VictorJuiz/thesis huggingface dataset:
Atomic structure and dynamics study of defects in graphene by aberration-corrected transmission electron microscope

Graphene has grabbed enormous research attention due to its multiple unique properties. These properties, however, can be strongly influenced by lattice imperfections. Aberration corrected transmission electron microscopy (AC-TEM) is one of the leading methods to image two-dimensional materials at the atomic level. This thesis addresses the issue of structure and dynamics characterization of dislocations and grain boundaries (GBs) in graphene with single atom sensitivity using the state-of-the-art AC-TEM in Department of Materials, University of Oxford.
My first goal is to understand the interaction between dislocation and the edge of graphene. When a dislocation is located near an edge, a decrease in the rippling and increase of the in-plane rotation occurs relative to the dislocations in the bulk. The increased in-plane rotation near the edge causes bond rotations at the edge of graphene to reduce the overall strain in the system. Dislocations are highly stable and remain fixed in their position even when located within a few lattice spacings from the graphene edge.
With the aid of an in situ heating holder, the high temperature behavior of dislocations is then investigated. Control of temperature enables the differentiation of electron beam induced effects and thermally driven processes. An analysis of the dislocation movement shows both climb and glide processes, including new complex pathways for migration and large nanoscale rapid jumps between fixed positions in the lattice. The improved understanding of the high temperature dislocation movement provides insights into annealing processes in graphene and the behavior of defects with increased heat.
The in situ heterogeneous nucleation and growth of graphene are also studied within the AC-TEM. The growth mechanism consists of alternating carbon cluster attachment and indentation filling to maintain a uniform growth front of lowest energy. The highly polycrystalline graphene seed is found to evolve with time into a higher order crystalline structure. The motion of GBs is discontinuous and mediated by both bond rotation and atom evaporation. These results provide insights into the formation of crystalline seed domains that are generated during bottom-up graphene synthesis.
Finally, the formation, reconfiguration and annihilation of GB loops are demonstrated. It is shown that the GB loop cannot fully relaxed under electron beam irradiation with its terminal state being isolated dislocations far apart from each other. Line defects composed of several adjacent excess-atom defects can be found during the reconfiguration process. This work gives detailed information about the stability and behavior of large GB loops in two dimensional materials.

Keywords: graphene
Advisor: Warner, J
Non-stabilized nucleophiles in cu-catalyzed asymmetric synthesis

This thesis describes the study of organozirconium reagents used in copper-catalyzed asymmetric synthesis. Explorations on the asymmetric allylic alkylation of linear substrates, the cyclic substrates and enantioselective desymmetrization of meso compounds including the oxabicyclic alkenes and meso-allyl substrates are reported here.
Chapter 1 has a brief overview about general methods used in asymmetric catalysis. In particular, more relevant introduction about catalytic asymmetric allylic substitution and asymmetric desymmetrization of meso compounds is given.
Chapter 2 describes the investigation of organozirconium reagents used in copper-catalyzed asymmetric allylic alkylation of linear substrates, and discloses a dynamic kinetic AAA system that employs cyclic allylic chlorides as substrates.
Chapter 3 presents the study on expanding the disclosed copper-catalyzed dynamic kinetic AAA chemistry by using more stabilized cyclic allylic phosphate substrates. Further exploration of its possible mechanisms uses substituted substrates, deuterated and enantiopure substrates are also discussed.
Chapter 4 demonstrates the study of organozirconium reagents used in copper-catalyzed enantioselective desymmetrization reactions. Investigation of oxabicyclic alkenes and mesoallyl substrates is reported.
Chapter 5 gives supporting information of this thesis.

Advisor: Stephen.P.Fletcher
Model or mirage?

Despite significant growth in the number of “good governance” initiatives promising to generate optimum developmental outcomes in resource-rich countries, there is surprisingly little empirical information about their sector and country-specific dynamics. This thesis focusses on how external “good governance” norms and institutions interact with domestic actors and organisations to shape the institutional landscape of resource-rich countries. This objective is pursued by means of an in-depth case study of Ghana, a Sub-Saharan African nation that has become a middle-sized exporter of crude oil since January 2011. More specifically, it scrutinises two major reform efforts designed to steer the country’s oil industry towards a developmental direction: the Extractive Industries Transparency Initiative (EITI), an international auditing and multi-stakeholder oversight mechanism, and the Public Interest and Accountability Committee, a home-grown citizens’ oversight initiative in Ghana. The analytical lens employed in the study is based on comparative political economy and comparative institutional analysis. They are employed to make sense of the dialectic between the promise of corrective “good governance” measures and the mirage of reform outcomes in the Ghanaian oil sector. The main argument advanced here is that “good governance” solutions in the oil industry are essentially weak instruments, due to their inability to grapple with deep-seated instrumental politics, perverse institutional environment, and elite capture that continue to undermine reform in Ghana. This point is adduced to highlight the shortcomings of the “good governance” agenda. The thesis draws from multiple data sources, collected through semi-structured interviews with various stakeholders, public officials, NGOs and community activists, development agencies, and oil companies. These are complemented by archival research, documentary sources, non-participant observation, and workshops.

