VictorJuiz/thesis huggingface dataset:
Cellular studies on the role of OGFOD1, a 2-oxoglutarate-dependent dioxygenase
Keywords: OGFOD1
2-oxoglutarate-dependent dioxygenase
RPS23
Ribosomopathy

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.
Pure states statistical mechanics: on its foundations and applications to quantum gravity
Keywords: Thermalization
Quantum Gravity
Black Hole
Quantum Information

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.
After antiquity: Joseph and Aseneth in manuscript transmission. A case study for engaging with what came after the original version of Jewish Pseudepigrapha.
Keywords: Syriac
transmission history
Armenian
Latin
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.
O-minimality, nonclassical modular functions and diophantine problems
Keywords: Diophantine Problems
Number Theory
O-minimality
Modular Functions
Andre-Oort
Zilber-Pink
Shimura Varieties
Logic
Model Theory
Pila-Wilkie Theorem
Unlikely Intersections

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.
An anthropology of processes of sensory learning and their implications for social differentiation in the field of contemporary perfumery
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

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".
From cohesion to fragmentation: a case study of the Ecuadorian indigenous movement
Keywords: Indigenous Movements
CONAIE
Ethnic politics
Social Movements
Pachakutik
Revolucion Ciudadana

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.
Transformational practices in fifteenth-century German music
Keywords: Schedels Liederbuch
Wolfenbüttel Lute Tablature
Glogauer Liederbuch
Neidhart
Lochamer Liederbuch
Buxheimer Orgelbuch
Oswald von Wolkenstein

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.
One startup's dream: an ethnography of a vision
Keywords: digital nomads
coworking spaces
ethnography
startups
paris
flexible work
coworking
worldmaking
startup
france
ethnomethodology
digital anthropology
marketing
western europe
entrepreneurship
workplace studies
digital nomadism

This is the story of how four people invented a whole new world and way of life—and how they attempted to establish it across the globe. Copass, a Parisian startup consisting of four cofounders, aimed to connect hundreds of the world’s shared workspaces under their new global federation. But the main objective of this startup, in contrast to most, was not to build capital. It was to build a universe: a future where white-collar workers would be liberated from the shackles of office life to work anywhere in the world, to meet exciting people and to have amazing experiences. Here, workdays were permanently mixed with holidays. Work was fun, workplaces were play-places and workers were adventurers. The ambition of these four cofounders was to turn the way they wanted things to be for them into the way things ought to be for everyone else. To turn their desired lifestyle into a global social movement that enrolled, as they saw it, hundreds of cities and thousands, tens of thousands, even millions of people. In short, they created a company to fulfil a dream. This is an ethnography of that one startup’s dream, analysed at length to demonstrate innovative ways of worldmaking employed by an ambitious tech company seeking success. A company dissatisfied with the world that, instead of changing it, decided to create a new one.
Essays on labor market dynamics with worker heterogeneity
Keywords: Life cycle models
Labor economics
Search and matching models

This thesis is comprised of three chapters which discuss topics related to labor market dynamics from a macroeconomic perspective. Although each chapter is self-standing in terms of research question and methodology, they are united by a common interest for the macroeconomic implications of worker heterogeneity. The chapters vary with respect to the time horizon over which they study aggregate dynamics, covering business cycle frequency, the economy's long run steady state, and households' life cycle. Furthermore, they develop the concept of heterogeneity across different dimensions: stages of the life cycle, households' income and wealth, observed worker characteristics, and worker-firm productivity levels. The overall purpose of this thesis is therefore to contribute to the study of labor markets and labor policies through a multi-faceted approach.
Landscape and connections: petroglyphs of the Altai in the 2nd and 1st Millennium BCE
Keywords: 1st millennium BCE
Mongolia
Connections
ArcGIS
Xinjiang
Landscape
Altai Republic
Altai
GIS
2nd millennium BCE
Northern China

This thesis presents a holistic study of connections in the Altai Mountains of the eastern Eurasian Steppe, as shown by rock-art. Currently divided by four countries, pecked images (petroglyphs) and painted images from the 2nd–1st millennium BCE have been subjected to very separate research traditions, exacerbated by language barriers. This thesis focusses on the entire Altai Mountain range as a study area, integrating research published in Chinese and Russian, with supplementary literature in Kazakh and Mongolian consulted.
To demonstrate the potential for connectivity and, consequently, movement, a map of accessibility was generated, showing that there are various optimal routes for movement throughout the Altai. The locations of rock-art sites relative to these routes indicate that movement was a key feature contributing to the creation of rock-art. Examining topographic features in the vicinity of rock-art sites of three regions (Mongolia, Russia, PRC) highlighted an association between watercourses and sites, whilst studying the micro-landscape within panels found that the creators of rock-art were not representing the tangible spatial relationship of figures to the landscape. More broadly, similarities between motifs at rock-art sites, as well as on portable art, demonstrate that the people making them, regardless of whether they were aware of it or not, were part of a wider understanding of how to depict subjects. Evidence of this understanding can be found even in regions with very different cultural backgrounds to the Steppe, such as the Chinese Central Plains, demonstrating that groups outside of the Steppe were aware of and using this way of representing. By combining analysis of motifs with that of the landscape, this thesis demonstrates that rock-art as a practice was inherently linked with to the landscape, whereas content and style are more indicative of a wide-ranging belief system amongst Steppe pastoralists, which was expressed aesthetically.
Investigations into the regulation of subventricular zone neuroblast migration by protein kinases
Keywords: Migration
Kinase
Regeneration
Subventicular Zone
Neurogenesis

The subventricular zone (SVZ) of the mammalian brain serves as one of only two sources of adult born neurons. Adult born neural progenitors – known as neuroblasts – acquire the ability to migrate and travel large distances to their destination in the olfactory bulb. Disruption of neuroblast migration is associated with learning and memory deficiencies and, following injury, neuroblasts are re-routed to promote neurodegeneration. While a lot of research has attended to augmenting the production and survival of neuroblasts, the body of evidence for pharmacological targets or compounds that promote migration is comparatively sparse.
This thesis set out to identify novel strategies to modulate neuroblast migration for brain repair by studying proteins known to modulate migration and identifying new ones through compound screening.
Firstly, an explant migration assay from the mouse SVZ was used to investigate the potential to use growth factors to stimulate neuroblast migration. This confirmed that that insulin-like growth factor 1 (IGF1) and IGF2 regulate neuroblast migration, as previously reported by other research groups. The role of IGF2 is investigated further using a mouse model in which the binding of IGF2 to IGF2R is disrupted, resulting in increased proliferation in the embryonic cortical SVZ, brain overgrowth and perinatal lethality.
In the second half of this thesis I try to tackle one of the major bottlenecks limiting the search in for pharmaceutical interventions targeting neuroblast recruitment: the lack of high-fidelity in vitro migration assays. Drawing concepts from existing in vitro migration assays and cerebral organoid models, I developed a novel neuroblast spheroid migration assays that permits the investigation of large numbers of interventions, concurrently, in 3 dimensions.
Using the spheroid assay I successfully screened 1012 small molecule kinase inhibitors for their effects on neuroblast migration. Several compounds were identified that significantly increased or decreased neuroblast migration. Two genes: MUSK and PIK3CB were selected from the screen as putative biological targets and genetic knockdown of these genes validated that interruption of their activity increased neuroblast migration. In the future these compounds could be studied further to explore their potential for augmenting the recruitments of new neurons to sites of injury so support neuroregeneration, or for decreasing invasion of brain malignancies.