VictorJuiz/thesis huggingface dataset:
Completeness of the ZW and ZX calculi
Keywords: String diagrams
ZX calculus
Applied category theory
Quantum computing
ZW calculus

This thesis looks at two quantum motivated graphical calculi, the ZW calculus and ZX calculus. These two calculi are intended to perform qubit calculations using string diagrams. Both calculi are universal in the sense that they are able to represent all qubit maps, but they lack the completeness which means that they don't allow all qubit computation. The main goal of the thesis is to address the completeness issue.
The ZW calculus was completed by Hadzihasanovic in his DPhil thesis. We build on his work to do a completion for a fragment of the ZW calculus which describes operations in the fermionic quantum circuits. In the process, we discovered an important family of maps, the even and odd projectors. The even projectors is particularly important for the completion process. Next, we further restrict the calculus to only "even" maps and complete this fragment too. The odd projectors are important for this completion process. We give an interesting story for the even fragment ZW calculus: it describes a world without "real" particles, and the fermionic particles are manifestation of the curvature of spacetime and self 'fermionic' intersection and interaction of spacetime.
The ZX calculus was not complete and we solve this issue in this thesis. The technique used is a refinement of the one used in the paper on 'A Complete Axiomatisation of the ZX-Calculus for Clifford+T Quantum Mechanics' by Jeandel, Perdrix, and Vilmart. The basic idea of the technique is to translate the ZX calculus to the ZW calculus to analyse the problem, then translate it back. We also obtained many interesting generalising results which includes the completeness for the Clifford+T fragment and any fragments containing the Clifford+T fragment.
Finally, we end off with some interesting possible continuation of the thesis. Many of them are low hanging fruits. One of them is the extension of the calculi to represent qudits maps. The other is to generalise the ZW calculus to take semi-ring parameters which may be suited for other areas of computer science.
Staging language in Bermuda: phonology and parodic performance of Bermudian English
Keywords: Racialisation
Language mocking
Dialect parody
Bermuda

This thesis examines the link between social conditions and linguistic practice in Bermuda, a British Overseas Territory in the North Atlantic Ocean. Bermuda is an under-studied, often misunderstood context, home to a unique dialect of English which is under-represented in the literature on Lesser-Known Varieties (LKVEs). It is also an unusual, not-quite-post-colonial, ‘offshore’ setting with an unusual immigration pattern to match, which has led to intense debates about the meaning of national identity and ‘authentic’ Bermudian-ness. These debates are, inevitably, related to and reflected in language.
This thesis argues that Black Bermudian English (BBerE) is a sub-variety of BerE arising from a history of enslavement, segregation and socioeconomic inequality, and goes on to show that BBerE is both mocked and simplified in parodic dialect performances, both written and spoken, common among white Bermudian men. The first part of the thesis gives a phonological overview of BBerE, and introduces Bermuda as a sociolinguistic setting, providing a foundation for further analyses of the variety. The second part focuses on various forms of dialect performance among a white male community of practice well-known for theatrical stylisations of BerE.
Qualitative and quantitative analyses of performances which occurred during sociolinguistic interviews find them to be a form of racialised mock language. Contextual analysis shows that they construct a caricature with socially undesirable tastes, skills, and habits, and link these qualities to salient features of BBerE. Sociophonetic analysis compares the pronunciations of phonological variables among black and white speakers, and finds that white speakers’ performances target black variants missing from their own repertoire, while failing to produce the same complex patterning found in the black group.
The speakers interviewed for this thesis overtly express the view that their performances represent legitimate self-parody, based on the idea that all Bermudians are immigrants from somewhere or another; ‘there’s no such thing as a native Bermudian.’ I argue, however, that the performances themselves reveal contradictions in this ideology. A ‘colourblind’ political stance is invoked to justify the appropriation of a black variety which the performers do not themselves speak, and which they deploy in ways that reproduce racist stereotypes; at the same time this appropriation is motivated by an essentialist idea of black Bermudian speakers as being ‘authentic’ in a way white speakers are not. The thesis introduces a wealthy island context to the literature on racialised dialect parody, prompting further investigation into privileged peripheries like Bermuda and advocating a nuanced and particularistic approach to the difficult sociolinguistic problem of authenticity.
Minimum data sets in women’s health: Opportunities and challenges explored within the context of developing a core outcome set for pre-eclampsia
Keywords: routinely collected data
randomised controlled trials
minimum data sets
qualitative methods
consensus development study
clinical practice guidelines
systematic review
observational studies

