VictorJuiz/thesis huggingface dataset:
Kähler groups and Geometric Group Theory

In this thesis we study Kähler groups and their connections to Geometric Group Theory. This work presents substantial progress on three central questions in the field:
Which subgroups of direct products of surface groups are Kähler?
Which Kähler groups admit a classifying space with finite (n-1)-skeleton but no classifying space with finitely many n-cells?
Is it possible to give explicit finite presentations for any of the groups constructed in response to Question 2?
Question 1 was raised by Delzant and Gromov.
Question 2 is intimately related to Question 1: the non-trivial examples of Kähler subgroups of direct products of surface groups never admit a classifying space with finite skeleton.
The only known source of non-trivial examples for Questions 1 and 2 are fundamental groups of fibres of holomorphic maps from a direct product of closed surfaces onto an elliptic curve; the first such construction is due to Dimca, Papadima and Suciu.
Question 3 was posed by Suciu in the context of these examples.
In this thesis we:
provide the first constraints on Kähler subdirect products of surface groups (Theorem 7.3.1);
develop new construction methods for Kähler groups from maps onto higher-dimensional complex tori (Section 6.1);
apply these methods to obtain irreducible examples of Kähler subgroups of direct products of surface groups which arise from maps onto higher-dimensional tori and use them to show that our conditions in Theorem 7.3.1 are minimal (Theorem A);
apply our construction methods to produce irreducible examples of Kähler groups that (i) have a classifying space with finite (n-1)-skeleton but no classifying space with finite n-skeleton and (ii) do not have a subgroup of finite index which embeds in a direct product of surface groups (Theorem 8.3.1);
provide a new proof of Biswas, Mj and Pancholi's generalisation of Dimca, Papadima and Suciu's construction to more general maps onto elliptic curves (Theorem 4.3.2) and introduce invariants that distinguish many of the groups obtained from this construction (Theorem 4.6.2); and
construct explicit finite presentations for Dimca, Papadima and Suciu's groups thereby answering Question 3 (Theorem 5.4.4)).

Keywords: Geometry and Topology
Complex geometry
Geometric Group Theory
Kähler groups
Advisor: Bridson, M
Exploring the use of mercury in reconstructing the environmental impacts of Large Igneous Provinces

Large Igneous Provinces (LIPs) represent geologically rapid emplacements of vast quantities of igneous material into/onto Earth’s crust. There is a marked correlation in the known ages of LIPs and Mesozoic extinctions and other environmental perturbations, suggesting a possible causal link between these events. However, uncertainties in matching LIP basalt ages to the stratigraphic record of Mesozoic events mean that a sedimentary tracer of volcanism would better indicate a precise coincidence between the two phenomena. Mercury (Hg) has shown potential as such a proxy. Volcanism is a major source of Hg to the natural environment, and its relatively long atmospheric residence time (0.5–2 years) allows global distribution of the element before it is deposited to sediments. However, questions remain about how the manner of LIP emplacement might influence its impact on the Hg cycle, as well as how sedimentary processes may locally overprint any global signal. Here, the Hg records of three Mesozoic events are investigated: the end-Triassic extinction (TJ: ~201.5 Ma), Cretaceous Oceanic Anoxic Event 2 (OAE 2: ~94 Ma), and the latest Cretaceous (K–Pg: ~67–66 Ma). These events coincided with markedly different LIPs: OAE 2 with multiple submarine LIPs; the K–Pg and TJ with subaerial LIPs; with the TJ also featuring release of additional thermogenic volatiles from intrusion of organic-rich lithologies by LIP sills. Additionally, mercury is used with osmium and carbon isotopes to study the temporal relationships between volcanism, weathering, and the carbon cycle during the Toarcian Oceanic Anoxic Event (~183 Ma). This work highlights the links between LIP volcanism and other surface processes, and shows that subaerial LIPs featuring thermogenic emissions are most likely to perturb the global Hg cycle, with the record of such perturbations dependent on the nature of the sedimentary archive.

Keywords: Palaeoclimate
Geochemistry
Mercury
Volcanism
Mass extinctions
Advisor: Jenkyns, H
Mather, T
Hesselbo, S
The evolutionary impact of resource availability

Evolution is the change in heritable characteristics in a population over successive generations that is driven by mutation, selection and random genetic drift. Understanding the factors affecting sequence evolution and the interactions between them is of fundamental importance and facilitated by the recent proliferation of genome data. One factor that is not well understood is the role that resource availability plays in determining sequence evolution. The aim of the research described in this thesis is to address this gap in our knowledge by presenting three papers on the theme of species and sequence evolution. First, I report the discovery of a new species of Phytomonas, a single-celled eukaryotic plant parasite. Second, using a comparative analysis of Phytomonas and other single-celled plant- and animal-infecting parasites, I reveal the importance of dietary nitrogen in determining biased patterns of nucleotide use in genome and transcript sequences. Third, I examine the interaction between codon biosynthetic cost and translational efficiency in a range of bacterial species. The new results reported in this thesis identify and quantify the impact of resource availability on sequence evolution. By elucidating the contribution of resource availability to sequence evolution, and investigating how selection acting on codon resource use interacts with selection acting on codon translational efficiency, the research presented in this thesis makes a significant contribution to our understanding of sequence evolution.

