VictorJuiz/thesis huggingface dataset:
Radical chemistry for selective modification of native residues in proteins

The chemical modification of proteins has provided a toolbox enabling many experiments in chemical biology. However, new strategies are required to be able to specifically target (hetero)aromatic residues. Fluorine atoms installed in proteins can serve as useful tags, but methods for efficient and selective chemical fluorination are limited. This thesis has explored the modification of native residues in proteins with fluoroalkyl radicals to address the shortage in current methodologies. The study began with the investigation of trifluoromethylation, using biocompatible oxidative generation of CF3 radicals from a sulfinate precursor, and resulted in a robust protocol for selective modification of tryptophan residues. Proteins modified with this minimally perturbing tag could be readily studied by protein observed 19F NMR. To evaluate possibility of 18F-trifluoromethylation, the automated radiosynthesis of the radical precursor was achieved, but unfortunately, the protein radiolabelling proceeded with a limited efficiency. On the other hand, the study of protein difluoroethylation, using the same radical generation system, revealed an unexpected N-modification of proteins, for which the mechanism was proposed (oxidative hydrolysis of fluoroalkyl sulfinates). To reduce this side reactivity, an improved fluoroalkylation protocol was developed, based on the photoredox activation of heteroaryl sulfones as radical precursors. The platform was used to study reactivity and selectivity trends of various fluoroalkyl radicals, which resulted in the detailed investigation of difluoromethylation. The preference for the formation of unstable difluoromethyl tryptophan products was used for the development of selective C-formylation of proteins, relying on a key step of the denaturative hydrolysis of the CF2H group. As such, a new method was established for the installation of a masked aldehyde, also serving as a minimal size fluorescent probe. Overall, the studies of radical fluoroalkylation of proteins yielded useful methods for modification of typically solvent inaccessible residues (specifically tryptophan), under-targeted in protein chemistry, with applications in protein observed NMR and bioconjugation.

Keywords: radical chemistry
fluoroalkylation
trifluoromethylation
protein modification
proteins
Advisor: Gouverneur, V
Davis, B
Essays in household finance

This thesis contains three essays on household finance focusing on household consumption and savings decisions. The first paper studies household demand for flexibility in debt repayment. Based on evidence from a natural experiment, I find that few households apply for flexibility in debt repayment, although all households weakly prefer flexibility in a standard consumption- savings model. The paper studies how self-control problems and a desire for commitment, as well as inattention and inertia can explain observed household behavior. The second paper untangles reasons for the credit card debt puzzle describing the co-holding of high-cost debt and low-yield assets. I test existing theories for co-holding and provide evidence on the contribution to co-holding of intra-household financial pooling and of anchoring to minimum credit card payments. The final paper studies household heterogeneity in insuring against cohort-level earnings shocks using: (i) investment income flows; (ii) the tax-and-transfer-system; and (iii) credit markets. The insurance mechanisms vary by household socio-economic characteristics captured by housing tenure.

Advisor: Ferrero, A
Cryogenic, near-field quantum logic chips with passive field nulling on 43Ca+

This work describes the design and implementation of a new apparatus to achieve quantum information processing in trapped ions using microwave methods. The apparatus involves many design improvements over a previous quantum processing experiment which achieved the highest single-qubit gate fidelity, longest coherence time, and highest microwave based two-qubit fidelity. The goal of this new experiment is a two-qubit gate speed and a fidelity improvement of a factor of 10, making microwave based gates much more feasible as quantum processors. To this end, a novel clock qubit within 43Ca+ is chosen, and the ion height is nearly halved. An anticipated heating rate increase is counteracted by the use of cryogenics. A novel ion chip design is implemented via wafer-scale fabrication and subsequently attached using a novel eutectic bonding technique. The implementation required many design and fabrication problems to be solved; these are described. The vacuum system reaches < 10−11 mbar even at room temperature, lowering experimental difficulty and allowing for performance comparisons at a wide temperature range. A new experiment control system, ARTIQ, and corresponding Sinara hardware is used for control. Experimental results achieved so far include a study of contributing factors to the ion loading rate, and a comparison between the designed and measured microwave fields. All results achieved to date are compatible with the main speed and fidelity goal, which should be achieved in the near future.