Keywords: Oil
Institutions
Ghana
Good governance
Advisor: Mustapha, AR
Branching processes with spatial structure in population models

We consider three different settings for branching processes with spatial structure which appear in population models.
Firstly, we consider the effect of adding a competitive interaction between nearby individuals in a branching Brownian motion. Each individual has a mass which decays when other individuals are nearby. We study the front location: the location at which the local mass density drops to o(1). We show that there are arbitrarily large times t at which the front location is order of t^(1/3) behind the maximum displacement of a particle from the origin.
Secondly, we study the strength of selection in favour of a particular allele in a spatially structured population required to cause a detectable trace in the patterns of genetic variation observed in the contemporary population. We suppose that the effective local population density is small. We show that whereas in dimensions at least three, selection is barely impeded by the spatial structure, in the most relevant dimension, d=2, selection must be stronger (by a factor of log(1/m) where m is the neutral mutation rate) if we are to have a chance of detecting it.
Finally, we model the behaviour of what are known in population genetics as hybrid zones. These occur when two genetically distinct groups are able to reproduce, but the hybrid offspring have a lower fitness. We prove that on an appropriate time and space scale, the hybrid zone in our model evolves approximately according to mean curvature flow. We also give a probabilistic proof of a (well-known) analogous result for a special case of the Allen-Cahn equation.
In the last two cases, we use the spatial Lambda-Fleming-Viot process to model the population (with different selection mechanisms), and our proofs rely on a duality with a system of branching and coalescing particles.

Advisor: Etheridge, A
Critical assessment of the role of cannabinoid receptor 2 in inflammation

Cannabinoid receptor 2 (CB2R) is a G protein-coupled receptor (GPCR) expressed in the periphery by immune cells, such as B cells, natural killer (NK) cells, neutrophils, macrophages and T cells. It belongs to the endocannabinoid system which also comprises CB1R, endogenous lipophilic agonists called endocannabinoids and the enzymes responsible for their synthesis and degradation.
During inflammatory diseases the endocannabinoid system is dysregulated and increased expression levels of endocannabinoids and cannabinoid receptors are observed. Therefore there is a continuing interest to target the endocannabinoid system to restore homeostasis in patients who suffer from a number of inflammatory diseases, such as multiple sclerosis, atherosclerosis, neuropathic pain and others. However, to date there has been no good anti-inflammatory drug in the market or clinical trials that acts via CB2R. The main aim of this DPhil thesis was to critically assess the role of this receptor in health and inflammation with a particular focus on innate immune cell recruitment.
Here I describe my findings regarding the immunophenotype of a CB2R knockout (KO) mouse strain at steady state and under acute systemic inflammation. I showed that CB2R KO mice display a trend in neutrophil accumulation and in monocyte egress in the bone marrow, as well as higher myeloperoxidase activity in the liver. These findings support the view that this cannabinoid receptor plays a pivotal role in innate immune cell trafficking during homeostasis.
Furthermore, I discovered that CB2R KO animals display exacerbated immune cell recruitment to peripheral tissues in a model of low dose endotoxemia. In particular, I found more neutrophils in the lungs and spleens of CB2R KO mice at the model’s peak time point. These observations are consistent with a model in which CB2R plays a non-redundant role in the inhibition of neutrophil migration to injured tissues after an inflammatory insult.
My in vitro experiments showed that CB2R-selective agonists had no anti-inflammatory effects during macrophage activation. Looking for a mechanistic explanation for this result, I found that the expression levels of the receptor are severely downregulated upon challenge with lipopolysaccharide (LPS) and interferon-γ (IFN-γ) which suggests that it is possible that CB2R is differentially regulated in immune cells during inflammation.
Collectively, the data presented in this thesis support the view that CB2R plays an important role in health and disease in pre-clinical models, but further studies are required to make more soluble CB2R-selective agonists and to understand which immune cells we should aim to target therapeutically.

