dissent while others do not? Specifically, what motivates some people to be the first to dissent when there is no safety in numbers, and no guarantee that others will join? The willingness of some individuals to seemingly disregard the high personal risk of dissent, evincing a readiness to bear costs, puzzles scholars in the social sciences.
This project draws on semi-structured interviews, archival evidence, and secondary sources from the United States, Burma, and the United Kingdom to investigate first movers in Burma and their attempts to initiate dissent that took place between 1988-2011. Based on my data, I developed a narrative-driven grounded theory on what motivates some individuals to become first movers – the initiators – of high-risk dissent against authoritarian regimes at high personal risk.
This project’s overarching theoretical claim is that first movers are made, not born. My cumulative three-part theory is as follows: The individuals in my sample who became first movers of high-risk dissent had been experienced dissenters who (1) acquired informal political education and had undergone socialization among dissenters; (2) were radicalized by state repression into becoming “devoted dissenters”; and ultimately (3) viewed participation in high-risk dissent to be in their self-interest.
First movers are the human catalysts for every political event that has the potential to snowball into a consequential episode of dissent in an authoritarian country. This question is important because the kind of mass protests that upend authoritarian regimes cannot transpire without this subset of high-risk political dissidents who instigate dissent activity. This project will attempt to play a role in better understanding this small group of people whose human agency can lead to lasting changes to undesirable regimes.

Keywords: micromobilization
Dissent
first movers
protest
democratization
Burma
Authoritarian countries
political dissent
Advisor: Tudor, M
Music and the epic meta-category: case studies from the long twentieth century

The last few decades have seen a dramatic rise in uses of the term ‘epic’ in vernacular discourse, regarding increasingly varied subject matter including music. As a noun, ‘epic’ is assumed to be a genre or tradition; as an adjective, it seems to be little more than a marker of great scale, elevated status, or high value. These uses have often been at odds with definitions found in academic criticism, but this is beginning to change in more recent scholarship. This thesis reimagines ‘epic’ as a meta-category that has been and continues to be shaped by a diverse array of media and theoretical concepts. Although musicology’s use of ‘epic’ has been limited, I argue that the discipline and meta-category have a reciprocal relationship. By examining case studies by Sibelius, Mahler, Vaughan Williams, and Howard Shore, this thesis considers how music can affirm, subvert, and critique seemingly conventional aspects of the epic meta-category. Focusing on the long twentieth-century, a period characterised by substantial shifts in definitional ideas around the meta-category, this thesis draws on recent re-evaluations of epic to embrace its inherent ambiguity and reflect its usefulness for musicological study. Each case study presents a different type of interaction between music and media more commonly invoked in discourse on the epic, namely literature and film, to offer a starting point for how music can participate in that same discussion. Going beyond merely asking whether a musical work “is” an epic, the conclusions drawn here are merely an initial suggestion of how music fits into and could provide greater understanding of this highly complex critical sphere.

Advisor: Grimley, D
The geometry and stability of fibrations

This thesis concerns two topics. First is the existence of optimal symplectic connections on holomorphic submersions, and links to algebro-geometric stability of fibrations. The main result is that a fibration admitting an optimal symplectic connection is stable with respect to a large class of fibration degenerations. The second topic is the deformation theory and families of Kähler metrics with weighted constant scalar curvature. Here we study the existence of such metrics when either the complex structures or the weight functions vary, and also prove the existence of a weighted Weil--Petersson metric associated to a family of these metrics. The results are new even in the fibrewise extremal and Kähler--Ricci soliton settings.

Keywords: Holomorphic submersions
K-stability
Optimal symplectic connections
Weighted cscK metrics
Canonical Kähler metrics
Advisor: Kirwan, F
Dervan, R
Macrophage-matrix interactions in the breast tumour microenvironment: the case of tenascin-C

Tumour-associated macrophages (TAMs) are key immune-suppressive constituents of the breast tumour microenvironment (TME) and correlate with poor prognosis. Tenascin-C (TNC) is an immunomodulatory extracellular matrix (ECM) protein which is upregulated in breast tumours, and is associated with increased metastasis and worsened prognosis. Our previous work showed that perturbation of the breast TME by tumour-derived TNC skews macrophages towards an immune-suppressive phenotype featuring downregulated antigen-presentation. Using TNC as an exemplar perturbant, this thesis sought to understand how macrophage effector functions such as antigen presentation become enhanced or suppressed within the TME. To achieve this, single-cell RNA sequencing (scRNAseq) was performed on infiltrating myeloid cells derived from syngeneic, orthotopically-engrafted, murine breast tumours that were engineered to express high or low levels of TNC. scRNAseq revealed marked heterogeneity in the intra-tumoural myeloid compartment with 7 distinct subsets observed, 5 of which were macrophages (Mac1-5). Notably, macrophages delegated key effector functions including antigen presentation (Mac2) and chemokine production (Mac3) to discrete subsets that were phenotypically, spatially and temporally distinct at the protein level by flow cytometry and confocal immunofluorescence imaging. The role of TNC was predominantly exerted at the level of subset abundance (rather than gene transcription), with 4 out of 7 myeloid subsets exhibiting TNC-dependent changes in abundance, including two macrophage subsets (Mac1 & Mac2). Over time, TNC modestly weakened the segregation of Mac2 and Mac3 phenotypes, suggesting it may drive dysfunctional delegation of effector functions. Pseudotemporal analysis of scRNAseq data implicated the epigenetic regulator, Kdm6b, in governing the acquisition of Mac3 effector function, and pharmacological inhibition of KDM6B in vivo shifted the proportion of Mac3 via TAM reprogramming. Finally, mouse-derived myeloid subsets were well-conserved in the most comprehensive scRNAseq atlas of human breast cancer, and gene signature analyses in bulk clinical datasets demonstrated significant differences in prognosis for patients with distinct myeloid ‘ecotype’ profiles. Together, these data demonstrate functionally divergent roles for TAM subsets in breast tumour progression and metastasis, while providing mechanistic insights into the impact of ECM-derived cues such as TNC on shaping the myeloid compartment, with potential therapeutic and prognostic implications for breast cancer patients.

