VictorJuiz/thesis huggingface dataset:
Galois representations attached to algebraic automorphic representations

This thesis is concerned with the Langlands program; namely the global Langlands correspondence, Langlands functoriality, and a conjecture of Gross.
In chapter 1, we cover the most important background material needed for this thesis. This includes material on reductive groups and their root data, the definition of automorphic representations and a general overview of the Langlands program, and Gross' conjecture concerning attaching l-adic Galois representations to automorphic representations on certain reductive groups G over &Qopf;.
In chapter 2, we show that odd-dimensional definite unitary groups satisfy the hypotheses of Gross' conjecture and verify the conjecture in this case using known constructions of automorphic l-adic Galois representations. We do this by verifying a specific case of a generalisation of Gross' conjecture; one should still get l-adic Galois representations if one removes one of his hypotheses but with the cost that their image lies in CG(&Qopf;l) as opposed to LG(&Qopf;l). Such Galois representations have been constructed for certain automorphic representations on G, a definite unitary group of arbitrary dimension, and there is a map CG(&Qopf;l) → LG(&Qopf;l) precisely when G is odd-dimensional.
In chapter 3, which forms the main part of this thesis, we show that G = Un(B) where B is a rational definite quaternion algebra satisfies the hypotheses of Gross’ conjecture. We prove that one can transfer a cuspidal automorphic representation π of G to a π' on Sp2n (a Jacquet-Langlands type transfer) provided it is Steinberg at some finite place. We also prove this when B is indefinite. One can then transfer π′ to an automorphic representaion of GL2n+1 using the work of Arthur. Finally, one can attach l-adic Galois representations to these automorphic representations on GL2n+1, provided we assume π is regular algebraic if B is indefinite, and show that they have orthogonal image.

Keywords: Automorphic Representations
Galois Representations
Langlands Program
Advisor: Wiles, A
The ecology and evolution of complex microbial communities

Microbial communities colonise virtually every habitable environment on earth. They live on us, inside us, and all around us, and are key components of the earth’s ecosystem. However, due to the complexity of microbial communities we still understand relatively little about the mechanisms that drive their ecology and evolution. The aim of this thesis is to develop novel experimental and mathematical approaches, in order to investigate complex microbial communities. Specifically, this thesis is split into two parts, focussing in turn on how environmental complexity, and interspecies interactions shape microbial ecology and evolution. In the first part I have studied microbial evolution in porous environments such as one might find in soil or aquifers. Here I have combined microfluidic experiments, mechanistic models, and game theory to study how hydrodynamics mediate competition between bacterial genotypes. With these I have demonstrated how even subtle environmental complexity can fundamentally affect microbial competition, enabling slow growing genotypes to outcompete their faster counterparts. In the second part of this thesis I have investigated how interspecies interactions influence the stability and initial assembly of microbial communities. Here I have developed new tools – from theoretical ecology – in order to study the microbial communities within the mammalian gastro-intestinal tract. With these I have demonstrated how strong, cooperative interactions between species can undermine both the stability, and the assembly of communities. Moreover, I have illustrated how these tools can be applied to real microbiome data, in order to better understand these important communities. In sum, this thesis explores two key drivers of microbial ecology and evolution, and presents a new set of tools for the future investigation of complex microbial communities.
Consentius' De barbarismis et metaplasmis: Critical edition, translation, and commentary

This thesis consists of a critical edition, English translation, and commentary of Consentius' De barbarismis et metaplasmis. Consentius probably lived in Gaul in the fifth century, and this work was presumably part of a larger grammatical treatise; as it stands, it is the most extensive discussion of language deviations (errors in ordinary language and poetic licences) in the Latin grammatical tradition.
The critical edition has taken advantage from the availability of a manuscript and several sources of indirect tradition that were not used by previous editors. In the introduction, I provide a discussion of the tradition with a stemma codicum. The new text is quite close to that of previous editions, but arguably has several improvements. I also provide the first English translation of this work.
In the commentary, I look at the text from the points of view of historical linguistics and the history of linguistics.
The section on metaplasms is tightly embedded in the Latin grammatical tradition. This allows us to look into the grammatical approach to the poetic language. In particular, the role of archaisms is crucial in the grammarians' appreciation of poetry, and I analyse their views on this while also explaining the history and use of the forms Consentius and other grammarians discuss. An appendix to the discussion of metaplasms is the final section on the scansion of verses, which displays some original, if sometimes bizarre, views.
The section on barbarisms is most interesting for the language historian: as Consentius discusses errors that arise in spoken language, he provides evidence for substandard Latin that is unparalleled in ancient grammatical texts. I assess such evidence by looking at other grammatical treatises, substandard texts (literary or not), and the Romance languages. Several forms mentioned by Consentius foreshadow Romance developments. The text also provides us with information about the regional diversification of Latin.