Advisor: Greaves, D
New reactions of titanium imido and hydrazido complexes

This Thesis reports the synthesis and reactions of titanium-nitrogen multiply bonded compounds. Reactions with both acidic and hydridic element-hydrogen bonds are explored along with unsaturated small molecules in general.
Chapter One provides a background on imido and hydrazido complexes, starting with the relevance of the hydrazido ligand to nitrogen fixation. Group 4 alkylidene hydrazide and alkoxyimide complexes are also reviewed. The Chapter focuses in particular on the synthesis, structure, and stoichiometric and catalytic reactions of these complexes with unsaturated substrates.
Chapter Two describes the synthesis of new titanium imido complexes and the reactions with molecules containing N–H or O–H bonds, internal alkynes and nitriles. The analogous reactions of the hydrazido compound Ti(N2iPrNMe)(NNPh2)(py) are also investigated.
Chapter Three details the reactions of the imido compound Ti(N2iPrNMe)(NXyl)(py) with terminal alkynes. Unusual reaction products are described and a full mechanistic study into their formation along with their synthesis and characterisation is presented. In addition, the relevance of these reactions to the catalytic hydrohydrazination of terminal alkynes and diphenylhydrazine with Ti(N2iPrNMe)(NNPh2)(py) is discussed.
Chapter Four describes the reactivity of the hydrazido compound Ti(N2iPrNMe)(NNPh2)(py) with a range of silanes and boranes. These reactions are then explored through an in-depth experimental and computational study.
Chapter Five presents full experimental procedures and characterising data for the new complexes reported.

Advisor: Mountford, P
Harnessing demographic data for cross-scale analysis of forest dynamics

Forests are a critical biome but are under threat from unprecedented global change. The need to understand forest dynamics across spatial, temporal and biological scales has never been greater. Critical to this will be understanding how the demographic rates of individuals translate into patterns of species diversity, biomass and carbon turnover at much larger scales.
In this thesis, I present a modelling framework focussed on demography. In Chapter 2, I introduce methods for translating forest inventory data into population models that account for the size-dependency of vital rates and persistent differences in individual performance.
Outbreaks of forest pest and pathogens are increasing in frequency and severity, with consequences for biodiversity and forest structure. In Chapter 3, I explore the impact of ash dieback on the community dynamics of a British woodland, describing a spatially explicit individual based model that captures the effect of an opening of the canopy on local competitive interactions.
Chapter 4 introduces methods to infer the impact of historical deer herbivory on the juvenile survival of forest trees. The approach is generalisable and could be applied to any forest in which patterns of regeneration and community structure have been impacted by periodic disturbance (e.g. forest fires).
Finding meaningful ways of incorporating species diversity into global vegetation models is increasingly recognised as a research priority. In Chapter 5, I explore the diversity of demographic rates in a tropical forest community and identify groups of species with similar life history strategies. I discuss the potential of integrating demographic and physiological traits as a way to aggregate species for inclusion in global models.
In summary, translating measurements of individuals into population dynamics provides opportunities to both explore small-scale community responses to disturbance events, and to feed into much larger scale vegetation models.

Keywords: Demography
Vital rates
Forest dynamics
Integral Projection Models
Ash dieback
Tropical trees
Advisor: Leimu-Brown, R
Hector, A
Metcalf, J
Impact of drops upon surfaces with complex morphology

Drop impacts are ubiquitous in nature forming a vital pathway for the transport of liquids, primarily water, and any dissolved substances. The axisymmetric impact of drops has been heavily studied but less work has been done on droplet impacts in which axial symmetry is broken. To analyse such impacts we used a two phase lattice Boltzmann code capable of simulating high density differences
.
We studied the impact of droplets on cylindrical surfaces, with radius of curvature similar to that of the drop. We found that the symmetry breaking nature of these surfaces leads to droplets bouncing faster and in elongated shapes. The origin of this eﬀect is a positive feedback mechanism through which the momentum asymmetry resulting from the impact grows during retraction.
We next looked at how varying the size of the cylinder affected this phenomenon. We found that smaller cylinders increased the contact time reduction, as long as they were still bigger than the droplet, but that below this limit the drop contacted the ﬂat surface and entered a new regime.
The work was expanded to look at other types of bouncing asymmetry, using a simple, exactly solvable Lagrangian model. We found that contact time reduction can result from an asymmetric droplet shape, an initially asymmetric velocity or if the surface has an asymmetric drag.
A study of the impact of liquid drops containing embedded air bubbles was also undertaken. This was found to lead to jet formation from the bottom of the bubble. We showed how the jet velocity depended on the physical parameters of the drop and impact. In particular the jet formation was very sensitive to the position of the air bubble inside the drop.

Keywords: Wetting
Hydrodynamics
Advisor: Yeomans, J
Molecular pharmacology of native and exogenous vascular ion channels

