VictorJuiz/thesis huggingface dataset:
Exploring new paths towards biological anion recognition by lanthanide complexes

Anions are ubiquitous in nature. In order to understand them in their natural setting, this thesis focusses on developing lanthanide complexes as hosts for the recognition of biologically relevant anions, particularly chloride and sialic acid. Chapter-I introduces lanthanide chemistry encompassing macrocyclic complexes, luminescence, and MRI. An account of anion recognition and lanthanide complexes used as hosts for biologically relevant anions are reviewed.
Chapter-II focuses on developing receptors for chloride recognition. The concept of binuclear lanthanide complexes, bridged by flexible ethane/propane spacer, for chloride recognition is envisioned. The proposed complexes are synthesised, and their anion binding properties are studied by luminescence, NMR spectroscopy, and X-ray crystallography. The study demonstrates the versatility of these binuclear complexes as the strongest chloride binding receptor to function in water and buffers to date. Thus, the work described here, hits a new milestone in anion coordination chemistry, ameliorating detailed exploration. Chapter-III builds on the drawbacks from these neutral complexes towards anion binding, and proposes tryptophan-conjugated cationic binuclear complexes for halide recognition. Initial studies show promising results towards halide recognition in water from this cationic coordination complex.
Chapter-IV revisits a ditopic approach of arylboronate-conjugated lanthanide chelates for sialic acid recognition, a tumour biomarker. However, the complexes suffer from protodeboronation, leading to the cleavage of boronic acid which is reported for the first time with structural evidence. The resulting boron free complex binds to L-lactate and D-gluconate. Chapter-V employs the ditopic approach, but with the incorporation of rigid anthracene and dansyl spacers between them, to improve the stability of the arylboronate during complexation. However, the anthracene-based receptor proved synthetically challenging. The success in making the dansyl-functionalised ligand extents the possibility of investigating sialic acid binding.
Chapter-VI summarises the work embodied in this thesis and Chapter-VII describes the complete experimental procedures followed in accomplishing the results reported in Chapters II-V.

Keywords: chelation
chloride
sialic acid
host-guest chemistry
lanthanides
luminescence
photoinduced electron transfer
f-block chemistry
X-ray crystallography
anion recognition
Advisor: Faulkner, S
Single-cell analysis of alternative splicing in normal and malignant stem/progenitor cells

Alternative splicing is the process of utilising a different combination of exons to generate different isoforms from the same gene. Therefore, alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression. To date, high-throughput single-cell RNA-sequencing (scRNA-seq) analyses have focused on characterising gene expression programme, whereas alternative splicing remains challenging to investigate. One possible reason for the sparsity of single-cell alternative splicing studies is the lack of single-cell alternative splicing analytical frameworks. To this end, we have developed analytical frameworks to comprehensively capture the alternative splicing landscape in health and disease models, and to prioritise actionable spliced genes for downstream experimental studies.
The developed frameworks consist of MARVEL, VALERIE, and IMPACT. MARVEL is an R package that provides comprehensive functionalities for the detection and quantification of alternative splicing events to enable dimension reduction analysis, differential splicing analysis, and functional annotation of differentially spliced genes. Functional annotation features include biological pathway enrichment analysis and nonsense-mediated decay prediction. VALERIE is an R package for visual-based validation of differentially spliced genes identified from MARVEL. IMPACT is an integrated in-house database consisting of a collection of pre-processed publicly available myeloid neoplasm and cancer cell line data for prioritising clinically relevant and druggable spliced genes validated by VALERIE.
We validated and demonstrated the application of our analytical frameworks on scRNA-seq data generated from both plate- (e.g., Smart-seq2) and droplet- (e.g., 10x Genomics) based library preparation methods derived from homogeneous cell lines and heterogeneous haematopoietic stem and progenitor cells in health and disease states. We believe our analytical frameworks will be advantageous to biologists to reveal novel biological insights from scRNA-seq data.

Keywords: next-generation sequencing
splicing
genetics
cancer
single-cell
Advisor: Mead, A
Thongjuea, S
Two-scale method for wall-bounded flows

