VictorJuiz/thesis huggingface dataset:
A molecular genetic investigation into the regulation of the chloroplast TOC complex

Chloroplasts are ancient organelles that house photosynthesis in all green plants. Most proteins required for chloroplast function are imported into the organelles from the cytosol via the coordinate action of two translocons – the TOC and TIC complexes. A recent forward genetic screen revealed that the TOC complex is conditionally targeted for degradation via the action of SP1, a chloroplast-resident E3 ubiquitin ligase. SP1 functions within the newly-described CHLORAD pathway – a pathway for the ubiquitination, membrane extraction, and degradation of chloroplast proteins. The CHLORAD pathway is activated by stress and developmental cues, but the mechanistic basis of this regulation is poorly understood. In this thesis, a genetic and functional link between chloroplast protein import, CHLORAD, and the SUMO system is described. Arabidopsis mutants representing most components of the SUMO pathway are shown to suppress the pale phenotype of TOC complex mutant ppi1 with respect to chlorophyll accumulation. This suppression is also linked to increases in the accumulation of TOC proteins and enhanced chloroplast development. Conversely, the overexpression of SUMO1 or SUMO3 accentuates the ppi1 phenotype. Protein/protein interaction studies demonstrate that key components of the SUMO system (the E2 SUMO conjugating enzyme, two E3 SUMO ligases) physically interact with TOC proteins at the chloroplast outer envelope, and SUMOylation assays indicate that TOC proteins are directly SUMOylated. This work is complemented by a forward genetic screen for additional regulators of the TOC complex. In this screen, a pale TOC complex mutant, ppi2-3 is chemically mutagenized and 28 viable suppressor mutants are identified, named, and characterised. Together, these two projects provide new insights into the regulation of chloroplast protein import and, perhaps, the CHLORAD pathway.

Advisor: Jarvis, P
Electrician not electrishion? Implicit and explicit knowledge of word stem and affix morphemes for children’s spelling

This study investigated the extent to which implicit and explicit knowledge of morphology contribute to children’s spelling in English. Children acquire some understanding of morphemes for spelling through their everyday encounters with words, but this could be enhanced to a more explicit level through direct instruction. Intervention studies have reported the advantage of teaching children about morphemes for spelling, but the vast majority of this research has been restricted to affixes, with limited attention to teaching word stems or combining instruction of stems and affixes together. In response, the current study compares a child’s knowledge of morphemes with implicit or explicit instruction of two related morphological spelling rules: the conservation of word stems in derived words and the distinction between the affixes of -ion and -ian.
A sample of 270 children in Years 3 and 4 from three state-supported schools participated. Three experiments were conducted: one examined implicit versus explicit teaching of the morphological rule for stems; a second investigated if explicit teaching of one morphological principle (e.g. word stems) leads to explicit knowledge of another (e.g. affixes); and a third combined instruction of stems and affixes together. A pre-test, immediate post-test, and delayed post-test design was employed for each experiment in which children were randomly assigned to one of two intervention groups or a control condition that did not receive any form of instruction. In the pre- and post-tests, the children’s spelling of stems and affixes in derivatives was assessed. The interventions involved training games in which the children spelled derived words after seeing the stem forms; the explicit groups discussed the connection between the spellings whereas the implicit and control conditions did not.
Analyses of variance revealed that explicit teaching of word stems and affixes led to more significant spelling improvements than implicit or no teaching, and that this effect held at both immediate and delayed post-test. Combining instruction of stems and affixes within the same teaching session was also reported to noticeably aid a child’s spelling accuracy. It was concluded that explicit teaching combined with appropriate spelling games shows a sustained effect on children's spelling. The evidence supports the integration of morphemes into current educational policy and teaching practice.

Keywords: morphemes
explicit teaching
Children
implicit teaching
spelling
Advisor: Nunes, T
Evangelou, M
Illuminating strategies for enhancing photosynthesis

While population growth and resource limitation increasingly clash, there is a growing need for sustainable intensification of agriculture. Improving yields by crop enhancement is a promising solution to this challenge, however, knowledge about which genes to engineer in crop species is lacking. To that end, the genetic regulation of photosynthesis was investigated. Initially, phylogenetics was used to infer a gene regulatory network that regulates C3 photosynthesis in rice. This revealed that, compared to the model plant Arabidopsis thaliana, as much as 81% of this network was unresolved in grasses. Gene expression data were analysed by correlational and machine learning approaches to fill in gaps in this rice network. Combined with the phylogenetic analysis, these approaches enabled the assembly of a grass regulatory network for photosynthesis and facilitated exploration of the regulation of photosynthesis in maize. Through de-etiolation experiments it was found that different wavelengths of light differentially activated chloroplast maturation networks in mesophyll and bundle sheath cells. This provided evidence that subdivision of light signalling networks is a key component of cellular partitioning of C4 photosynthesis in maize. Finally, the results of the gene regulatory network analysis and the de-etiolation experiments in maize were used to devise a strategy to engineer enhanced photosynthesis in C3 plants. This strategy was validated through transgenic experiments in both Arabidopsis and rice plants. Phenotypic analyses showed that photosynthetic rates were enhanced in these plants by 20-40%. Thus, the findings presented here reveal a new strategy by which crop yield enhancement can be brought to light.