Keywords: Microwave gates
physics
Quantum computing
Lasers
Ion trap fabrication
Quantum Information
Cryogenic
Ultra high vacuum
Ion trapping
Advisor: Steane, A
Holistic, instance-level scene parsing with deep neural networks

Humans have long fantasised about the notion of a machine that sees and interprets a scene in ways that simulate the human visual system. As effortless as it appears to us, however, making sense of a scene is highly challenging for computers, due to the unbounded complexity and unlimited variations of a real-world scene. This thesis focuses on solving instance-aware pixel-level scene understanding with deep neural networks, which have potential applications in autonomous navigation, security systems, object counting, medical image analysis, amongst many others.
This thesis first proposes an instance-level human parsing network, which is capable of producing category-, instance-, and part-level segmentation of human in a single forward pass. The proposed network is trained end-to-end given detections, and exploits a differentiable conditional random field (CRF) defined over a dynamic number of part instances for every image. It is the first work to perform human parsing at an instance level and can be trivially adapted to parse other objects. At the time of publication, it achieves state-of-the-art performance on public leaderboards.
Prompted by the large amount of labour and cost required for annotating a pixel-level dataset, this thesis then seeks to reduce the reliance of instance-level scene parsing methods on fully labelled examples, by proposing a weakly-supervised training strategy that makes use of image-level tags and bounding boxes as supervision. Using the proposed weak supervision scheme leads to massive reductions in required annotation time per image and attains a high percentage of the performance achieved by fully supervised oracles. This thesis also presents the first weakly-supervised panoptic segmentation model.
Finally, realising that a CRF-based instance segmentation pipeline has several limitations in terms of optimisation and capacity, this thesis presents a new panoptic segmentation pipeline which exploits a fully connected -- and yet lightweight -- instance affinity term. Unlike the prior art, this approach can directly supervise panoptic segmentation outputs and train end-to-end, thanks to a differentiable mechanism for propagating panoptic logits according to predicted instance affinities. At the time of publication, this method also obtains state-of-the-art results on public leaderboards.

Keywords: conditional random fields
instance segmentation
probabilistic graphical models
scene understanding
computer vision
object parsing
semantic segmentation
deep learning
scene parsing
deep neural networks
semi supervised learning
panoptic segmentation
weakly supervised learning
Advisor: Torr, P
An institutional perspective on entrepreneurial ecosystems: variation, evolution, agency in and across organisational fields

Entrepreneurial ecosystems (EEs), understood as a type of organisational environment conducive to fostering high-growth and technology oriented startups, are currently deemed important for economic and employment growth. However, while the flagship case of Silicon Valley is widely researched and invoked, our knowledge of variation in how EEs develop is limited, and insufficiently theorised. In response, this thesis adopts an institutional perspective, conceptualising EEs as organisational fields, and addressing how the interplay between agency and structure result in different developmental trajectories of location-based EEs. The thesis consists of three empirical papers that examine several cases of EEs in Japan and India focused on Information and Communication Technology. The in-depth inductive studies are anchored in interview and participant observation data generated during multiple fieldwork visits.
The findings illuminate key novel concepts: 1) a field development mechanism of intra-field cross-generational support (uncovered in an emerging field of Tokyo EE examined in relation to domestic large corporations); 2) a comparative framework of Varieties of Entrepreneurial Ecosystems (derived from an analysis of Tokyo and Bangalore – the biggest EEs in their respective countries); 3) an institutional infrastructure-related element of place cohesion (identified from a comparison of Osaka-Kyoto and Fukuoka – smaller EEs developing within one institutional context where the dominant EE is already present).
Together, the papers show that differences in EE developmental trajectories stem from the interplay of EE stakeholders’ agency to develop a desired EE institutional infrastructure (which is similarly conceptualised across locations), and the underlying elements for such infrastructure (which can be very time- and location-specific). Particular agency-related mechanisms that are crucial to EE development, depend on the EE relations to other fields. Overall, the thesis contributes to the scholarship on EEs and organisational fields, enhancing more contextualised understanding of EEs, and suggesting how to better study fields in a comparative and interconnected perspective.

Keywords: Organisational fields
Japan
Entrepreneurial ecosystems
Comparative research
Startup entrepreneurship
India
Institutional work
Institutional infrastructure
Organisation theory
Advisor: Whittaker, D
Sako, M
Plasticity and maintenance of the virulence plasmid in Shigella flexneri and Shigella sonnei

