VictorJuiz/thesis huggingface dataset:
Catalytic enantioselective methods for challenging polar addition reactions

Chapter 1 serves as an introduction to the fundamental principles of organocatalysis and enantioselective synthesis. Seminal contributions to the evolution of modern superbase catalysis are discussed.
Chapter 2 describes the development of a novel enantioselective direct aldol reaction catalysed by a bifunctional iminophosphorane. The ability of a BIMP catalyst to activate high-pKa aryl methyl ketone pro-nucleophiles is emphasised against the backdrop of traditional Cinchona and thiourea organocatalysis. The broad downstream utility of the β-hydroxy ketone products is demonstrated, along with an efficient scale-up protocol showcasing catalyst recyclability. Finally, mechanistic considerations are discussed based on NMR studies and reaction observations.
Chapter 3 outlines the development of an efficient aza-Michael addition/condensation strategy for the preparation of enantioenriched 2-pyrazolines. A simple one-pot protocol affords useful heterocycles from readily accessible enones. Highly reactive hydrazines are made amenable to enantioselective catalysis by in situ conversion to the corresponding hydrazone, which subsequently engages in an enantio-determining aza-Michael addition. The Cinchona alkaloid-derived catalyst is recyclable, and the large-scale utility of the method was demonstrated with the preparation of over 80 grams of a product in a single reaction.

Keywords: catalysis
enantioselective synthesis
organocatalysis
organic synthesis
Michael addition
Advisor: Dixon, D
Cardiac small heat shock proteins and their roles in maintaining the integrity of the cytoskeletal system

Small heat shock proteins (sHsps) are a family of ubiquitous proteins that defend the first line for proteostasis. They have specific regulatory roles to fulfill their chaperone functions or maintain the physiological structures of tissues through interactions with their native or dysfunctional partners. This thesis will focus on the sHsps and their substrates in the human heart and skeletal muscles, using various biophysical and structural techniques to probe their structures and interactions. Among the sHsps, cardiovascular heat shock protein (cvHsp, HspB7) and HspB8 (Hsp22) perform their primary functions in cardiac tissues and skeletal muscles. Firstly, I find that, unlike the well-studied human sHsps like Hsp27 or αB-crystallin forming large oligomers based on dimeric building blocks, cvHsp is dominantly monomeric at dynamic conditions. I solve the crystal structure of cvHsp to explain that oligomerization and dimerization are much less favored for cvHsp. Then I study the actin-linking protein filamin C (FLNC) and confirm its dimerized domain 24 (d24) is the binding substrates of cvHsp. The monomeric cvHsp binds to the dimerized FLNCd24 and competes to its dimerization. This process can be regulated under stress conditions. Phosphorylation at FLNCd24 T2677 or Y2683 residues at different stress conditions has opposite effects in mediating the FLNC dimerization and interaction with cvHsp, which might be a potential target for mediating cancer development. To study this interaction at the atomic level, I reveal the binding surfaces for the cvHsp-FLNC interaction and obtain the crystal structure of the complex. cvHsp uses its β4 strand to bind FLNCd24 strand C, which is involved in the dimer interface. Some hydrophobic contacts within the interface make this interaction strong and specific. Both T2677 and Y2683 residues show up clearly in the structural analysis. We further research the FLNC clearance system, the chaperone-assisted selective autophagy (CASA) complex, which involves HspB8, BAG3, Hsp70, FLNC, and other components. We have obtained the stable construct of HspB8, and the purification of non-structured BAG3 is still going on. Overall, our studies provide new and deep insight into cardiac sHsps and their roles in maintaining proteostasis.

Advisor: Benesch, J
Acceleration in first-order optimization methods: promenading beyond convexity or smoothness, and applications