Future pre-eclampsia research should ultimately improve patient care. For this to be possible, randomised trials must select, collect, and report outcomes that genuinely reflect the perspectives of key stakeholders, including healthcare professionals, researchers, and women with pre-eclampsia.
The objective of this study was to develop a core outcome set for pre-eclampsia, along with standardised definitions, to ensure outcomes and outcome measures are consistently selected, collected, and reported across future primary research, secondary research, and clinical practice guidelines.
A long list of 116 potential core outcomes was developed by undertaking a systematic review of 79 published pre-eclampsia trials and thematic analysis of 30 in-depth interviews of women with lived experience of pre-eclampsia.
The long list of potential core outcomes was entered into a modified Delphi method. Four hundred and thirty-two participants, including 281 healthcare professionals, 41 researchers, and 110 patients, representing 31 high-income countries and 25 low- and middle-income countries participated in a three-round Delphi survey. One hundred and fifty-nine participants (37%) withdrew. Forty-seven consensus outcomes were identified and entered into a modified nominal group technique. Eleven healthcare professionals, two researchers, and three women with lived experience of pre-eclampsia prioritised 14 maternal, four fetal, and four neonatal core outcomes.
A long list of 86 potential definitions were identified by reviewing four formal definition development initiatives, eight international and national guidelines, 11 Cochrane systematic reviews, and 79 pre-eclampsia trials. During a consensus development conference involving ten healthcare professionals and three researchers, consensus definitions were successfully developed for all core outcomes.
Embedding the core outcome set within future pre-eclampsia research could make a profound contribution to advancing the usefulness of research to inform clinical practice, enhance patient care, and improve maternal and offspring outcomes.
Functional diversity of vascular macrophages in atherosclerosis
Keywords: Macrophages
Atherosclerosis

Atherosclerosis is a multifactorial chronic inflammatory disease of the artery. Diverse macrophage subsets in the atherosclerotic artery contribute to the pathogenesis of the disease. The dendritic cell immunoreceptor (DCIR) 1 is a C-type lectin receptor that inhibits immune responses in myeloid cells. DCIR1 plays both protective and detrimental roles in autoimmune diseases and pathogen-induced infections, respectively. However, to date, the role of DCIR1 in macrophage biology and atherosclerosis remains unknown.
In this thesis, I identified six macrophage subsets by single cell technologies in the murine atherosclerotic aorta. These consist of three “resident” and three “recruited” subsets, which include two novel subpopulations (CD209b+ resident and CCR2+ recruited macrophages). DCIR1 is preferentially expressed by resident vascular macrophages and maintains the balance between resident and recruited macrophage subsets. A novel mouse strain LysMCre Dcir1-DTRflox enables ablation of vascular resident macrophages, together with the majority of tissue macrophages. DCIR1-mediated macrophage ablation opens the niche to Ly6C+ monocytes which can re-acquire DCIR1. This indicates that DCIR1 expression defines tissue resident macrophages.
A comparative study using apolipoprotein E (ApoE)-/- and ApoE-/- Dcir1-/- mice showed that DCIR1 protects against atherosclerosis by maintaining the resident vascular macrophage niche in the aorta. The loss of DCIR1 alters the myeloid cell dynamics in the atherosclerotic aorta, promoting the recruitment of monocytes and macrophages and exacerbating disease evolution.
In conclusion, DCIR1 is a potent regulator of myeloid homeostasis which acts to sustain the resident macrophage niche in the majority of organs. In atherosclerosis, DCIR1 alleviates the disease progression by sustaining the survival of two vascular resident macrophage subsets and limiting monocyte influx to the artery.
Eighteenth century women and the domestic mock heroic
Keywords: British literature
eighteenth century
Great Britain
mock-heroic
domesticity

