VictorJuiz/thesis huggingface dataset:
Cellular studies on the role of OGFOD1, a 2-oxoglutarate-dependent dioxygenase

2-Oxoglutarate (2-OG) and iron (Fe2+) dependent Oxygenase Domain containing protein 1 (OGFOD1) is an evolutionarily conserved prolyl hydroxylase enzyme in mammals, invertebrates (Sud1 in D. melanogaster) and yeast (TPA1 in S. cerevisiae and Ofd1 in S. pombe). This enzyme modifies a residue corresponding to Proline-62 in humans of the small ribosome protein S23 (RPS23) that occupies a critical site within the decoding centre of the eukaryotic ribosome. A number of cellular phenotypes have been reported following OGFOD1 inactivation, including altered ribosome decoding, activation of translational stress pathways and reduced proliferation. In addition, studies in S. pombe have assigned a novel signalling function for Ofd1 in the regulation of sterol response genes via the Sre1 transcription factor. Collectively, these studies indicated functions for OGFOD1 in both translation and transcription. However, it was not known whether these functions are conserved in mammalian cells or if they are linked.
To inform on OGFOD1-dependent cellular phenotypes, OGFOD1 defective cells were generated by genome editing using the CRISPR methodology. Clones re-expressing the OGFOD1 transgene under the control of a doxycycline regulable promoter were subsequently derived, facilitating comparison of OGFOD1 status within an isogenic setting. These cells were validated by the generation and use of antibodies specific to the modification site (Pro-62) in RPS23. Surprisingly, genetic inactivation of OGFOD1 did not mimic the reported phenotypes observed by RNA interference.
To improve understanding of OGFOD1 function, immunoprecipitations of ectopic and endogenous OGFOD1-containing protein complexes were analysed by proteomic methods. The transcriptional regulator, Thanatos associated protein 11 (THAP11) was identified as a novel high stoichiometry OGFOD1-interacting protein across a range of cell lines. Analysis of the THAP11 transcriptional programme in SW620 cells defined a repressive action of OGFOD1 overexpression on THAP11 DNA binding and target gene expression. Reciprocal regulation of THAP11 signalling was not associated with OGFOD1 knockdown or genetic inactivation suggesting that THAP11 is not limiting in the steady state. Protein interaction studies revealed a direct association between the two proteins that was mediated by a region of THAP11 that shares sequence homology to the Ofd1-binding domain of Sre1. This, together with the observation that THAP11 forms a discrete association with the translational machinery, raises the interesting possibility that OGFOD1 performs an analogous regulatory function in mammalian cells to that described in S. pombe. These results provide a focus for future work dissecting the interrelationship between OGFOD1-dependent effects on transcription and translation.

Keywords: OGFOD1
2-oxoglutarate-dependent dioxygenase
RPS23
Ribosomopathy
Advisor: Cockman, M
Ratcliffe, P
Pure states statistical mechanics: on its foundations and applications to quantum gravity

The project concerns the study of the interplay among quantum mechanics, statistical mechanics and thermodynamics, in isolated quantum systems. The goal of this research is to improve our understanding of the concept of thermal equilibrium in quantum systems.
First, I investigated the role played by observables and measurements in the emergence of thermal behaviour. This led to a new notion of thermal equilibrium which is specific for a given observable, rather than for the whole state of the system. The equilibrium picture that emerges is a generalization of statistical mechanics in which we are not interested in the state of the system but only in the outcome of the measurement process. I investigated how this picture relates to one of the most promising approaches for the emergence of thermal behaviour in quantum systems: the Eigenstate Thermalization Hypothesis. Then, I applied the results to study the equilibrium properties of peculiar quantum systems, which are known to escape thermalization: the many-body localised systems. Despite the localization phenomenon, which prevents thermalization of subsystems, I was able to show that we can still use the predictions of statistical mechanics to describe the equilibrium of some observables. Moreover, the intuition developed in the process led me to propose an experimentally accessible way to unravel the interacting nature of many-body localised systems.
Then, I exploited the "Concentration of Measure" and the related "Typicality Arguments" to study the macroscopic properties of the basis states in a tentative theory of quantum gravity: Loop Quantum Gravity. These techniques were previously used to explain why the thermal behaviour in quantum systems is such an ubiquitous phenomenon at the macroscopic scale. I focused on the local properties, their thermodynamic behaviour and interplay with the semiclassical limit. The ultimate goal of this line of research is to give a quantum description of a black hole which is consistent with the expected semiclassical behaviour. This was motivated by the necessity to understand, from a quantum gravity perspective, how and why an horizon exhibits thermal properties.