Acceleration in optimization is a term that is generally applied to optimization algorithms presenting some common methodology that enjoy convergence rates that improve over other more simple algorithms for the same problem. For example, Nesterov's Accelerated Gradient Descent improves over the gradient descent method for the optimization of smooth and convex functions. In this thesis, we investigate the acceleration phenomenon and its applications for three previously studied research questions in optimization and online learning: geodesically convex accelerated optimization in Riemannian manifolds, approximation of a proportional fair solution under positive linear constraints, also known as the 1-fair packing problem, and regret minimization in a decentralized cooperative stochastic multi-armed bandit problem with no reward collisions. We improve over previously studied approaches by using acceleration as a key element in all of our algorithms: we obtain an accelerated method for some non-convex problems in the first case, we exploit a local decrease condition of our problem in the second case, avoiding the use of poor and non-global smoothness, and in the third problem, we design a solution for which we can effectively apply an accelerated gossip protocol to spread and use information.
In particular, we provide an extensive overview of acceleration techniques that provide context for ours proofs. In Riemannian optimization, we design the first global accelerated algorithm for the optimization of smooth functions that are geodesically convex or geodesically strongly convex and that are defined in manifolds of constant sectional curvature. We reduce these problems to a Euclidean non-convex problem and design a global accelerated method, obtaining a solution with the same rates of Accelerated Gradient Descent in the Euclidean space, up to logarithmic factors and constants depending on the initial distance to an optimum and on the curvature. We also provide some reductions. Regarding our fairness problem, we present a deterministic, accelerated, distributed and width-independent algorithm for the 1-fair packing problem. We obtain a quadratic improvement in the number of iterations and remove polylog(width) factors with respect to the previous best solution. In our bandit problem, we design a decentralized upper confidence bound algorithm to minimize the expected regret. It allows for the use of delayed and approximate estimations of the arms' means which we can obtain fast with an accelerated gossip communication protocol. We provide theoretical and empirical comparisons showing we obtain lower regret than previous state of the art.

Keywords: Riemannian optimization
Accelerated first-order methods
Cooperative multi-arm bandit problem
Proportional Fairness
Advisor: Kanade, V
Rebeschini, P
Synthesis and characterization of molecular wires with small bond-length alternation

This thesis presents the synthesis, characterization, and single-molecule charge transport studies of two families of molecular wires, cumulenes and cyanines, both of which have small bond-length alternation (BLA) in their linear conjugated systems. Normally, the single molecule conductance of a family of molecular wires will decrease as the molecules become longer, which would hinder the molecular wires from mediating long distance charge transport. Our experimental and computational studies showed that a small BLA contributes to more efficient charge transport through molecular wires.
Chapter 1 introduces the research field of molecular electronics, including the main techniques for studying single-molecule charge transport, scanning tunnelling microscope break-junction (STM-BJ) and mechanical controlled break-junction (MCBJ), and the mechanism of charge transport through single molecules. We also discuss how BLA influences the conductance of the molecules.
Chapter 2 introduces our research into cumulene molecular wires. Cumulenes are molecules with consecutive double bonds. We synthesized a family of cumulene molecular wires, with 1, 2, 3 and 5 consecutive double bonds, then studied their charge transport properties by the STM-BJ technique and DFT calculations. Our results showed that the [3]cumulene and [5]cumulene have essentially the same conductance, suggesting that the structure of consecutive double bonds contributes to higher conductance of the molecular wires. We attribute this to the small BLA, which leads to a smaller HOMO-LUMO gap in cumulenes.
Chapter 3 introduces our research into cyanine dye molecular wires. Cyanines are molecules bearing a positive charge, which have ending groups connected by an odd-numbered polymethine bridge. For the short cyanine dyes, their positive charge fully delocalises through the molecule, leading to a ground state structure without BLA. When the molecules become sufficiently long, their positive charge starts localizing at one of the end groups, thus the ground state structure shows BLA in their polymethine chains. We synthesized a family of cyanine dye molecular wires, with 3, 5, 7, 9 and 11 carbon atoms in their polymethine chains, with PF6- and B(C6F5)4- as counter ions, then studied their charge transport properties by the STM-BJ technique and DFT calculations. All cyanine dyes showed similar conductance, except the Cy11·PF6, which has a lower conductance. Combined with the UV-vis-NIR spectroscopy and crystallographic studies, we conclude that a Peierls transition happens in the Cy11·PF6 molecular wire, leading to charge localization and a lower conductance of the molecule.

Keywords: organic synthesis
cumulene
molecular electronics
cyanine dye
Advisor: Anderson, HL
PMT studies and loop antenna development for the LZ dark matter experiment

The nature of dark matter remains one of the biggest mysteries of the universe. Extensions to the Standard Model of particle physics provide potential candidates for dark matter. Such dark matter particles can be searched for using direct detection experiments. LUX-ZEPLIN (LZ) is a next-generation search for dark matter currently under construction at SURF, South Dakota. LZ employs a two-phase, liquid xenon time projection chamber (LXe TPC). A dark matter particle would scatter of a xenon nucleus, which causes scintillation and electroluminescence light signals. The light is detected by Photomultiplier Tubes (PMTs) on the top and bottom of the detector. The sensitivity projection for a 1000 live day run with 5.6 tonne fiducial mass is 1.6 x  10-48 cm2for a 40 GeV/c2 mass WIMP at 90% confidence level.
The first part of this thesis is concerned with the precise modelling of PMT properties and their impact on detector performance. To optimise sensitivity to WIMP masses of less than 10 GeV, it is essential to understand the single photon PMT response in detail. A simulation model, including undersized PMT pulses, is developed based on data taken with spare LZ PMTs. Variation in the PMT single photon response impacts detection efficiencies, energy resolution and position reconstruction. The improved PMT simulation is used to assess the impact of PMT failures on LZ signal detection efficiency, signal to background discrimination and ultimately LZ sensitivity.
High voltage discharges, accompanied by sparks, are a potential danger to the PMTs and a known problem in liquid noble gas detectors. The second part of this thesis discusses the development of the first dedicated high voltage discharge monitoring sensor in a LXe TPC. The loop antenna provides useful information about the electromagnetic environment of the detector and monitors for such discharges.