Keywords: chloroplast development
genetic engineering
evolution
photosynthesis
plant genetic regulation
Advisor: Kelly, S
An epidemiological study of health, injury, and long term outcomes in baseball players 

Baseball injuries are a persistent and significant problem, with the greatest injury incidence to the elbow and shoulder. Baseball injuries can be prevented through a stepwise process that enables the identification of injury type, injury risk factors, etiology and injury mechanisms which is dependent upon high quality data. However, current injury risk and prediction research does not quantify the complexities related to athletic injuries. Therefore, the complex interaction of multiple risk factors and injury mechanisms are unclear and inhibits clinical examination and prevention. The primary aim of this thesis was to create an injury prediction model for shoulder and elbow injuries in a cohort of professional baseball pitchers. The secondary aims are to describe the musculoskeletal health and wellbeing of current and former baseball players and assess the clinical utility of the primary injury risk model.
I conducted a systematic scoping review of baseball health and wellbeing in 2019. It found that the greatest density of baseball research focused on injury incidence and prevalence. However, there was a paucity of research on the long-term health effect of baseball participation, health and wellbeing across all baseball playing standard, and injury prevention research.
I analyzed data of a survey of current and professional baseball players. Both current and former baseball players reported similar health related quality of life compared to the general population, high flourishing, and high physical activity. Former baseball players reported the greatest persistent joint pain prevalence to the shoulder and elbow, and decreased arm function compared to older total shoulder arthroplasty patients.
I conducted an interrupted time series analysis to assess the effectiveness of injury risk profiling and education on a five-year cohort of professional baseball players. Injury risk profiling and education decreased injury incidence by 33%.
I developed and internally validated an arm injury prediction model on a ten-year cohort of professional baseball pitchers. The prediction model demonstrated good discriminate ability and excellent calibration.
I developed and internally validated a humeral torsion prediction model on the same ten-year cohort of professional baseball pitchers. The prediction model demonstrated small error and excellent calibration.
I analyzed the clinical net benefit and utility of the developed injury prediction model in comparison to current evidence based practice. The prediction model demonstrated improved net benefit and utility compared to current practice standards.
Future research is needed to examine if findings are generalizable to different cohorts and playing standards, and the efficacy of this prediction model in a clinical setting

Keywords: Humeral Torsion
Arm Burden
Net Benefit
Decision Curves
Prediction
Advisor: Filbay, S
Collins, G
Arden, N
Connective tissue changes in patients with rectal prolapse

Rectal prolapse is a common and distressing condition in which the rectum either protrudes externally or telescopes insides itself (intussceception) resulting in evacuatory dysfunction. It has traditionally been viewed as being a disorder of multiparous women who sustain pelvic floor injury during childbirth. However, this explanation fails to account for the occurrence of the condition in nulliparous females, males and children.
This thesis seeks to study the relationship between connective tissue changes and the development of rectal prolapse.
Participants with rectal prolapse were prospectively recruited to the study (n=105) control tissue was taken from individuals undergoing colonic cancer surgery (n=12). Individuals were assessed for their connective tissue status and grouped according to parity and gender. Analyses focussed on presenting demographics and surgical outcomes in patients with respect to connective tissue status, changes in the extracellular matrix in relation to prolapse, systemic change in connective tissue components.
It was found that a proportion of patients have heritable predisposition to altered connective tissue biology in that they had benign joint hypermobility syndrome. These patients typically presented younger and had higher surgical re-intervention rates than those with normal connective tissue status. The extracellular matrix had a number of changes in association with the condition, collagen types 1 and 3 were altered in comparison to control and overall increase in the elastic fibres of the pelvic connective tissues was noted. Alterations in the elastic fibres within the dermis of patients were also identified and suggests that a systemic disorder of connective tissue may account for the development and progression of the condition in some individuals. The pelvic connective tissues themselves were noted to have a number of changes with respect to the disorder, an increase in MMP 1 was noted and this was linked to a reduction in connective tissue supports surrounding the rectum. The growth factor TGF β may play a role in modulating this process and a reduction in the expression of this growth factor was found to be associated with the development of external prolapse. We found that cellularity was increased in response to the process of prolapse in females, but in males this process was attenuated. In addition it was also noted that in some females the cells did not differentiate to the type normally identified in the pelvic connective tissues.
The experimental findings suggest that in some individuals a combination of a systemic connective tissue disorder, altered collagen ratios and an environment favouring tissue degradation may account for the development and progression of rectal prolapse.