Keywords: scRNAseq
TNC
tumour microenvironment
breast cancer
macrophage
TAM
epigenetics
tenascin-C
extracellular matrix
KDM6B
single-cell RNAseq
tumour-associated macrophage
ECM
Advisor: Midwood, K
Udalova, I
The microvariation of post-verbal negative particles in Old Gallo-Romance: a comparative study

This thesis is a microvariational analysis of post-verbal negative particles in varieties of Old Gallo-Romance between the years 1100 and 1500 A.D. It examines the internal and exogenous factors contributing to the survival of certain particles and the disuse of others. Using a mixture of verse and prose data from six oïl varieties and ten oc varieties of Old Gallo-Romance, it draws comparisons between them from the following perspectives: rates and degrees of grammaticalisation; the influence of discourse-pragmatics and information-structure on their presence, absence and frequency of occurrence; their diatopic and diachronic spread; and the effect that standardisation, linguistic prestige, and a scribal koiné had on the diminishing number of competing post-verbal negative particles in the grammar. In essence, it seeks to clarify why pas, as one of several hundred so-called ‘minimisers’, came to be the default sentential negator in French, rather than any other competing variant.

Keywords: Medieval
Langue d'oïl
Syntax
Gallo-Romance
Linguistics
Grammaticalisation
Negation
Middle French
Occitan
Post-verbal
Old French
Langue d'oc
Advisor: Wolfe, S
Experience teaches? How can the orientations to learning from experience framework (Hagger et al. 2008) be used by mentors and teachers to explore learning to teach on employment-based routes?

Recent changes within teacher education policy in England present a timely opportunity to consider the nature of teachers’ learning through experience on employment-based routes. This thesis draws on the Orientations to Learning from Experience Framework ((OLEF) Hagger et al. 2008), which uses five dimensions to describe the dispositions of beginning teachers to learning from experience, as identified in a three-year longitudinal study. In this study I investigated if and how this research product could be used by mentors and beginning teachers to explicate and develop participant teachers’ learning.
In the secondary school site of this qualitative study the majority of the teachers in their first or second years as teachers were undertaking, or had undertaken, ‘employment based’ routes of initial teacher education. Nine beginning teacher participants and their mentors were involved in data collection and analysis during their first years as teachers on School-Direct Salaried and Teach First routes. As a ‘Close-to-Practice’ study focussed on employment-based initial teacher education, it offers a fresh perspective on the complex, contextualised and idiosyncratic process of learning to teach.
The OLEF framework and other re-presentations of their practice stimulated rich data regarding the beginning teachers’ learning, thereby demonstrating the potential for OLEF to act as second stimulus in formative interventions. Furthermore, I developed the conceptual framework of OLEF by drawing in contemporary research through citation analysis as well as cross- and within-case analysis of the conversational data. Intentionality, one of the socio-cultural concepts of OLEF is considered in relation to self-efficacy, professional agency, self-regulation, adaptive expertise and deliberate practice. Five conditions which support high levels of Intentionality were found.
Few research studies have captured conversations between beginning teachers and their mentors in the recent English context. These conversations were recorded and analysed by participants, opening up their semi-private world. The role of mentors as mediators in supporting self-regulation and the development of a broader Frame of Reference is explored. The data contributes to discussion about the nature of teachers’ knowledge, learning, self-regulation and professional agency. Practical implications for beginning teachers and their mentors are offered.

Keywords: Initial teacher education
employment-based initial teacher education
mentoring conversations
teacher learning
double stimulation
mentorin
Advisor: Burn, K
Menter, I
The memory of Ignatius of Antioch: the martyr as a locus of Christian identity, remembering and remembered


The fundamental argument of my thesis is that the concept of ‘memory’ provides remarkable insight into the early second-century bishop and martyr, Ignatius of Antioch; my thesis seeks to explore the nature of this insight and unpack its significance. His palimpsestic literary legacy and personal preoccupation with remembering and its correlates make Ignatius uniquely suited among early Christians to be unlocked by the key of memory. This endeavour broadly takes its lead from Elizabeth Castelli’s Martyrdom and Memory (2004). She argues that ‘memory work’ done by early Christians on the experience of persecution and martyrdom was a form of ‘culture making’; Christian identity is coloured by memory of the religious suffering of others. My focal question is an extension of hers, and has three parts. Given that remembering in community is central to the development of the early church, its theology and self-understanding: 1) What is the nature of the memories inherited by Ignatius and his communities, and how are they engaged in the rhetorical and polemical context of his letters? 2) How does Ignatius construct himself as a figure to be remembered by Christian interpreters? 3) How was Ignatius in fact memorialised in early Christian history?
This thesis spans three centuries and three distinct parts. I therefore establish my argument by a combination of means: close reading of the ‘authentic’ middle recension letters, select and critical interaction with sociology and anthropology, and thorough analysis of the long recension and Ignatian martyrological accounts. The long recension has received only meagre scholarly attention, so my work constitutes a significant contribution to Ignatian scholarship with regard to this corpus in particular. Memory is demonstrated to afford a previously unnoticed hermeneutic from which to approach Ignatius, who is at once one remembering, one aspiring to be worthy of remembrance, and one indeed remembered.

Keywords: Remembering
Patristics
Ignatius of Antioch
Sacrifice
Girard
Memory
Remembrance
Theology
Martyr
Advisor: Edwards, M