Advisor: Kelly, S
Sweetlove, L
Synthesis and functionalisation of endohedral nitrogen fullerenes: towards quantum devices

Endohedral nitrogen fullerenes (ENFs) have been proposed as building blocks for quantum information processing due to very long relaxation time for their incarcerated electron spins. However, fabricating quantum devices based on this exotic material is still limited by the low yield of ENFs synthesis and various difficulties in subsequent molecular engineering, including the chemical sensitivity of the molecules, assembling approaches of the molecular architecture, and control of spin-spin coupling between qubits. My contributions towards removing the aforementioned limitations by studying the synthesis and functionalisation of ENFs are presented herein. My aim has been to pave the way towards quantum devices based on ENFs.
Firstly, I enhanced the ENFs production yield by a factor of five. I accomplished this by optimizing the ion implantation apparatus and parameters during the synthesis of raw ENFs, in addition to adjusting the column and eluent during the purification of ENFs by high performance liquid chromatography (HPLC).
Secondly, I established (for the first time) a spin-compatible protocol for performing Bingel reactions on ENFs. Utilizing the developed method, I also demonstrated the feasibility of chemically modifying ENFs for different molecular requirements via synthesizing a series of ENF derivatives with rigid configuration, long molecular aspect ratio, and amphiphilic properties.
Subsequently, I covalently assembled ENFs at microscopic levels and axially aligned ENFs at macroscopic levels, respectively. At the microscopic scale, I synthesized ENF- containing dyads and dimers, and developed a method of coaxially dimerizing ENFs with rigid bridge molecules, which provides material foundation for multi-qubit manipulations with spin couplings. At the macroscopic scale, I achieved the best orientational alignment of ENFs reported to date by embedding elongated ENF derivatives within a liquid crystal, which is critical for ensemble qubit with anisotropic spin properties. Benefiting from the good alignment, a controllability of the ensemble spin anisotropy is demonstrated with zero-field splitting of ENF derivatives.
Finally, I studied the electron spin dipolar coupling in ENFs by measuring and comparing of the coupling strength at different conditions. I discovered that the electron spin dipolar coupling in N@C60-CuPc dyads can be chemically tuned by altering the lengths of the spacing groups between the two spin centres, and be physically adjusted by changing the sample concentrations to aggregate the sample and suppress the Cu electron spin.
In summary, aiming for ENF-based quantum devices, I made progress in both the material production and the molecular engineering of ENFs.

Advisor: Porfyrakis, K
Briggs, G
Neural network modelling of the primate ventral visual pathway

The aim of this doctoral research is to advance understanding of how the primate brain learns to process the detailed spatial form of natural visual scenes. Neurons in successive stages of the primate ventral visual pathway encode the spatial structure of visual objects and faces. However, it remains a difficult challenge to understand exactly how these neurons develop their response properties through visually guided learning. This thesis approaches this problem through the use of computational modelling. In particular, I first show how the brain may learn to represent the spatial structure of objects and faces through a series of processing stages along the ventral visual pathway. Then I propose how understanding the two complementary unsupervised learning mechanisms of translation invariance may have useful applications in clinical psychology. Next, the potential functional role of top-down (feedback) propagation of visual information in the brain in driving the development of border ownership cells, which are thought to play a role in binding visual features such as boundary edges to their respective objects, is investigated. In particular, the limitations of traditional rate-coded neural networks in modelling these cells are identified. Finally, a general solution to such binding problems with the use of a more biologically realistic spiking neural network is presented. This work is set to make an important contribution towards understanding how the visual system learns to encode the detailed spatial structure of objects and faces within scenes, including representing the binding relations between the visual features that comprise those objects and faces.