Keywords: rectal prolapse
Advisor: Urban, J
Applications of parallel radiofrequency transmission to ultra-high-field magnetic resonance imaging

Increasing the static magnetic field (B0) strength of magnetic resonance imaging (MRI) scanners improves the signal-to-noise ratio (SNR). Higher SNR may be used for more sensitive, faster, and higher resolution imaging.
Despite its potential, the biggest challenges for ultra-high field MRI is inhomogeneity in the radio-frequency field (B1+), which causes spatially varying flip angles when using fixed-frequency pulses, leading to undesirable perturbations in signal and contrast. The most flexible solution to B1+ inhomogeneity at UHF is parallel transmission (pTx). A pTx enabled system consisting of more than one RF transmit channels which may be independently driven.
This thesis seeks to extend the methodology and applications of pTx magnetic resonance imaging (MRI) in the brain at 7 tesla. Specifically, this thesis focuses on two spin labelling techniques: arterial spin labelling (ASL) that measures cerebral perfusion and T2-Relaxation-Under-Spin-Tagging (TRUST) that measures venous oxygenation.
The ASL study demonstrates that labelling efficiency can be improved by the incorporation of pTx static shimming in the labelling pulses, but indicates that the temporal SNR does not yet exceed optimised 3 tesla protocols in the absence of further developments. The TRUST study investigates the use of spatially-selective pTx pulses in a modified TRUST sequence to measure regional oxygen extraction fraction (OEF) in the brain. Results show that localised saturation was achieved by repeatedly exciting (using pTx pulses) and saturating spins outside the region-of-interest.

Keywords: TRUST
PCASL
perfusion
parallel transmission
ultra-high field
arterial spin labelling
Advisor: Jezzard, P
Clarke, W
"Multiplex est modus": elements of accommodation in the early Jesuit missions to India, 1545-1575

My project explores the methodologies of missionaries of the Society of Jesus in southern India between Francis Xavier's arrival in 1542 and the policy reforms under Alessandro Valignano in 1575, investigating the presence of cultural accommodation within the attitudes and decisions of various Jesuits. During the three decades between the Society’s foundation and Valignano’s arrival in India, Jesuits faced a number of issues both internally and externally, suggesting an organization prone to the influences of various individuals and contemporary ecclesiastical and secular politics. I argue that these factors presented limits to the development of more adaptive techniques which characterised cultural accommodation of the late sixteenth and early seventeenth century through Matteo Ricci and Roberto de Nobili, and that analysing these can help illustrate why such a policy did not manifest during earlier decades.
Nevertheless, elements of accommodation appear in the voices of some Jesuits active during this period through their opinions regarding the primary objectives of mission. Although accommodation did not exist in a complete form in this period, I shall show that the basic underpinnings did emerge through the opinions and attitudes of some individuals on multifarious particulars, such as education, language, conversion, and identity. Following an ideological commitment to simultaneous contemplation and action, members of the Society of Jesus were afforded greater flexibility and mobility than their religious contemporaries, labouring across diverse environments throughout South Asia and beyond. Analysing the questions regarding Jesuit organisational procedures and relations with convert communities, non-Christians, the Portuguese state in India, and other clergy, this thesis aims to better illuminate the multiple ways individual Jesuits interpreted their purpose as well as pinpoint instances where elements of accommodation appeared through their interpretations.

Keywords: Portuguese India
global history
early modern history
cultural accommodation
Jesuit missions
conversos
Society of Jesus
Advisor: Strathern, AL
Davidson, NS
Deep ensemble learning-based quality control for automatic segmentation in cardiovascular magnetic resonance imaging