Keywords: LZ
Dark Matter
Advisor: Kraus, H
Inkjet printing of liquid crystals and polymer composites for novel thin-film optical elements

This thesis investigates the drop-on-demand inkjet printing of liquid crystal (LC) inks, from drop formation and deposition, through to substrate selection. Inkjet printing is a particularly attractive fabrication method as it is a precise, scalable and highly cost-effective additive manufacturing process. These benefits, along with the ability to deposit pico-liter volumes of particulate suspensions, viscous and complex fluids, have led to inkjet printing being considered as an attractive alternative fabrication technique in a range of established fields such as the display, pharmaceutical and bioengineering industries. However, the unique considerations of using liquid crystalline inks, such as their anisotropic properties and alignment criteria is barely touched in the literature. This thesis describes the design and build of an inkjet printing system capable of depositing a range of different functional inks such as LCs and polymer solutions. Drop generation of a nematic LC in a piezoelectric printhead and the role of different printing substrates on the final droplet configuration is considered in detail. This knowledge is used to fabricate novel, variable-focus microlens arrays that can be deposited as pre-programmable arrays on to a variety of different substrates. The unique properties of inkjet printing are then leveraged to describe two new methods of producing patterned, single layer polymer dispersed LC films. A prototype switchable, patterned polymer-dispersed LC film, produced by inkjet printing, is demonstrated. This work shows the feasibility of inkjet printing LC and polymer formulations and has important technological implications in the manufacturing of small and large area, polymer dispersed LC films for a variety of applications.

Keywords: printed displays
microlenses
Inkjet printing
fabrication of optical thin film elements
3D printing
smart windows
additive manufacturing
liquid crystals
Advisor: Morris, S
Castrejon Pita, A
Deterritorialising climate: ocean-based approaches to adaptation governance


This research asks how the Pacific climate system of El Niño Southern Oscillation (ENSO) is conceived and represented in the boundary-making practices of three knowledge communities: a) ocean science (i.e. Pacific marine biogeographies), b) environmental governance (i.e. Pacific adaptation frameworks), and c) local and traditional environmental knowledge (i.e. coastal subsistence communities in Timor-Leste). Ultimately, the project asks whether these disciplinary delineations of ENSO-related climate events promote effective adaptation governance.
There are four main findings: the ontological foundations of environmental law and governance frameworks work against fundamental aims in climate adaptation governance; there is an imperative to decolonise environmental law and governance frameworks in postcolonial contexts; local and traditional practices offer alternative ways of delineating adaptive geographies; and, lastly, principles from marine scientific boundary-making practices could inform governance frameworks in conceptualising assemblages of environmental change that move over space and time.

Keywords: climate change
Timor-Leste
Pacific adaptation governance
ENSO
ocean ontologies
The Wikipedia news network: understanding collective response to current events through the internet’s encyclopaedia

Wikipedia is the primary authoritative information resource on the web for billions of people, and perhaps the most important reference work in human history. Its modernised notion of the encyclopaedia is a widely accessible and rapidly updatable record for both historical knowledge and current events. The trove of available trace data from its users' browsing patterns also means that the site acts as an appealing, representative barometer for wider patterns of collective attention.
Studies of news media are often concerned with news values—properties of events—that together define newsworthiness—how likely an event is to be chosen for news coverage. In essence; what makes an event news? Traditional study, however, has frequently focussed on data directly from news media, journalists, or even news sharing on social media rather than independent "extra-media" data. This raises concerns of selection biases, platform-specific network effects, and endogeneity. To counter these issues I turn to Wikipedia and the way its users access its information for an audience-centric perspective on current events, news values, and newsworthiness.
In this thesis I conduct three studies designed around understanding collective response to current events. In the first study, I explore how events are represented on Wikipedia and accessed by is audience. To do this I develop a temporal community detection approach towards identifying the topics primarily browsed by users. Secondly, by combining the extra-media data of Wikipedia with a matched news article database I address and reformulate foundational hypotheses of news values and newsworthiness theory. In the third study, I more directly analyse the peaks of collective attention that emerge when a subject is in the news. I develop a time series clustering algorithm to identify the characteristic shapes of these peaks and propose a forecasting model for their growth and decay.
This thesis makes significant contributions to research on online representations of current events, modern understandings of news value theory, and models of collective attention dynamics. By not directly studying news media itself, this 'altmetric' style approach to studying the impact of news events is an important practical and theoretical advancement. It also has deep implications for newsrooms employing editorial analytics and for how platforms, including Wikipedia, serve content on current events to users. More widely, since newsworthiness and attention influence what information is popular—even acceptable—online, studies from novel, independent settings such as this are crucial to informing future journalistic and online speech policies and regulations.