Recent findings on wall-bounded turbulence prompt a new impetus for modelling development to capture and resolve the Reynolds-number-dependent influence of outer flow on near-wall turbulence in terms of the ‘foot-printing’ of the large-scale coherent structures and the scale-interaction associated ‘modulation’. A two-scale method is developed to couple a locally embedded near-wall fine-mesh DNS block with a global coarser mesh domain. The influence of the large-scale structures on the local fine-mesh block is captured by a scale-dependent coarse-fine domain interface treatment. The global near-wall coarse-mesh region outside the local fine-mesh block is governed by the augmented flow governing equations with forcing source terms generated by upscaling the space-time averaged fine-mesh solution. The validity and effectiveness of the method are examined for canonical incompressible channel flows at several Reynolds numbers. It is shown that the mesh-count scaling with Reynolds number is potentially reduced from O(Re^2) for the conventional fully wall-resolved LES to O(Re) for the present locally embedded two-scale LES. The method is also extended to the implementation in boundary layer flows. A 2-dimensional roughness element is used to trip a turbulent boundary layer. It is observed that large-scale disturbances originating from the trip have a much shorter lifetime and weaker foot-printing signatures on near-wall flow compared to those long streaky coherent structures in well-developed wall-bounded turbulent flows. For the tripped turbulent boundary layer, a Chebyshev block spectral mapping is adopted to propagate source terms, driving the upscaled equations to a target solution. The overall mesh count - Re scaling is estimated to reduce from O(Re^1.8) for the full wall-resolved LES to O(Re^0.9) for the present two-scale solution.

Keywords: turbulence
computational method
Advisor: He, L
Performing the Arthurian legend in late Elizabethan and early Jacobean England c. 1575-1610

This thesis offers a critical analysis of various forms of Arthurian “play” performed across a spectrum of dramatic and quasi-dramatic entertainments between 1575 and 1610, and of the texts that record and reimagine them. By looking at the historical convergence of aesthetic forms, textual artifacts, social practices, and the human actors involved, this thesis emphasises the variety of groups and individuals engaged with the legend and the different uses to which it was put. Rather than a period characterised either by the absence or atrophy of the legend, attending to the transmission of performed Arthuriana transforms our conception of the genres, people, and institutions that we consider part of Arthurian literary history, and provides us with a fuller view of the range and valence of cultural reference in play during the period.
This thesis finds no single version of the Arthurian legend and no one Arthur. Rather, by scrutinizing progress entertainments, archery pageants, Inns of Court plays, tournament shows, and court masques, it reveals how performance cultures in this period shaped and were shaped by the Arthurian legend. Allegory and satire dislocate Arthurian figures from the compendious narratives of earlier centuries and reimagine them through classical mythology. The traditional associations of Arthur’s Round Table fellowship with individual aristocratic and amorous exploits are repurposed to perform corporate, civic virtue. Translation and imitation are deployed in pseudo-classical tragedy to reimagine Arthur’s fall as a cultural conquest. Tournament shows parallel the dangers and wonders of privateering with those of romance and so expand the bounds of chivalry. And Ben Jonson adapts the legend’s Elizabethan associations for a new reign. These experimental entertainments evidence an ongoing creative investment in King Arthur, and provide a new narrative about the negotiation of political and poetic authority in early modern England.

Advisor: Ashe, L
Kewes, P
Designing main group compounds for small molecule activation

This thesis reports on work aimed at designing main group compounds for small molecule activation, and includes studies of the reactivities of Frustrated Lewis Pairs (FLPs), low valent group 13 (gallium) compounds and low oxidation state group 14 compounds of tin and germanium towards H2 and CO.
Chapter 3 discusses the synthesis of several xanthene and acridine based FLPs which can activate H2 and CO reversibly. For the xanthene-based P/B FLP, H2 can be activated under high pressure (4 atm), and the acridine-based bis-borane FLP systems are capable of capturing gaseous carbon monoxide. In the case of the –BArf 2 system CO uptake can be shown by VTNMR studies to occur reversibly.
In Chapter 4, we report on the development of a mono-anionic phosphino-amide ligand based on a xanthene backbone, together with the synthesis of the corresponding Ga(I) complex, (PON)Ga, as a probe of its coordination properties in low valent main group chemistry.
In Chapter 5, we use a boryl substituted tin halide as a precursor to synthesize low oxidation state tin compounds. Here we describe the formation of formally SnI and Sn0 compounds and their transformation into [B]4Sn6 ([B] = (HCNDipp)2B); the mechanism has been studied by DFT methods and shown to proceed via a bisborylstannavinylidene intermediate. Moreover, we also isolated the tin cyclobutadiene dianion analogue of tin K2[B]4Sn4 which can react with benzoic acid to give a neutral Sn4 ring [B]4Sn4H2. DFT studies shows that K2[B]4Sn4 is not aromatic but the putative dication [[B]4Sn4]2+ could be aromatic.
In Chapter 6, we used K2[B]2Ge2 as nucleophile to react with LiI and catBBr, generating two planar digermene species Li2[B]2Ge2 and [B]BcatGeGeBcat[B]. The latter was found to react with CO to form a boryl/borylcarboxylate stabilized digermyne, [B]CO2Ge2[B]; the mechanism for the formation of [B]CO2Ge2[B] is proposed to proceed through a bisborylgermavinylidene intermediate. K2[B]2Ge2 can also react with electrophile (IPrMe)GeCl2 to form a Ge3 unit which dimerizes on carbene abstraction leading to the formation of a [B]4Ge6 cluster, the germanium analogue of [B]4Sn6.