Keywords: Thermalization
Quantum Gravity
Black Hole
Quantum Information
Advisor: Vedral, V
Consensus in conflict - the making of a common intellectual culture in Germany, c. 1920-1950

This study analyses intellectual continuities in bourgeois periodicals from Weimar to the early post-war period. Whereas publication bans and censorship in Nazi Germany have been researched in depth, my work focuses on journals that were continuously published from the 1920s to the 1940s and 50s. It seeks to analyse the compatibility of National Socialism with a whole range of worldviews and mind sets, which allowed educated Germans to fit in equally well in the Third Reich and the democratic systems by which it was preceded and followed whilst retaining a strongly intact sense of having ‘not been a Nazi’.
By examining intellectual overlaps in a variety of liberal, conservative, nationalist, Social Democratic, and Christian journals, this work revises our understanding of how Nazism was anchored in the intellectual culture of the Weimar Republic. It follows discussions of widespread catchwords, such as ‘masses’ and ‘elites’, ‘progress’ and ‘decline’, ‘Sachlichkeit’ and ‘Romanticism’ in order to identify common patterns of thought, which united a wide range of both supporters and opponents of the Nazi movement. While historians have traditionally described the 1920s and early 1930s as a period ridden by political clashes, my work thus reveals a hidden intellectual convergence underlying Germany’s open and violent conflicts.
Based on these observations, my dissertation then engages with different and often contradictory interpretations of Nazi ideology within the supposedly ‘unified’ framework of Nazi dictatorship after 1933. This study argues that middlebrow intellectuals of different political backgrounds, such as high school teachers or civil servants, often lived in the illusion of still pursuing their own ideals rather than simply conforming to the demands of the regime. Accordingly, the political integration of the educated middle classes required far less ‘conversion’, ‘unification’ and ‘Gleichschaltung’ from above than previously thought. Hence, instead of relying on these classical historiographical categories, this work sheds light on the mechanisms by which a plurality of ‘Nazisms’ was embedded in much older, deeper, and continuous traditions of German intellectual culture.

Advisor: Stargardt, N
O’Rourke, K
After antiquity: Joseph and Aseneth in manuscript transmission. A case study for engaging with what came after the original version of Jewish Pseudepigrapha.

The story of Joseph and Aseneth expands a few verses from the book of Genesis into a novella- length work. In recent years, the story has attracted considerable scholarly attention. Interest has focused on questions of provenance: whether the 'longer' or 'shorter' version of the text has prior- ity, and what this means for its interpretation. Like other works of the so-called 'Jewish Pseud- epigrapha', it is increasingly used as a source for Judaism and Christianity at the turn of the Com- mon Era. But few have engaged with the story's manuscript witness and transmission.
This thesis returns to the sources. It considers how the redaction and translation of Joseph and Aseneth affected its interpretation, and looks at the interests of the redactors and copyists. It warns against placing too much weight on details that lack such an importance in the manuscript tradition.
The introduction surveys modern secondary literature on the story. Section 1 investigates the translation and transmission context of the two earliest preserved versions, the Syriac and Armeni- an translations. Despite their text-critical importance, they have received little attention. Section 2 focuses on the Greek manuscripts of the three longest families (f, Mc, a). It argues that these re- dactions, and the variety within their witnesses, need to be understood within a Byzantine context, in particular, within hagiographic trends for works produced in monastic environment. Section 3 looks at how the story could be abridged and edited. It identifies the key elements of the story shared by redactors. Four versions are compared: family d, E, Latin 1 and so-called "early modern Greek". The appendices contain a synoptic presentation of Greek versions of the story, an edition and translation of the story from manuscript E, and a translation of the Greek text from manu- script 661.

Keywords: Syriac
transmission history
Armenian
Latin
Pseudepigrapha
Advisor: Salvesen, A
Weak integrability breaking and full counting statistics

In this thesis two questions of equilibrium and non-equilibrium properties in many-body quantum mechanical systems are investigated.
The first part is focused on probability distributions of quantum observables in many-body quantum systems. After an introduction to probability distributions, full counting statistics and the transverse field Ising model we give a brief overview over related experiments and then derive an expression for the probability distribution of the transverse field magnetization of a finite subsystem in any Gaussian state. We study the probability distribution in ground and thermal states as well as in a non-equilibrium setting after a quantum quench. We find an analytic expression for the time evolution after the quench and compare to numerics.
The second part of the thesis is concerned with the stability of exact quasi-particle excitations of an integrable model after weak integrability breaking perturbations are introduced. For this we first discuss the stability of excitations in integrable systems and then give an introduction to the Heisenberg XXX-model in a magnetic field. After constructing exact excitations we calculate the decay rate in leading order perturbation theory using methods of integrability.