Shigella is the major cause of human bacillary dysentery worldwide. Shigella flexneri and Shigella sonnei account for >90% of shigellosis globally, and evolved from commensal Escherichia coli following acquisition of a large plasmid, pINV. This plasmid is essential for virulence as it harbours genes encoding a Type three secretion system (T3SS) on a 32 kb pathogenicity island (T3SS PAI). pINV is present in the bacterium in low copy number, and possesses multiple partitioning systems and toxin-antitoxin (TA) systems whose role in plasmid maintenance is unclear. Furthermore, during growth in the laboratory both S. flexneri and S. sonnei spontaneously lose T3SS expression, becoming avirulent.
In this work I evaluated how insertion sequences (IS), TA systems and partitioning systems influence the maintenance of virulence in S. flexneri and S. sonnei. I demonstrate that in S. flexneri avirulence mainly results from discrete deletions involving the T3SS PAI mediated by insertion sequences (IS). Repositioning of vapBC, which encodes a TA system essential for pINV maintenance, near the T3SS PAI prevents loss of the PAI, indicating that VapBC maintains the entire plasmid as well as local sequences. IS also mediate reversible integration of pINV into the chromosome, which results in down-regulation of T3SS expression, and reversible avirulence. In contrast, S. sonnei becomes avirulent by mainly losing pINV, which I found is caused by the absence of the two TA systems present in S. flexneri, CcdAB and GmvAT, as well as amino acid substitutions in VapBC. The contribution of the partitioning system ParAB on pINV maintenance is influenced by bacterial growth conditions and the presence of TA systems. However, the function of the second partitioning system StbAB is unknown. The absence of this system in S. sonnei pINV suggests that the two partitioning systems may be redundant.
Finally, I have designed and evaluated CRISPR-Cas to induce the loss of virulence or reduced viability in Shigella by targeting T3SS genes and vapBC, thus, validating a novel approach to treat shigellosis.

Keywords: Insertion sequences
Virulence plasmid
Toxin-antitoxin systems
Partitioning systems
Shigella flexneri
Shigella sonnei
Advisor: Tang, C
A ketone ester for diabetes mellitus

Various studies have reported that type 2 diabetes mellitus (T2DM) may be reversed by following a ketogenic diet, although it is not clear if this is due to carbohydrate restriction or a consequence of elevating the concentration of ketone bodies in the blood (ketosis). A recently developed ketone ester (KE) drink, which elevates human circulating D-βhydroxybutyrate (βHB) levels by ~3 mM within minutes, allows to isolate the effects of ketosis and carbohydrate restriction.
The aims of the work described in this thesis were to determine; if sustained exogenous ketosis is safe and well tolerated in healthy adults, L-Alanine’s contribution to the glucose-lowering effect of ketone bodies, the impact of acute ketosis on myocardial energetics and, if sustained ketosis is safe and tolerated in patients living with T2DM. In the first study (Chapter 3), twenty-four healthy adults (1:1 sex ratio, between 18 to 70 years old) drank 25 ml of the KE three times a day for 28 days. Anthropomorphic measurements, plus blood and urine biochemistry remained unaltered. All adverse effects of the KE were mild according to the participants.
In the experiments presented in Chapter 4, ten healthy adults fasted for 24 hours prior to the ingestion of 25 ml of the KE with or without 2gr of L-Alanine. Raising L-Alanine blood concentration attenuated the KE glucose-lowering effect by almost 50% (p<0.01). No significant differences in blood βHB, Free Fatty Acids (FFA), lactate and C-peptide were found when adding L-Alanine to the KE drink.
The work described in Chapter 5, involved twelve healthy adults who fasted for 24 hours and afterwards, drank 25 ml of the KE. Myocardial Phosphocreatine/Adenosine Triphosphate ratio (PCr/ATP) was measured before and 30 minutes after the KE drink using 31P Magnetic Resonance Spectroscopy at 7 Teslas. No significant differences in PCr/ATP were detected between measurements.
Finally, in Chapter 6, twenty-one type 2 diabetes patients, drank 25 ml of the KE three times a day for 28 days. Glycated haemoglobin (HbA1c) dropped from 7.7% to 7.2% and fructosamine concentrations from 335 to 290 µM. Overall time in the euglycemic range was assessed using continuous glucose monitors and improved by 2.3% (p < 0.01) while drinking the KE. Once again, anthropomorphic measurements, blood and urine biochemistry remained unaltered. All adverse effects of the KE were mild according to the participants and no events of ketoacidosis were documented.
In summary, the work described in this thesis has demonstrated; a close interaction between blood L-Alanine, ketone bodies and glucose concentrations and that a single KE drink has no effect on myocardial PCr/ATP in healthy participants. This work is the first to demonstrate, in the general population and in patients with T2DM, that sustained exogenous ketosis, is safe, well-tolerated, and may improve glucose control in T2DM.