Advisor: Aldridge, S
Egypt and the Hellenic economy: culture as a non-tariff trade barrier in the Atheno-Egyptian grain trade, 665-204BC

Without sufficient food for her population, and in the absence of the empire which had sustained her before the Peloponnesian War, fourth-century BC Athens relied on regular supplies of foreign grain. While the trade in grain has been subjected to sustained scholarly interest, few academics have considered why Athens chose one grain source above another. Most agree that at least a third of Athens’ grain requirements were satisfied from the Euxine, which was vulnerable to infrequent crop failure and sits at the end of a precarious and navigationally challenging shipping route exposed to danger from the Spartans, Byzantians and pirates. Conversely, there is insufficient evidence that Egypt, a voluminous grain source closer (by ancient sailing practices) than the Black Sea, contributed much to Athens’ food supplies before the Battle of Chaironeia (338BC). This thesis contributes one solution to this conundrum: that cultural differences constituted such a significant transaction cost to Atheno-Egyptian trade that it outweighed the dangers of the Euxine route. Applying approaches derived from New Institutional Economics to the Atheno-Egyptian case-study, this thesis pre-empts the Finleyan shibboleth that ancient trade cannot be considered economically rational by demonstrating the real economic costs of linguistic, religious, ethnic, philosophical, governmental, diplomatic and legal differences. Through charting a gradual convergence in these areas between the seventh and third centuries BC, a new perspective is offered on Egypt’s transition into a Hellenic economy which undermines the long established ‘Classical’-‘Hellenistic’ and ‘Western’-‘Oriental’ dichotomies which still pervade literature on the ancient economy.

Keywords: Athens
Egypt
Saite
Classical Athens
ancient economy
grain trade
ancient
Advisor: Moreno, A
Reliable attribution and projection of extreme heat events altered by human influence on the climate

Anthropogenic greenhouse gas emissions are now well-understood to be causing damaging changes to the climate. One of the many ways in which the climate is changing is through extreme weather events. Given the severe consequences of such events, understanding how human influence on the climate is affecting them is vital. This is the aim of the young field of 'extreme event attribution'. There now exist many established methods for attributing individual weather events to climate change, from probabilistic approaches utilising large climate model ensembles to deterministic storyline approaches. However, questions still remain over the reliability of these approaches, especially when considering the most unprecedented events. In this thesis, I show how weather forecast models could provide us with such reliable information about human influence on extreme weather --- focusing on extreme heat. These models are state-of-the-art and can be shown to be unequivocally able to simulate the detailed physics of specific extreme weather through successful prediction. I develop a perturbed initial- and boundary-condition approach within an operational forecasting system that aims to produce forecasts of individual events as if they had occurred in a world without human influence on the climate. These 'counterfactual' forecasts can be used to assess how not only the intensity, but also the probability of such events has changed. Although extreme weather attribution typically focuses on the past, the same approach could be used to produce forecasts in warmer future worlds --- thus providing vital information about how the most damaging weather may be expected to change in the future. I explore this theme of extreme weather projection, examining a novel approach to producing large climate model ensembles that span the range of uncertainty in future extreme weather. This work complements the specific nature of extreme event attribution, and they could together provide crucial information about climate risk.

Keywords: extreme value theory
numerical weather predictoin
extreme weather
climate modelling
extreme event attribution
climate change
Advisor: Allen, M
Weisheimer, A
Revenue patterns of piped water services in rural Africa