This thesis examines women’s mock-heroic verse on domesticity, focusing on four female poets of the eighteenth century. Despite critical work on women’s poetry, on the mock-heroic, and on the rise of a cult of domesticity during the period, there has been little sustained criticism of women’s verse about domesticity, and even less about women’s use of mock-heroics. This thesis closes a gap in the work of the past few decades by adding the work of women poets to the discussion of domesticity and mock-heroic verse. The mock-heroic has been identified as ‘the exemplary mode of the eighteenth century’ and ‘the dominant idiom of the age’: a form which late seventeenth and early eighteenth century poets developed to criticise the status quo. The fact that female poets wrote mock-heroic poems and sections of poems in the mock-heroic mode, as well as the range of poems by women which may be considered mock-heroic, demonstrates that women’s use of what might be called the domestic mock-heroic merits more and different critical attention than it has received until now. This dissertation traces the use of mock-heroic poetry by four different female poets of the eighteenth century: Mary Leapor, Mary Jones, Elizabeth Moody, and Anna Letitia Barbauld. It demonstrates that the mock-heroic poems written by women differed significantly from those written by Scriblerians such as Alexander Pope, Jonathan Swift, and John Gay – both in form and in tone. Further, it argues that mock-heroics by women contributed significantly to the form’s development throughout the century and to the intellectual shifts that occurred throughout the century.
Vapour-deposited hybrid metal-halide perovskite thin films for photovoltaic applications
Keywords: Vapor-Deposition
Metal-Halide Perovskites
Photocurrent Spectroscopy
Low temperature

Hybrid metal-halide perovskite semiconductors have recently shown to be excellent photoabsorbers for photovoltaic devices. There are a variety of techniques that can be used to fabricate hybrid metal-halide thin films, from facile low temperature solution processing methods to vapour deposition methods. Physical vapour deposition, in particular thermal evaporation, is one such technique, which is easily up-scalable and widely used in industry. Additionally, vapour deposition is a solvent-free technique that yields smooth, uniform and pin-hole free thin films.
This thesis reports an investigation of hybrid metal-halide perovskite, CH3NH3PbI3 (MAPbI3) thin films, and their subsequent implementation in photovoltaic devices. The initial investigation follows the formation dynamics of the MAPbI3 thin films from sequentially depositing the precursors, PbI2 and CH3NH3I (MAI), whilst keeping the substrates at 273 K. Upon heating the substrates to room temperature, the MAI diffused into the PbI2. The diffusion is tracked using Fourier transform infrared spectroscopy (FTIR) and x-ray crystal diffraction analysis. The results show that exposing the films to moist air facilitates the diffusion and aids in creating a crystalline perovskite thin film.
Dual-source vapour deposition is a technique whereupon both the precursors are evaporated at the same time, yielding a perovskite thin film immediately. An investigation on how different substrates influence the perovskite thin film, was carried out. It is found that perovskite growth on TiO2 induces regions of amorphous perovskite at the interface. The presence of amorphous perovskite explains why photovoltaic devices which have a TiO2/MAPbI3 interface show current-voltage hysteresis. However, incorporating a layer of continuous fullerene thin film on the substrate leads to the formation of crystalline perovskite at the interface, and the corresponding photovoltaic devices show no hysteresis.
MAPbI3 photovoltaic devices were carefully investigated at low-temperatures (15 K – 350 K) using Fourier transform photocurrent spectroscopy (FTPS). The photocurrent spectra of MAPbI3 devices showed that the excess PbI2 usually found in MAPbI3 thin films contributes to the photocurrent. Furthermore, a lower limit of the exciton binding energy of 9.1 meV was extracted for MAPbI3 by comparing the low temperature absorption spectra with the photocurrent spectra.
Finally, organic bulk heterojunction photovoltaic devices were investigated. The effect of UV light on the devices for 18 hours was carefully tracked using FTPS. Initially, the results show a decrease in external quantum efficiency (EQE) at high photon energies. A closer look at the EQE spectra reveal a change in the sub-band gap absorption, indicative of a change in the micromorphology of the bulk heterojunction. These findings indicate the need to find non-fullerene acceptors.
Developing and applying modelling and Bayesian inference tools for developmental biology
Keywords: Bayesian statistics
Approximate Bayesian computation
Model comparison
RNA localization