Keywords: ketosis
ester
Beta-hydroxybutyrate
diabetes mellitus
ketone bodies
Advisor: Clarke, K
Evans, R
Using positioning theory to understand marginalized students’ identities work and their learning experiences in English language arts classrooms

There are various dimensions of diversity that affect the learning experience of students. These might include aspects such as social background, ethnic and cultural origin, languages spoken, perceived learning ability, physical abilities, gender, sexuality, religion, and race. These work in dynamic ways and are influenced by both spatial and temporal social factors akin to general social transformations like globalization, migration, changing labour markets, and so forth. Whereas a lot of the social science literature in education has viewed these aspects of student identity and diversity as separate from each other, this qualitative, multi-modal study examines how these factors work intersectionally. As 16, 17, and 18-year-olds answer the question of who they are and explore the formative role that the learning environment—such as conversations they engage in and the texts they read—plays in identities development, this study uses a Discourse Analysis approach drawing upon Positioning Theory and Critical Incident Technique to analyse the discursive events around different social contexts across four Texas upper- secondary English Language Arts (ELA) classrooms. By analysing students’ dialogic interactions with their peers and their teacher, an interpretation of the agentic moves students make develops. The way in which these agentic actions affect learning experiences and the marginalizing forces that strengthen or diminish a student’s learning outcome also emerge. In thinking about how to treat students’ voices honourably, while reflexively focusing on my own positionality in relation to ethics, this study makes a positive contribution to both culturally responsive teaching and the field of education research.

Keywords: English language arts classrooms
identity
marginalized students
culturally responsive teaching
marginalized
identity formation
English
identities
marginalised
Positioning Theory
discourse analysis
Advisor: Elliott, V
Ingram, J
Todd, J
Copper-catalysed autocatalytic reactions

The work contained within this thesis describes the development and study of self-reproducing systems, created from simple chemical building blocks, that exhibit emergent, life-like properties. Several different autocatalytic systems that are driven by copper-catalysed azide-alkyne cycloaddition (CuAAC) reactions are reported.
Chapter 1 introduces the fundamental concepts relevant to the bottom-up construction of minimal living systems and highlights relevant synthetic advances in the field of systems chemistry. The following two chapters describe an autocatalytic system where surfactant formation from phase-separated components is linked to a CuAAC reaction.
In Chapter 2, the influence of product seed on the rate of the reaction and the impact of surfactant tail length on the kinetics of the reaction is investigated. Chapter 3 expands upon this system by exploiting the link between the secondary catalyst and the autocatalytic cycle to drive new reaction outcomes. A mechanistic model is formulated that rationalises the kinetic profiles based on the phase behaviour of the coupling partners and the catalyst.
Chapter 4 presents an out-of-equilibrium self-reproducing protocell system that models biological cells more faithfully. Selection and inhibition processes are observed between competing replicators and orthogonal downstream chemical reactivity is incorporated.
Chapter 5 describes the ongoing development of an asymmetric autocatalytic CuAAC reaction through formation of enantioenriched polytriazole ligands via dynamic kinetic resolution of allylic azides. An initial finding shows that this new class of chiral ligand induces chirality in asymmetric CuAAC reactions.
Finally, Chapter 6 offers concluding remarks and details future work that may improve upon the reported systems.

Keywords: Autocatalysis
Origin of life
Self-reproduction
Out-of-equilibrium
Protocells
Advisor: Fletcher, S
Studies of breakdown and pre-breakdown phenomena in high-gradient accelerating structures

Vacuum breakdown is a complex process and an important limiting factor of the performance of normal-conducting high-gradient particle accelerators, and can result in loss of luminosity in particle collider applications, as well as damage to accelerating structures. The work presented here was done in the context of the Compact Linear Collider (CLIC) study, but is also relevant to a variety of applications such as medical linear accelerators or high-electric-field vacuum electronics. The aspects of vacuum breakdown discussed in this thesis together provide the theoretical basis for important technological parameters for the design of normal-conducting high-gradient devices: the influence of radio-frequency design and material properties on the achievable field, and the mechanism of conditioning. The first part of this thesis discusses the development of an improved quantitative limit which determines the maximum accelerating gradient at which a given structure geometry could operate, with the intention of guiding the design of improved accelerating structures. It models the coupling of radio-frequency power to a breakdown, giving a value for surface electric field when loaded by a nascent breakdown. Calculations were performed on various cases that were tested experimentally, showing excellent consistency and the potential to become a very general model of vacuum breakdowns. The second part presents an experimental study of dislocation dynamics in copper surfaces subject to high electric fields, to better understand the mechanism of the nucleation of breakdowns. This is believed to involve stochastic deformation of microscopic features under high-electric-field stress. Field-emitted current from radio-frequency structures, as well as electrodes subject to a static electric field were precisely measured, revealing small fluctuations in the latter case. The dependence of the rate of events on the surface field and the distribution of time intervals between events was found to match prior theoretical predictions. The rate of fluctuations was also found to decrease with the cumulative number of voltage pulses applied, supporting the idea of work hardening due to stress from pulsed electric fields as a mechanism for conditioning.

Keywords: dislocation
linear accelerator
compact linear collider
CLIC
radiofrequency
fluctuation
dark current
vacuum breakdown
nucleation
RF
field emission
high gradient
Advisor: Burrows, P
Wuensch, W