Rural Africa lags behind all other global regions in progress towards establishing universal and equitable access to safely managed drinking water. This challenge is marked by a notional interest in piped water for achieving service level goals while increasing demand and financial viability. Yet, a paucity of reliable information and evidence perpetuates unrealistic assumptions of how infrastructure and payment collection alternatives influence seasonal revenue generation. The emergence of professional service delivery models offers new sources of operational and financial data with potential to address knowledge gaps and inform viable, resilient, and equitable drinking water investments.
The primary aim of this project is to understand how seasonal patterns of domestic water use and payments affect revenue from piped water services in rural Africa. Empirical analyses have drawn on longitudinal records from Ghana, Kenya, Malawi, Rwanda, Tanzania, and Uganda that cumulatively span more than 500 service-years. In contrast to conventional assumptions, findings suggest household-level services exhibit similar seasonal revenue variability as off-site services and are not consistently associated with higher revenue when tariff level is controlled. Piped service areas with consistent seasonal rainfall have a third less revenue during wet months. Furthermore, prepaid credit payments do not consistently improve revenue generation compared to conventional payment approaches.
Three recommendations for rural water policy and practice are highlighted from this research. First, the threat of seasonal revenue variability to rural piped water services can be characterised by assessing rainfall patterns on localised, intra-seasonal scales. Second, complementary revenue patterns of on- and off-premises services can be leveraged at incremental stages of infrastructure investment. Third, caution should be exercised when considering prepaid credit over conventional payment approaches to prevent unrealistic revenue expectations and perverse outcomes.

Keywords: archetype analysis
rural water supply
seasonality
sustainable development goals
Africa
financial sustainability
Advisor: Hope, R
Koehler, J
Safer (cyber)spaces: reconfiguring digital security towards solidarity

As technology increasingly mediates our relationships, it also enables existing patterns of coercion, abuse, and control. This thesis investigates digital safety and security in the context of intimate violence and coercive control. I first develop a feminist critique of cybersecurity: namely, that due to the discipline’s engineering focus on defending networks and information, cybersecurity neglects the human element, and particularly differences in power and relationships between humans that produce (in)security. Feminist and critical theories, which centre gender and power in interpersonal relationships, provide a useful corrective to this highly masculinised and avowedly apolitical field. Taking this critique as a starting point, I present a set of studies that answer the overarching research question: “how can we reconfigure cybersecurity to account for tech-facilitated coercive control?” I focus on responses to the phenomenon of technology-enabled coercive control, or ‘tech abuse’ as a site for examining alternative security practices.
I then present three studies that reconfigure cybersecurity through running participatory workshops with excluded and marginalised groups, interviewing advocates who support survivors of technology abuse and addressing intimate violence in cybersecurity design. The model of cybersecurity that emerges from these studies is relational, made up of communal ‘networks of care’ rather than devices and individuals. This carries weight for questions of epistemology and academic knowledge production; my work centres the knowledge of unconventional and unacknowledged experts, such as survivors of abuse and community practitioners who support them. These people are cybersecurity experts due to their on-the-ground understanding of how technology is co-opted for abuse. Security practitioners should recognise the expertise inherent in these care networks to build on and strengthen them with a mindset of solidarity rather than turning these social problems into opportunities to pitch new technical products. Cybersecurity which starts with people (not machines), especially marginalised people, points our attention to dismantling the broader structures that create insecurity rather than patching technical vulnerabilities. In doing so, this reconfigured security becomes a call for solidarity.

Keywords: coercive control
participatory action research
technology abuse
surveillance
feminism
solidarity
domestic violence
cybersecurity
migrant domestic workers
Advisor: Neff, G
Webb, H
Wright, J
The privilege against self-incrimination in England and Canada

Historically, the concept of protection against testimonial self-incrimination was not an inherent part of the English system of justice. Formal oaths and formal acts to be performed by the defendant were a part of both civil and ecclesiastical trials. The only procedural protection that existed was the requirement that there be "due presentment", i.e., there had to be a specific charge and the solemn accusation before the defendant was required to make any response. When the Church, and subsequently the Star Chamber, adopted an inquisitional procedure, due presentment was by-passed, and there was a great outcry by dissenters. Gradually, the inquisitorial procedure became the focal point of opposition to church and state, and the phrase nemo tenetur setpsum prodere, which formed part of a Statement of law relating to due presentment, was snatched from its context and used as a slogan of the revolution. Common law courts supported the development of the privilege because it provided a means of controlling the jurisdiction of their rivals - the ecclesiastical courts. The fight against the tyranny of kings and bishops was successful, and the privilege became a fundamental rule of English trial procedure.
Canada inherited the privilege against self-incrimination from England, but in 1893 the right of a witness not to answer incriminating questions was abolished and replaced by a rule requiring an answer to be given while affording immunity against its use in subsequent proceedings. A comparison of the privilege in the two countries reveals that while the scope of the privilege is essentially the same, its actual operation is very different. Surveys conducted in conjunction with this research showed that the percentage of accused persons choosing not to enter the witness box is substantially higher in Canada than in England. Likewise, the Canadian immunity provision is used much more frequently by witnesses in Canada than is the common law privilege by witnesses in England. The reasons for and the implications of this difference are examined.
Continued in thesis ...

Keywords: privilege
self-incrimination
incrimination
Canada
England