Advisor: De Milo, W
Long range monocular SLAM

This thesis explores approaches to two problems in the frame-rate computation of a priori unknown 3D scene structure and camera pose using a single camera, or monocular simultaneous localisation and mapping. The thesis reflects two trends in vision in general and structure from motion in particular: (i) the move from directly recovered and towards learnt geometry; and (ii) the sparsification of otherwise dense direct methods.
The first contributions mitigate scale drift. Beyond the inevitable accumulation of random error, monocular SLAM accumulates error via the depth/speed scaling ambiguity. Three solutions are investigated. The first detects objects of known class and size using fixed descriptors, and incorporates their measurements in the 3D map. Experiments using databases with ground truth show that metric accuracy can be restored over kilometre distances; and similar gains are made using a hand-held camera. Our second method avoids explicit feature choice, instead employing a deep convolutional neural network to yield depth priors. Relative depths are learnt well, but absolute depths less so, and recourse to database-wide scaling is investigated. The third approach uses a novel trained network to infer speed from imagery.
The second part of the thesis develops sparsified direct methods for monocular SLAM. The first contribution is a novel camera tracker operating directly using affine image warping, but on patches around sparse corners. Camera pose is recovered with an accuracy at least equal to the state of the art, while requiring only half the computational time. The second introduces a least squares adjustment to sparsified direct map refinement, again using patches from sparse corners. The accuracy of its 3D structure estimation is compared with that from the widely used method of depth filtering. It is found empirically that the new method's accuracy is often higher than that of its filtering counterpart, but that the method is more troubled by occlusion.

Keywords: Scale drift
Monocular
Direct optimisation
Advisor: Murray, D
The man on the land: classics in colonial Australia

The 'man on the land', in his various guises – pioneer, bushman, farmer, Anzac – is an iconic figure in Australian culture. The nationalist tradition of which he is part has often been seen as vernacular and anti-British, with roots in the democracy of the bush in the nineteenth century. This thesis argues that ‘the man on the land’ was not autochthonous, and owes much to the classicising influences at work in New South Wales from European settlement to the First World War. It suggests that he is, in many of his manifestations, from smallholding farmer to dutiful soldier, a Virgilian figure, and that Virgil and other Greek and Roman texts were critical to shaping the narratives through which colonial Australians made claims to land. The role of the Classics in Australian culture in the nineteenth century has been largely overlooked, and needs to be reconsidered in the light of recent work on classical receptions in other postcolonial cultures. I look first at the reception of the Georgics in New South Wales; Virgil was central to the popular narrative in which the colony appeared as a nascent Rome. I then turn to counter-narratives in which the Australian continent appears as a classical underworld. I argue that Aboriginal Australians were compared to ancient peoples as part of a discourse that reinforced the idea that they were doomed to extinction. I examine debates over the value of classical education that took place in connection with the establishment of the University of Sydney; the reception of Tiberius and Gaius Gracchus in New South Wales; and the reinvigoration of the Virgilian tradition in C. E. W. Bean’s Anzacs. It is argued that recent Australian classical receptions need to be seen in the context of this long and diverse tradition of engagement with the classical past.

Advisor: Macintosh, F
The role of the lysine demethylases KDM5 and KDM6 in bone malignancies

Methylation of histone lysine residues functions as a dynamic, reversible mechanism for regulating gene expression and aberrations in this process have been linked with the development of cancer. Members of the lysine demethylase (KDM) family remove methyl marks from histones. KDM5B removes methyl marks from histone H3 lysine 4 (H3K4) whereas KDM6A and KDM6B remove methyl marks from histone H3 lysine 27 (H3K27).
In this thesis, GSK-J4, an inhibitor of KDM5B, KDM6A and KDM6B, is shown to impair viability in a range of cancers affecting bone including multiple myeloma, Ewing sarcoma and chordoma. GSK-J4 induces a biphasic transcriptional response, characterized by an early, massive rise in the expression of a number of cysteine-rich metallothionein genes followed by induction of ATF4 via phosphorylation of eIF2α by GCN2. Induction of ATF4 leads to apoptosis in myeloma cells and cell cycle arrest in Ewing sarcoma. Ectopic overexpression of metallothioneins is shown to be sufficient to induce the ATF4 response. GSK-J4 is shown to alters cellular metabolism by impairing glutaminolysis. ChIPseq demonstrates a global increased H3K27me3 in response to treatment with GSK-J4 with a decrease in H3K4me3 around transcription start sites of genes not involved in the ATF4 response. Combined knockdown of KDM6A and KDM6B recapitulates the cellular response to GSK-J4 whereas inhibition of KDM5B is not sufficient to reproduce the effect.
A model is presented suggesting that the increased requirement for incorporation of cysteine into protein due to the expression of metallothioneins leads to the presence of uncharged cysteinyl-tRNA molecules that are sensed by GCN2 leading to activation of an ATF4-driven integrated stress response.