Cardiovascular magnetic resonance (CMR) imaging is a powerful tool for research and clinical applications. To extract useful clinical information from the acquired CMR images, time-consuming and laborious manual delineation of cardiovascular structures is currently required. Despite promising overall performance across medical imaging applications, the current state-of-the-art automated image segmentation methods still fail in some cases, potentially jeopardising the reliability of clinical diagnosis. Thus, it is important to develop not only automation of image segmentation but also quality control of segmentation, to empower efficient and reliable CMR image data analysis.
To address both segmentation and quality control problems, I have developed a novel quality control-driven (QCD) framework in this thesis. Extending upon deep ensemble learning, the framework utilises multiple convolutional neural network-based models to generate segmentation candidates, the agreement of which is exploited via additional regression models to predict segmentation quality measured by Dice similarity coefficient (DSC). The DSC prediction not only provides a quality estimate but also enables a novel approach to select a final, most optimal segmentation on-the-fly from multiple candidates, improving segmentation robustness. Following the DSC prediction, a segmentation quality classification scheme is implemented to alert human operators only when manual intervention is recommended, intended for more efficient allocation of time and labour resources for large-scale image processing pipelines.
Through both quantitative and qualitative evaluation, the QCD framework has demonstrated excellent performance in both segmentation and quality control. More importantly, the framework has been successfully applied across CMR imaging techniques, anatomical structures, and large-scale datasets acquired at different sites, with high adaptability and generalisability. The QCD framework could pave the way towards large-scale automated imaging data analysis pipelines, with both efficiency and reliability, in real-world clinical applications.

Keywords: Image segmentation
UK Biobank
Ensemble learning
Cardiovascular magnetic resonance
Quality control
Medical image analysis
Uncertainty estimation
Deep learning
T1 mapping
Advisor: Piechnik, S
Ferreira, V
Neubauer, S
Unruly technics in the French literary avant-garde: technological writings of the Third Republic and their afterlives in contemporary thought

This thesis traces a particular genealogy of thinking and writing about technics which germinates in French avant-garde writings of the late nineteenth and early twentieth centuries, takes root in the mid-twentieth century in the work of major French philosophers, and continues to bloom in the contemporary ‘nonhuman turn’ in Anglo-American theory that draws inspiration from those philosophers. The place of those early literary figures in this lineage has never before been traced, yet they are crucial to understanding why we think the way we do, and to identifying what our contemporary modes of thought overlook, as we face a moment of rapid technological change. In nine linked chapters, this thesis shows how these writers and thinkers are united by a common concern with technics as a mode of relation to self, other, and world, through which change happens and things come into being. Through close reading of primary material, I explore technics as a source of subject matter and conceptual metaphors, but also probe how ideas and words are modes of technicity through which we shape and reshape the world. I highlight how, in this particular genealogy, it is impossible to separate these modes of unruly technicity out from one another. Tracing the unruly transition from Catholic vocabularies of grace, potentiality, and actuality to the modern and contemporary secular lexicon of agency, virtuality, and affect, I identify an ambitious and original mode of approach to a field of enquiry whose importance is only set to increase.

Keywords: Third Republic
Nonhuman
Avant-garde
Technics
Catholicism
Advisor: Lübecker, N
Modification of the metal lattice in transition metals by light elements: synthesis, characterisations and catalytic applications

Heterogeneous catalysis plays an important role in the pharmaceutical and petrochemical industries. Due to the poor chemical selectivity in many processes, it is essential to design novel catalysts to resolve this problem. Recently, interstitially modifying transition metal NPs with light elements has become a potential strategy for adjusting surface energy and tuning catalytic activity. However, this new class of catalysts remains relatively unexplored due to a lack of adequate characterisation evidence.
Herein, the work presented in this thesis continues the structural characterisation of the Pd-intB/C and Pd-intLi/C, reported from previous work, by using a novel combination of analytical techniques that span from the atomic to the macro level. Initially, these characterisations showed that after B and Li incorporation the Pd lattice maintains a face-centred cubic structure, but tolerates structural distortion. These structural distortions can further result in the local formation of the HCP structure. Additionally, the combination of STEM-EELS and ptychography was attempted to directly observe the presence of B and Li at the atomic level.
Meanwhile, in order to broaden the scope of the light element modified catalyst family, attempts were made to alloy Li into the Pt host metal system. It was found that the unit cell of the Pt contracts after thermal treatment at elevated temperature, indicating the formation of the Pt-subLi nano bimetallic alloy. The combination of XPS and ssNMR confirms the presence of Li in the metal framework, in addition to the SXRD. The STEM-ADF imaging reveals the presence of the Pt7Li. Seemingly, this is the first report of Pt-Li based NPs synthesis to date. This catalyst displays premium 2,5-bis(hydroxymethyl)furan (BHMF) selectivity when catalysing HMF hydrogenation; this is due to the Li blocking specific, undesired reaction pathways. It is anticipated that such an in-depth investigation will help influence the future design and characterisation of novel, light element alloyed systems.

Keywords: characterisation
catalysis modification
catalytic hydrogenation
Heterogeneous catalysis
Advisor: Tsang, E
Nellist, P