Advisor: Essler, F
O-minimality, nonclassical modular functions and diophantine problems

There now exists an abundant collection of conjectures and results, of various complexities, regarding the diophantine properties of Shimura varieties. Two central such statements are the Andre-Oort and Zilber-Pink Conjectures, the first of which is known in many cases, while the second is known in very few cases indeed.
The motivating result for much of this document is the modular case of the Andre-Oort Conjecture, which is a theorem of Pila. It is most commonly viewed as a statement about the simplest kind of Shimura varieties, namely modular curves. Here, we tend instead to view it as a statement about the properties of the classical modular j-function. It states, given a complex algebraic variety V, that V contains only finitely many maximal special subvarieties, where a special variety is one which arises from the arithmetic behaviour of the j-function in a certain natural way.
The central question of this thesis is the following: what happens if in such statements we replace the j-function with some other kind of modular function; one which is less well-behaved in one way or another? Such modular functions are naturally called nonclassical modular functions. This question, as we shall see, can be studied using techniques of o-minimality and point-counting, but some interesting new features arise and must be dealt with.
After laying out some of the classical theory, we go on to describe two particular types of nonclassical modular function: almost holomorphic modular functions and quasimodular functions (which arise naturally from the derivatives of the j-function). We go on to prove some results about the diophantine properties of these functions, including several natural Andre-Oort-type theorems, then conclude by discussing some bigger-picture questions (such as the potential for nonclassical variants of, say, Zilber-Pink) and some directions for future research in this area.

Keywords: Diophantine Problems
Number Theory
O-minimality
Modular Functions
Andre-Oort
Zilber-Pink
Shimura Varieties
Logic
Model Theory
Pila-Wilkie Theorem
Unlikely Intersections
Advisor: Pila, J
An anthropology of processes of sensory learning and their implications for social differentiation in the field of contemporary perfumery

In this thesis, I explore distinct modes of developing sensory knowledge in the field of practice of perfumery. In particular, I discuss the often confrontational relationship that the classically educated perfumers have with the self-trained ones and argue that different practices can subsist within the reality of contemporary perfumery, leading to sometimes overlapping skills but completely different practices. Considering both cognitive and metacognitive approaches to enskilment, I opt for the latter given that the subject of enskilment is olfaction and that I look at sensory anthropology from a phenomenological perspective. I, thus, reject common ideas of knowledge transmission according to motor-based representations of kinaesthetic and proprioceptive information, in favour of Ingold's (2001) theorisation of “education of attention” following Gibson (1979).
Through an analysis of "learning-in-practice" (Lave and Wenger, 1991) in terms of social capital and social participation, I carry on with my thesis connecting Lave and Wenger's (1991) formulation of "legitimate peripheral participation" to Bourdieu's (1977, 1990) "theory of practice". On this premise, I see the reproduction of the dominant social group, which is objectively recognised as the perfumers' community of practice, in conjunction with tactics of exclusion and inclusion depending on the kind of training that a perfumer underwent. Regardless of institutionally trained perfumers' strong opposition to self-training, I identify any practitioner who made an occupation out of perfumery as a "perfumer".

Keywords: Jean Carles Method
Community of practice
Raw materials
Anthropology of knowledge
Institutional training
Habitus
Sensory anthropology
Contemporary perfumery
Policing of knowledge
Ethnographic portraiture
Transmission of knowledge
Perfumery
Perfumery school
Self-training
Social capital
Misappropriated knowledge
Olfactory memory
Scents
Givaudan
Bespoke perfumery
Institutional perfumers
Education of knowledge
Perfumes
Independent perfumers
Trainee perfumers
Legitimate knowledge
Advisor: Banks, M
From cohesion to fragmentation: a case study of the Ecuadorian indigenous movement

The following research tries to find a causal explanation of the transformation of the Ecuadorian Indigenous Movement, from its rise to its progressive decay in the first decade of the 21st century. The method used to understand this process has been the implementation of qualitative research, namely fieldwork interviews and path tracing processes to find critical junctures and the use of archive material. As a result, I will argue that the mechanisms that made the weakening of the Indigenous movement possible rely on two aspects: the movement’s decision to not pact with mestizo parties after the failed alliance with the ex-president Lucio Gutierrez and the instrumental use of the movement’s framing by Rafael Correa and his political project.