Advisor: Oppermann, U
Athanasou, N
Optimising the left ventricular lead for endocardial and epicardial cardiac resynchronisation therapy

Cardiac Resynchronisation Therapy (CRT) is an effective treatment for selected patients with heart failure. The left ventricular (LV) lead used to achieve this can be hard to place via the coronary sinus in a proportion of patients, and in addition may not be in an optimal position in others.
In this thesis, I initially discuss CRT and its technical limitations. Using a large meta-analysis, I elucidate contemporary rates of LV lead placement failure. An alternative method of LV lead placement is endocardial, and I discuss results to date, again using a meta-analysis to summate prior trials and the technique’s risks and benefits. The main subject of the thesis is assessing a novel method of LV endocardial pacing via the interventricular septum. I report a trial of 19 patients in whom conventional CRT was not possible or unsuccessful, showing clinical response to CRT delivered in this manner to be similar to conventional CRT, with acceptable risks.
LV lead location in endocardial CRT has been little studied. I go on to investigate optimal LV lead positioning in this group, by assessing acute haemodynamic response (AHR) to CRT with a high-fidelity pressure wire and a multi-level modelling analysis. I show that this technique is reproducible. I compare placement at sites of late mechanical activation and late electrical activation, showing little difference in this cohort or in a parallel study of AHR in 22 patients undergoing conventional CRT. With a multivariate analysis I show that only electrical delay is a consistent predictor of acute response.
These results support the use of this novel technique for CRT as a second-line procedure, and I discuss future directions for this. Lead site selection at a site of late electrical activation is supported by my work, and again I summarise the context of this.

Advisor: Betts, T
The orientalising phenomenon on Crete, 9th-7th centuries BC

This thesis compiles and assesses orientalising artefacts from EIA Crete, which by definition are those that emulate Near Eastern models in design, style or technique. While oriental imports discovered on Crete have been the subject of several recent publications, there are currently no studies that deal with orientalising finds from the island in a similarly comprehensive manner. The aim of the present work is to fill this gap in scholarship and to provide a solid basis for interpretation. Following a multifaceted approach, the thesis offers an in-depth investigation of relevant pottery, terracottas, sculpture and metal finds. These classes of objects are investigated in terms of types, contexts and iconographies; they are then compared to potential Near Eastern models, which are examined in equal detail where appropriate. Based on this evidence, presumed connections to the Near East are challenged or substantiated while novel links are added, offering fresh insights into the meaning of the Cretan material. A critical revaluation of Cretan contacts with the Near East puts gained findings into a larger perspective of socio-political relations. The final part of the thesis suggests a new interpretation of the material, stressing the importance of Cretan agency, cultural self-definition and the multivalent nature of the orientalising phenomenon on the island.

Keywords: Crete
orientalising / orientalizing
Advisor: Lemos, I
Functional DNA nanotechnology