Developmental biology allows us to answer crucial questions about how patterned, polarized cells can organize robustly and repeatably to form living tissues and organisms. Quantitative imaging data is now available that can provide deep insights into developmental processes, but to make best use of these data, we need mathematical and computational models. Linking complex mechanistic models to quantitative experimental data is challenging, but Bayesian inference provides a principled framework for this. Together, mechanistic models can guide hypothesis-driven experiments, while quantitative experimental data can inform modelling through a data- driven framework for inference and testable predictions. However, challenges remain in developing methodological tools to relate mechanistic models to data effectively. We address a number of these challenges in this thesis, and demonstrate the use of such tools in an integrative framework to address hypotheses about the robustness and points of control governing mRNA localization during development. We begin by studying the bottlenecks controlling the regulation of mRNA transport, using a fine-grained stochastic model of transport within a single cell and relate this model to experimental data. We then study this stochastic model in a more general setting and ask how experimental design, such as the sampling frequency of observations via imaging, affects parameter estimation. Summary statistics are frequently used to simplify inference for problems with high-dimensional data. It is not clear how to select and combine summary statistics for approximate Bayesian computation, although much previous work has been done in this area. We address this problem with an adaptive algorithm that aims to maximize the distance between prior and approximate posterior distributions. Finally, we return to our study of mRNA localization by developing a coarse-grained model to address questions about how robustness of mRNA localization is regulated during development. Using a simple differential equation model, we make testable predictions, which demonstrate the surprising robustness of mRNA localization, and subsequently reveal crowding as a mechanism for regulation of this process. Together, the contributions of this work are towards developing modelling and inference tools to enable quantitative hypothesis-driven study of developmental and cell biology.
Programming patchy particles to form complex ordered structures
Keywords: Soft matter
Cholesteric phases
Patchy particles
Self-assembly
Dodecagonal
Quasicrystals
Helical nanotubes
Monte Carlo

This thesis explores by numerical simulations the rational use of patchy particles to control material properties, by designing particles to either assemble into or apply internal stress to a target structure. Increasingly complex and fine-tuned patchy-particle assemblies are being reported, which may have a wide range of interesting properties and thus immense value for meso-scale materials, devices, and technologies. Understanding the behaviour of patchy-particle ensembles is also useful for understanding natural systems, such as viruses and condensed matter.
I introduce a systematic, rational design scheme for a set of patchy particles to form a unique periodic structure. Torsional restrictions encoded in my patches assist assembly, by controlling second-nearest neighbour bonding. As a proof-of-concept, I demonstrated the robust assembly of five complex, extended, three-dimensional targets. In contrast, previous structures assembled from patchy particles are mostly simple, two-dimensional, and/or finite. I also considered simplified versions of the successful designs (e.g. fewer patches, no torsional interactions), finding them sufficient in some cases but not others.
I further extend the structural complexity by assembling three-dimensional dodecagonal quasicrystals, building on earlier two-dimensional work which was recently realised via DNA origami. This is the first demonstration of the self-assembly of any three-dimensional quasicrystal from patchy particles. I use two systems: unary, with wide, non-selective patches; and ternary, with narrower, selective patches. Assembly is more complicated than in two dimensions (e.g. due to de-mixing), but robust nonetheless. I characterised the structures by their diffraction patterns. I unexpectedly observed screw dislocations in the unary system (the ternary system's narrower patches disfavour defects), and in an approximant.
Finally, I deliberately introduce internal stress into a helical, tube-like structure via imperfectly aligned patches. Recently, a new mechanism of cholesteric ordering was identified (in DNA origami filaments) - solenoidal shape deformations due to mechanical stress. However, the results for my tubes were inconclusive, with no clear trend in solenoidal shape deformations being yet apparent. This was at least partially due to the tubes' stiffness, which reduced the shape fluctuations, but may also reflect the complex network of axial and lateral interactions controlling the tubes' mechanics.
Generalised networks for protein interaction analysis
Keywords: Systems Biology
Network Science
Protein-Protein Interaction
Machine Learning