Advisor: Stringer, S
Humphreys, G
Electronic and magnetic properties of iron-based superconductors

This thesis presents experimental studies of the electronic and magnetic properties of several iron-based unconventional superconductors, primarily using the techniques of magnetotransport and torque magnetometry in high magnetic fields and synchrotron-based angle-resolved photo-emission spectroscopy (ARPES). Superconductivity in the iron-based superconductors is always found in proximity to a magnetic phase, and the details of the electronic structure and Fermi surface are also important in determining the strength of interactions, and ultimately superconductivity. This motivates the experimental studies of electronic, magnetic and superconducting properties of Fe-based superconductors presented in this thesis. First, quantum oscillation measurements using high-field torque magnetometry are used to provide a partial determination of the Fermi surface of superconducting LiFeAs. The data are compared with density functional theory calculations, finding strong mass enhancements on the observed electron bands, however the hole bands are not observed. A large portion of this thesis concerns experiments on FeSe, which uniquely has a structural transition but is not magnetically ordered at any temperature. High field magnetotransport measurements show quantum oscillations, revealing small quasi-two dimensional Fermi surfaces, and it is argued that both hole and electron pockets are observed. The low-temperature Fermi surface consisting of one hole pocket and two electron pockets is also deduced from low-field magnetotransport. ARPES studies show that both hole and electron pockets undergo a significant elongation when cooling through the structural transition at ~90 K, interpreted as the result of orbital order. Measurements of the resistivity anisotropy above the structural transition are used to show that the structural distortion is electronically-driven. By combining these data sets, a complete picture of the symmetry-broken electronic structure of FeSe is constructed. The final chapter concerns another iron-based superconductor with a more complex crystal structure, the so-called
10-3-8" phase, and in particular finds an unusual field-induced magnetic transition.

Keywords: FeSe
LiFeAs
ARPES
quantum oscillations
Advisor: Coldea, A
Metabolomics in hypertrophic cardiomyopathy and other myocardial diseases

Despite the clinical importance of hypertrophic cardiomyopathy (HCM) and a recognition that aberrant energetics contributes to its pathogenesis, significant uncertainty remains regarding the determinants of the clinical phenotype. The central hypothesis underlying this thesis is that the clinical manifestations of HCM are causatively influenced by perturbations in cellular metabolism, and that the metabolome in HCM, both at rest and during stress, is distinct from that of healthy hearts and other cardiac diseases manifesting left ventricular hypertrophy (LVH). Aortic stenosis, the most common valvular heart disease in the western world, and often presenting with a prominent phenotype of LVH, was the principal comparator disease state.
The metabolome of coronary sinus effluent from densely phenotyped patients with HCM, aortic stenosis with LVH and controls was systematically studied. These patients were assessed under different physiological states (at rest and during stress induced by pacing). The present work focused on fatty acid, carbohydrate and amino acid metabolism. The metabolomic changes identified were then validated by metabolomic and an orthogonal transcriptomic analysis of genes regulating these metabolic pathways in separately recruited patient cohorts.
Most prominently, this study identified substantial metabolic dysregulation in aortic stenosis, consisting of impaired fatty acid β-oxidation at rest and a trend towards reduced uptake of citric acid cycle intermediates and branched chain amino acids (BCAAs) during chronotropic stress (pacing). Transcriptomic analysis revealed only partial and ineffective upregulation in PPARA expression, with a corresponding downregulation of several PPARα target genes regulating fatty acid metabolism. In contrast, there was a seemingly appropriate upregulation of citric acid cycle activity and BCAA metabolism in HCM patients during stress. During discovery and validation stages selected metabolites differentiated the control vs aortic stenosis and HCM vs aortic stenosis cohorts with relatively similar and high area under the curve (AUC) values on receiver operating characteristic (ROC) analysis.
This work presented in this thesis represents the first comprehensive analysis of changes in metabolic pathways (transcriptional to metabolome) in aortic stenosis, and its comparison to HCM. The findings represent a significant increase in our understanding of the underlying metabolic derangements accompanying these disorders and provide us with promising avenues into potential therapeutic targets (e.g. PPARα), with strong clinical translation potential.

Advisor: Ashrafian, H
Resource allocation in the legume-rhizobia symbiosis: an integration of modelling and experimental approaches

The symbiosis between plants of the legume family and nitrogen-fixing rhizobia underpins global food security. Legume crops are a major source of protein in human diets, either directly or indirectly as feed for livestock. Application of inoculant rhizobial strains is common practice in many areas, as plant growth is often nitrogen limited and the symbiosis can significantly enhance yields. However, rhizobial strains and outcomes of the symbiosis vary widely. This variation has also been studied by evolutionary biologists interested in the stability of mutualisms. They proposed that plants may prevent establishing symbioses with ineffective strains (partner choice), or provide them with fewer resources (sanctioning). I studied both mechanisms, combining modelling and experimental approaches.
Mathematical modelling was used to predict how plants should allocate resources to maximise growth rates, depending on rhizobial nitrogen provision and carbon requirements and on soil nitrogen conditions. The use of marked mutant strains – easily distinguishable and differing in a single rhizobial characteristic – overcame previous experimental difficulties. It was found that pea (Pisum sativum L.) plants are not able to exert partner choice, but do sanction in a more complex way than was previously established. In line with model predictions, resources were preferentially allocated to the single – best available – strain, so that resources allocated to an intermediate-fixing strain depended on whether or not a strain providing more nitrogen was available. Contrary to model predictions, there was no indication of discrimination based on rhizobial carbon requirements.
The results cannot be explained by resource allocation in proportion to nitrogen received, and indicate systemic integration of information from different nodules. I formulate a hypothesis about the underlying plant regulatory mechanisms, and discuss implications of the results for selecting inoculant strains and enhancing yields in the field. Future work will rely on further integration of theoretical and applied methods and perspectives.