This thesis sets out to further the field of functional DNA nanotechnology through the design of novel functional DNA scaffolds, and investigates their applications and efficacy. The work presented here comprises two parts: The design of a chiral DNA nanotube that acts as a scaffold for motor motion and for an enzyme cascade; and the design of two different tetrahedral scaffolds for selection of a combination of three ligands, which together have a greater binding effect than the sum of the individual components.
It begins by proposing the design of a DNA origami nanotube which distinguishes between the inside and outside face of the tube at the design stage, which most previous designs reported do not. The previous designs in the literature result in a distribution of 50:50, of one face forming the inside surface on one tube and the same face forming the outside surface of a different tube. In the design presented in this thesis, this distinction results from making the tube chiral, which forces it to roll up in a predetermined manner. Chirality is introduced by varying the positions of staple crossovers and this process is explained. The chiral tubes may stack end-to-end to form long polymers, or exist in monomeric form with stacking suppressed, by inclusion of different sets of staples at the ends of the tubes. We confirm tube formation and right-handed chirality with AFM and CD respectively.
The efficacy of the tube as a scaffold for an enzyme cascade is tested and discussed in context of the wider field. No significant enhancement is observed when enzymes are tethered to the inside of the tubes, compared to when they are tethered to the outside or are free in solution, although the same slight trend is always observed. Suggestions are made to better this experiment and further understand the underlying physics of such systems.
We propose using the tube as a scaffold for a DNA track, upon which a DNA motor may walk. DNA motors are introduced and we attempt to observe micron-scale, inter-tube motion within the confines of our origami tube. Initial experiments show the motor moving and we propose methods of fluorescent labeling via PAINT to better the experimental set-up for TIRF microscopy, which currently is limited by photobleaching.
The second part of this thesis proposes systems for selection of a combination of three ligands, which together have a greater binding effect than the sum of the individual components. Here we design two tetrahedral systems where either three ligands or three aptamers are brought together at a vertex of the tetrahedron to form a binding domain. The aptameric system allows for selection, amplification and reassembly of the strongest binders, because the functional and structural sequences are on one strand of DNA, following ligation. This design betters the initial tetrahedral system, where the coding/record strands for amplification are separate from the functional binding domain strands the ligands are attached to. This means it is not possible to reassemble this particular structure after amplification of the record strand.

Advisor: Turberfield, A
Plasticity associated with Up/Down states in the mouse barrel cortex

Slow wave sleep is characterised by synchronised slow oscillations, which manifest themselves in cortical neurons as depolarised Up states and more hyperpolarised, silent Down states. Up/Down states have been implicated in synaptic plasticity during sleep-associated memory consolidation. However, the underlying mechanism is not well-understood.
I used the mouse somatosensory barrel cortex as a model system to investigate whether Up states and Down states differentially facilitate synaptic plasticity. Initial experiments were carried out in vitro in slices of barrel cortex. Here, Up states were evoked by electrical stimulation, making it possible to precisely control onset timing. Perforated patch-clamp recordings were obtained from pyramidal neurons in layer 2/3 to determine whether pairing of inputs with electrically-evoked Up states results in plasticity of the paired input. I found that pairing a train of EPSPs at different frequencies with Up states resulted in synaptic depression. However, there was no significant difference between Up states and Down states in their propensity to mediate plasticity of paired inputs. This lack of state-dependent plasticity could have been due to an insufficient number of pairings, as well as differences between electrically-evoked and spontaneous Up states in their ability to facilitate plasticity of paired inputs in the barrel cortex. To overcome these issues, plasticity was studied using long-term extracellular recordings in vivo under anaesthesia. Here, spontaneous Up states were automatically detected and paired with whisker deflections. While persistently pairing inputs with Up states led to long-term depression of the whisker response in the barrel cortex, Down state pairings did not induce any long-term effects. Taken together, results from experiments in vivo, but not in vitro, suggest that Up states facilitate depression of inputs in an activity-dependent manner.

Advisor: Mann, E
Regulation of MITF and TFEB

The bHLH-LZ transcription factors MITF and TFEB have been implicated in human disease, with their overexpression increasing the risk of developing cancer. The manner in which their access to E-box target motifs is controlled is an important consideration, as it is via binding to these motifs that bHLH-LZ factors mediate changes in gene expression. In addition to controlling the level of a given transcription factor, mounting evidence suggests that modulating MITF target specificity and TFEB access to the nucleus constitute an important means of regulating their functional output. Post-translational modifications offer one mechanism by which stimuli can rapidly and reversibly alter MITF and TFEB binding to their transcriptional targets.
This thesis aims to expand upon the already substantial literature examining MITF and TFEB post-translational modifications. Specifically, we confirm that MITF can be acetylated and that this occurs within the basic region of the DNA binding domain. Using a naturally occurring acetylation-mimicking mutation, we study the possible functional implications of acetylation on MITF residue K206. Turning to the closely related TFE family member TFEB, we show that TFEB nuclear translocation in response to multiple stimuli is reversible and at least partially mediated by a novel nuclear export signal in the TFEB N-terminus. We show that phosphorylation of nearby S138 by GSK3 requires a priming phosphorylation on S142 and that this latter event may activate an adjacent nuclear export signal.

Advisor: Goding, C
Filippakopoulos, P