Keywords: Indigenous Movements
CONAIE
Ethnic politics
Social Movements
Pachakutik
Revolucion Ciudadana
Advisor: Payne, L
Receiver technology for radio astronomy and deep space communications

This thesis presents the design and development of a complete receiver system for a conversion project, which replaces the commercial receiver of a telecommunication antenna with a cryogenically cooled radio astronomy receiver. Part of the project is to explore the synergy between radio astronomy and deep-space communications, which share many technical requirements, but also have technical conflicts. Therefore, this thesis attempts to solve some of these technological issues and provides a design for a receiver system, where radio astronomy and communication applications can successfully share the same hardware and infrastructure.
The receiver system employs a FPGA-based digital signal processing backend, which enables the instrument to be used in three different operational modes, single-dish observation, interferometer observation, and deep-space communication.
The architecture of the receiver system includes a novel technical solution to stabilise gain drift when used in single-dish observation mode. Two stabilisation methods are discussed in detail, and their performance is verified by measurements. The white-noise stabilisation approach uses a modulated reference noise signal and the continuous-wave stabilisation approach uses a narrowband reference signal to track the change in am- plification. Both stabilisation methods showed excellent performance and are implemented to stabilise the gain drift of the receiver system.
A number of analogue signal components were specially designed for the receiver system in order to meet the requirements of the conversion project. One of these components is the compact quad-ridged orthomode transducer, which provides the transmission between the feed horn and the coaxial cables. Its design uses a novel approach to reduce significantly the transition length, while retaining a wide operational bandwidth.
Finally we present the design of the complete receiver system, which includes the development work and verification of the components that were built for this project.

Advisor: Jones, M
Holler, C
Current generation in photovoltaic cells

In this thesis we present an analysis of the operation of a particular type of hybrid photovoltaic device called a solid-state dye-sensitised solar cell. A mathematical model is used to describe the cell’s operation, from the moment the photon reaches the surface of the device, until it is collected at the end electrodes.
The invention of the solid-state dye-sensitised solar cells is recent and is part of the greater search for stable, low cost and efficient alternative means of energy generation. As the physical and chemical analysis has progressed in recent years, there is a need to establish a mathematical model to describe their behaviour. This thesis includes such mathematical analysis, based on our current knowledge of semiconductors and opto-electrochemical properties of solid-state material. The effect of these properties and of the geometry of the cell are examined in detail using analytical, but also numerical techniques that allow to circumvent the complexities involved.
In this thesis, we show how conducting electrons can be generated by absorbing photons within an internal dye layer and are then transported via diffusion in the device until they reach the electrodes connecting it to an external electric circuit. While there are several limiting factors in the analysis, including the geometry of the device, the mathematical model appears to agree qualitatively well with available data on the current generation of solid-state dye-sensitised solar cells.

Advisor: Breward, C
Please, C
Muench, A
Transformational practices in fifteenth-century German music

In this thesis I investigate transformational practices in the secular music of mid-fifteenth-century German sources. At the heart of the research are case studies of the Lochamer Liederbuch with its two sections—a song and a keyboard collection—and of the newly discovered Wolfenbüttel Lute Tablature. By analysing and comparing the different versions of pieces surviving in these and related sources I explore how they interacted and what the motivations and techniques behind their transformation were. The organist and lute player Conrad Paumann and his ‘School’ were central driving forces in this process, which led to numerous innovations, particularly in the development of instrumental music and its notation. I then investigate the question of the instrumental accompaniment of monophonic song and how the development of new instruments and techniques influenced and shaped the melody types in the late medieval sources. To do this, I consult the genre of Neidhart songs as an oeuvre of secular song that was cultivated and transmitted in sources from the thirteenth to the fifteenth centuries. The network of interdependencies between repertoires enables an analysis of transformational practices in the songs of Oswald von Wolkenstein, which are influenced by the Neidhart-genre. The analysis comes full circle with reworkings of his melodies in the Lochamer Liederbuch and related sources. The study shows that vocal music and instrumental intabulations influenced each other mutually to create new repertoires and styles. Amongst the most significant insights are the findings around the Wolfenbüttel Lute Tablature, which open up a field of hitherto unknown instrumental practices and playing techniques, particularly on the plectrum lute. The process of transferring intabulation techniques from the keyboard to other polyphonic instruments leads to the formulation of a coherent, ‘pan-instrumental’ style of solo intabulation in the fifteenth century.

Keywords: Schedels Liederbuch
Wolfenbüttel Lute Tablature
Glogauer Liederbuch
Neidhart
Lochamer Liederbuch
Buxheimer Orgelbuch
Oswald von Wolkenstein
Advisor: Strohm, R
Leach, EE