Protein interaction networks (PINs) are mathematical representations of interactions between proteins within organisms. Studying their properties can give insights into biological functions and the importance of proteins, and it can therefore aid in drug- discovery. Graphs are the most common mathematical object used to represent PINs. In this thesis, we investigate generalised mathematical representations of PINs. In particular, we examine multilayer networks (MLNs) and node-weighted networks. These mathematical objects allow the construction of temporal PINs and tissue-specific PINs by combining gene-expression data with PINs. We introduce promiscuity as an information-theoretical measure of a node’s distribution of neighbours across different layers in MLNs. We examine promiscuity in synthetic networks and tissue-specific PINs and find that the vast majority of proteins are not cell-type specific. Integrating temporal gene-expression data with PINs allows us to create temporal PINs in the form of MLNs. We investigate an eigenvector-based temporal centrality in a temporal PIN of yeast during the cell cycle. We thereby examine the change of proteins’ importance over time, which reflects their activity during the cell cycle. We then discuss the detection of community structure in node-weighted networks. For synthetic networks, we show that considering node weights can alter detected community structure. We combine a human PIN with gene-expression data to construct tissue-specific PINs and investigate their community structure. Comparing the detected communities with gene-ontology information, we find some tissue-specific functions of these PINs. Overall, the case studies in this thesis suggest that MLN and node-weighted networks are suitable for the integration of protein-interaction data with other biological data sets.
Cross-linguistic transfer of phonological awareness in Chinese children receiving English instruction: an intervention study
Keywords: Phonological training
Phonological Awareness
Cross-Language Transfer
Bilingual
Cantonese-English
Cross-Linguistic Transfer
Intervention

The aim of the research is to investigate whether children transfer phonological awareness between languages. There is theoretical and practical significance to study the transfer of phonological awareness across languages. We can gain a better insight into how bilingual children develop phonological awareness in both languages, and how children’s phonological awareness support learning to read in different orthographies. In practice, the transfer enables bilingual children to develop phonological awareness in their first language and transfer to their second language. The learning of second language can be made easier by transferring the prior phonological knowledge across languages. In Study 1, phonological measures were developed to assess the phonological awareness of English and Cantonese in parallel. The measures were rhyme oddity, initial phoneme deletion, and final phoneme deletion. The measures were evaluated, and the results showed that the English version and the Cantonese version of each measure were comparable to each other. In Study 2, phonological awareness was hypothesized as a language-general ability across languages. It was predicted that training English phonological awareness could enhance Cantonese phonological awareness and vice versa. One hundred and sixty-two Hong Kong children at age five were randomly assigned to English phonological training, Cantonese phonological training, or an active control of print concepts. The children were tested on English and Cantonese phonological awareness before and after the training by the three phonological awareness measures developed in Study 1. Results revealed that the English training group significantly outperformed the print concepts control group in all the Cantonese measures, whereas the Cantonese training group significantly outperformed the control group in all the English measures. The results provided strong evidence that there was a bidirectional transfer of phonological awareness between English and Cantonese, suggesting that phonological awareness is a language-general ability that can transfer across languages. Practical and theoretical implications of the findings of both studies were discussed.