Keywords: rhizobia
agriculture
nitrogen
mutualism
resource allocation
nutrients
evolutionary biology
symbiosis
mathematical model
legume
Advisor: Turnbull, L
Poole, P
Preston, G
Nonlinear optical probes for measuring membrane potential in neurons

Chapter 1: In Chapter 1, I discuss the design and mechanisms of existing optical techniques to measure membrane potential of live cells. I compare the different fluorescence and second harmonic generation- based methodologies developed over the years to test voltage sensitivity of dyes.
Chapter 2: I discuss the design, synthesis, and characterization of pyropheophorbide-based push-pull dyes as nonlinear optical probes. I show that the pyropheophorbides have different transition dipole moment for two-photon fluorescence and second harmonic generation in both 2D and 3D.
Chapter 3: In this chapter, I investigate the cellular localization of different donor-acceptor porphyrin-based dyes in a multiphoton microscope. The dyes possess the same hydrophobic electron-donor group and porphyrin group but different hydrophilic electron-acceptor groups. The dyes stain different types of cellular organelles depending on the type of hydrophilic headgroups.
Chapter 4: Here, I discuss the existing techniques to test voltage-sensitivity of organic dyes. I also discuss the design of a patch-clamp–based setup that I installed in the multiphoton microscope. I test the efficacy of the setup by testing the voltage sensitivity of commercial dyes. I also investigate the voltage sensing efficacy of plasma membrane bound porphyrinbased dyes.
Chapter 5: In this chapter, I discuss the design, synthesis, and characterization of a new tricationic porphyrin-based dye, AK-1. I also investigate the plasma membrane localization of AK-1 in HEK 293T cells, U-87 MG cells, HeLa cells, rat hippocampal neurons, mice brain slices, contracting neonatal myocytes, gram negative bacteria E.Coli, and giant unilamellar vesicles. I demonstrate the voltage sensitivity of the dye in contracting neonatal myocytes. I also demonstrate multimodal imaging efficacy of AK-1.
Chapter 6: In this chapter, I study the spatial characteristics of monocellular and multicellular spheroidal tumor models through two-photon microscopy. The spheroids display similar characteristics to real tumors.

Advisor: Anderson, H
A critical edition of the Book of Proverbs in Ethiopic

The manuscript Add. 1570 (Cambridge) has been chosen as the base text for this edition of Proverbs. Against it twenty one Ethiopic manuscripts have been collated, as well as the printed texts of the Bassano edition and the and'm commentary. Add. 1570 has been selected as the base for reasons of date and textual type.
The base text has been translated in a literal manner to retain, where possible, the idiosyncrasies of the Ethiopic version. The apparatus criticus records all the significant variants of the twenty one manuscripts and two printed texts. Points of interest relating to matters within Ethiopic, as well as to the relationship of one group of manuscripts to another and of these groups to likely original texts, are dealt with verse by verse in the notes.
The data in the apparatus provide evidence for four distinct textual traditions. The introduction brings together and analyses the data from these traditions, in relation to the antecedents and history of the Ethiopic Old Testament version. The following conclusions are drawn;-
No "pure" Ethiopic text is found – namely one which can be related to one textual Vorlage only. All groups of manuscripts Show a deep and thorough-going amalgamation of Greek and Semitic textual features. The Semitisms are found to be Hebraisms, with very scarce evidence of Syriac influences.
The nature of the Hebraic element is considered such an integral part of the Ethiopic tradition that it cannot be considered to be the product of revision alone, but must go back to the earliest stage of translational activity. No evidence is found to prove that the Hebrew sources used in Ethiopic were different from the Masoretic text known to us.
The structure and layout of the book are found to depend on the LXX (arrangement of chapters and verses). The Greek source used in the translation is identified with the main LXX tradition; influence from the versions of Aquila, Symmachus, and Theodotion is not found. But no particular strand of the LXX tradition is identified as influential upon Ethiopic.
The particular Ethiopia tradition in the text of Proverbs is investigated. An editorial process of implification (even at the expense of fidelity to the original texts) is noticed in later manuscripts; this takes the form of additions, explanation— and a tendency to make explicit what is thought to be implicit in the text.
Questions which remain unanswered include the date and authorship of the Ethiopic text, and the reconstruction of the plurality of stages through which the text must have passed. These questions, it is thought, cannot be answered in isolation for the Book of Proverbs alone; even tentative conclusions must await further analysis of the data in many more books of the Ethiopic Old Testament.

Keywords: proverbs
Ethiopic