Vascular Ca2+-activated chloride channels (CaCCs), are a class of ligand- and voltage-gated channels that couple agonist binding and inositol triphosphate (IP3) signalling to depolarisation of the cell membrane and smooth muscle contraction. The elucidation of the precise physiological role and the pharmacological profile of this channel has been accelerated by the recent discovery of the gene (TMEM16A) coding for these channels. Based on the rationale that depolarising membrane potential (Vm) causes contraction in vascular SMCs, the possibility of controlling vessel tone via the exogenous light-activated, depolarising Channelrhodopsin 2 (ChR2) channels was also investigated. The overall aim of this thesis is two folds: i) to define mechanisms of regulation of CaCCs by endogenous signalling molecules and pharmacological agents, and ii) to develop a new method of controlling vascular contraction by exogenous ion channels. The main findings of this thesis are:
1) Arteries (large conduit, systemic and pulmonary) obtained from mice lacking of one allele of TMEM16A gene (heterozygous knockouts) presented reduced response to α1-adrenergic receptor activation. This finding reinforced the view that TMEM16A proteins serve as key mechanism of modulation of artery tone.
2) Phosphatidylinositol 4,5-bisphosphate (PIP2), a lipid involved in the IP3 signalling cascade, is a key activator of native and cloned vascular TMEM16A channel. Furthermore, the closely related TMEM16B was inhibited by PIP2. These modulatory effect of PIP2 on these channels were especially pronounced in the physiological range of [Ca2+]i.
3) Anthracene-9-carboxylic acid (A9C), a general Cl- blocker, exhibited bimodal effects on TMEM16A-mediated currents. The inhibiting effect occurred via open-channel block mechanism while the activating effect was due to an increase in Po and a leftward shift in the steady-state activation curve. These mechanistic insights may help the design of novel drug (activators and inhibitors) that could be used to modulate blood vessel tone.
4) ChR2, a light-gated and non-selective cation channel, was introduced specifically into the SMC in mice (ChR2-SMC). Isolated arterial SMCs obtained from these mice showed light-dependent inward currents. ChR2-SMC artery rings also contracted in a light-dependent manner. The mechanism of lightinduced contraction involved voltage-gated Ca2+ channels (VGC) activation and Ca2+ influx.
To conclude, this work of thesis has shed light on the functional role of TMEM16A in various vascular SMCs types. The regulation of TMEM16A by membrane lipid will lay the foundation for the identification of the PIP2 binding site on these channels, which could also be exploited as a site for pharmacological intervention. The study of A9C mechanisms of activation and inhibition may aid the development of selective blockers and activators for TMEM16A channels. Lastly, the control of vascular tone by ChR2 in mice can be used to control blood perfusion to organs and tissues for experimental purposes.

Advisor: Tammaro, P
Development and characterisation of a cold molecule source and ion trap for studying cold ion-molecule chemistry

A novel apparatus, combining buffer-gas cooling, electrostatic velocity selection and ion trapping, has been constructed and characterised. This apparatus is designed to investigate cold ion-molecule chemistry in the laboratory, at a variable translational and internal (rotational) temperature. This improves on previous experiments with translationally cold but rotationally hot molecule sources. The ability to vary the rotational temperature of cold molecules will allow for the experimental investigation of post-Langevin capture theories.

Keywords: Ion trapping
Low-temperature physics
Molecular beams
Reaction dynamics
Cold chemistry
Ammonia
Laser cooling
Advisor: Vallance, C
Heazlewood, B
Pharmacoproteomic characterisation of human colon and rectal cancer

Colorectal cancer (CRC) is one of the top three most common cancers and among the top four causes of cancer-related deaths worldwide (Torre et al., 2015). CRC patients are well characterised on the transcriptome and proteome level, but proteomics data on representative cell lines as model systems for pre-clinical drug sensitivity studies lag behind. Here, label-free quantitative mass spectrometry was used to characterise the kinomes and full proteomes of 65 CRC cell lines, collectively termed the CRC65 cell line panel. This data was integrated with proteomics data on patient samples, as well as public transcriptome and drug sensitivity datasets, which were reanalysed from raw data in order to unify and streamline the data processing. Protein/mRNA ratios were constant across these datasets, enabling linear prediction of protein abundance from mRNA abundance after appropriate adjustment, which was used for mRNA-guided missing value imputation. An exploration of secondary imputation methods prompted the development of a complementary method for minimum-guided missing value imputation. Combining the proteomics datasets on cell lines and patients led to the discovery of integrated proteomic subtypes of CRC and enabled the identification of representative cell lines for each of them. Modelling publicly available dose-response data generated by four large-scale drug sensitivity studies as a function of kinome/full proteome profiles fuelled the prediction of drug sensitivity for cell lines and patients, allowed the identification of drugs differentially effective between the different integrated proteomic subtypes and revealed MERTK as a predictive biomarker for resistance towards MEK1/2 inhibitors. This predictive role of MERTK was subsequently confirmed using in vitro experiments, while immunohistochemistry of TMAs from 1,074 tumours generated as part of the QUASAR2 clinical trial unveiled that MERTK is also a prognostic biomarker in CRC. This dataset will be made available to the scientific community to facilitate the design of prospective clinical studies.

Keywords: QUASAR 2
proteomics
mass spectrometry
CPTAC
colorectal cancer
patient stratification
CRC65
Advisor: Feller, S
Knapp, S