Keywords: News Media
Collective Attention
Social Networks
Encyclopaedia
Wikipedia
Advisor: Yasseri, T
Lambiotte, R
In Extremis: Exploring gender, faith, and identity in the experiences of young South Asian British Muslim women who have joined or considered joining violent or non-violent extremist Islamist organisations

This thesis explores the role of gender, faith, and identity in the experiences of second-and third-generation South Asian British Muslim women who have joined or considered joining a violent or non-violent Islamist extremist organisation. It explores how growing up as a South Asian British Muslim woman in the UK has shaped the individual experiences of those who have joined or considered joining the so-called Islamic State of Iraq and Syria (ISIS) or Hizb ut-Tahrir (HT). Embedded in a feminist research framework, I draw on ethnographic fieldwork and interviews conducted between 2017-2018 to centre the voices of the women in the academic research that focuses on their lives. Conceptually I draw on a Bourdieusan framework alongside a rich history of theoretical research on women who participate in conservative religious movements and political violence to examine the ways in which their agency and experiences are embedded in the different social fields and normative frameworks which they navigate between. Focusing on the multiple choices they make, I explore the ways their embodied capacity to critically engage is shaped by the different social contexts and norms they inhabit, experience, resist, subvert, and perform daily. Consequently, I advocate for the introduction of ‘relationality’ to the study of ‘radicalisation’ to understand the mutually constituted relationship that unites agents and structures to tackle the overwhelming nomothetic nature of ‘radicalisation’ research. The accounts of the women who participated in this research raise some very worrying questions about the way Muslim minorities are treated in the UK. With this in mind, the title of this thesis: “In Extremis” is intended as a subversive reference to what the word “extreme” conjures in social consciousness. By definition, it refers to being in an extremely difficult situation and is crafted to draw attention to the difficult situations and challenges faced by all women in this thesis.

Advisor: Bano, M
Friedrichs, J
Improving the surgical patient care pathway through use of activity monitoring                                 

We can now monitor the physical activity levels of patients in the perioperative period. This has several potential applications including preoperative monitoring to assess patient fitness, postoperative monitoring to assess patient recovery, and to measure the impact of interventions aiming to improve cardiorespiratory fitness.
The research presented in this thesis set out to explore the relationship between daily physical activity levels and a patient’s cardiorespiratory fitness, and how measurement of daily physical activity levels can be used to improve patient fitness. To this aim, I developed two clinical study protocols to explore the use of activity monitoring as part of the surgical patient care pathway. A secondary aim was to improve the usability of activity monitoring for measuring physical activity levels in this population of patients. For this, a physical activity classification method and a system of remote activity monitoring was developed.
I found that there was a relationship between summary measures of daily physical activity levels as measured using a wearable accelerometer and patient fitness levels as measured using cardiopulmonary exercise testing. A feasibility study was commenced and successfully recruited six patients into a randomised controlled study involving daily physical activity monitoring and remotely supervised exercise intervention. Analysis of accelerometer data was shown to be a useful measure of the change in patient physical activity levels over a period of four weeks. Qualitative analysis of patient interview data revealed themes relevant to development of behavioural change techniques to improve adherence to preoperative exercise intervention.
The results from the novel study presented in this thesis showed how activity monitoring could be used in the surgical care pathway. From my studies, I have also identified the benefits and limitations of accelerometer measured daily activity in both the assessment of cardiorespiratory fitness and as a remote supervision and patient behavioural change tool during prehabilitation.

Keywords: preoperative assessment
surgical pathway
activity monitoring
accelerometer
cardiopulmonary exercise testing
prehabilitation
Advisor: Turney, B
Griffiths, J
Hamdy, F