VictorJuiz/thesis huggingface dataset:
How do sister DNAs become entrapped within cohesin rings?

Sister chromatid cohesion (cohesion) is a process that ensures accurate segregation of genetic material into daughter cells during mitosis in eukaryotic cells. Cohesion is mediated by a highly conserved ring-shaped protein complex called cohesin. Cohesion is thought to arise from the topological entrapment of replicated sister DNAs inside the cohesin ring. Although cohesin can load onto, and topologically entrap individual DNAs prior to DNA replication, cohesion is established during S-phase in concert with DNA replication. Analysis of small circular DNAs in yeast has revealed that cohesion establishment can occur by two pathways operating in parallel. Firstly, cohesin can load onto replicated sister DNAs de novo in a manner that is dependent on the cohesin loading protein Scc2. Secondly, there exists a ‘conversion’ pathway in which cohesin binds to unreplicated DNA during G1, and remains associated with DNA throughout S-phase during which it is converted into cohesive cohesin. This process is independent of Scc2 but requires a group of replisome-associated factors which include Ctf4. Whether this cohesin conversion pathway generates cohesion of yeast chromosomes, and the molecular mechanisms underlying conversion, remain largely unknown. It is thought that opening of cohesin’s Smc1-Smc3 hinge is crucial for entrapment of individual DNAs, but whether this is the case for entrapment of sister DNAs is currently unclear. I have developed a unique assay to measure cohesion generated solely by cohesin rings associated with DNA from G1. Using this assay, we show for the first time that conversion of non-cohesive cohesin to cohesive cohesin occurs on S. cerevisiae chromosomes during DNA replication, and that this process does not require opening of the Smc1-Smc3 hinge. Furthermore, the conversion observed was significantly reduced by deletion of Ctf4 but not significantly impacted by inactivation of the cohesin loader Scc2. These data provide crucial mechanistic insight into the process of cohesin conversion, and unequivocally demonstrate that while hinge opening is required for loading of cohesin rings onto DNA, it is not required for conversion of these rings into cohesive forms.

Advisor: Srinivasan, M
Nasmyth, K
Criss-crossing creativity: on creativity, Wittgenstein, and artificial intelligence

Until lately, the view prevailed that creativity is the last stronghold of human supremacy, unconquerable by even the most intelligent machines. Yet, recent advances in artificial intelligence (AI) cast doubt on this cherished conviction: there are now programmes that generate music in the style of famous composers or produce paintings that are displayed in renowned galleries. In the face of these awe-inspiring algorithmic achievements, this thesis pursues two main goals. First, it devises a new set of conceptual tools for analysing human creativity. It presents a novel practice-based account of creativity which captures the multifacetedness and distributed character of this phenomenon. Ludwig Wittgenstein’s later philosophy, especially his remarks on rule-following, serve as a crucial source of inspiration in this context. The framework that will be developed overcomes the shortcomings of existing definitions and theories that pervade the philosophical and scientific literature on creativity. Secondly, this thesis examines whether and to what extent creativity can legitimately be attributed to machines in the era of AI. It engages critically with influential objections to the notion of computational creativity and assesses the creative potential and limitations of state-of-the-art AI systems. The proposed approach challenges strong forms of anthropocentrism as well as the hyperbole evoked by recent developments in deep learning. So, the present work is not just a contribution to the emerging philosophy of creativity, but also to the blossoming philosophy of AI. The thesis concludes with a speculative exploration of possible conceptual futures for “creativity” in the face of potential future machines with superhuman creative powers.

Keywords: creativity
artificial intelligence
Wittgenstein
generative AI
AI
Advisor: Mulhall, S
Morgan, B
Weird music: reading John Ireland and Arthur Machen in tandem

John Ireland’s music divulges a more sophisticated relationship to literary influences than has traditionally been explored. Despite broad recognition of his literary interests, this thesis argues that Ireland’s enthusiasm for and engagement with the work of his professed favourite writer, Arthur Machen (1863-1947), is at best fractionally understood. This thesis submits that Ireland’s music is entwined preternaturally with a literary figure whose defining characteristic, ‘weirdness’, grants his music and life a comparable quality, thriving off a complex and ambiguous language of interdisciplinary systems and symbols, and contributing a singular body of work to the repertoire of early twentieth-century music.
Providing contextual frames for works by both artists, this study takes as its point of departure the concept of ‘weirdness’ as it pertains to Machen’s post hoc classification by S.T. Joshi as a progenitor of ‘weird fiction’. Reconstructing the worldview that inspired and sustained Machen’s writings through literary criticism, socio-cultural movements, and aesthetic and philosophical systems, it is demonstrated that Ireland’s subsequent compositions and artist-persona emerged from an absorption of the defining principles of Machen’s work with an emphasis on schematizations of weirdness. As such, it is argued that Ireland’s life and work can only be properly perceived within the context of Machen’s own writings; they must be read in tandem.
By placing Machen’s writings within concurrent aesthetic and cultural contexts animating notions of weirdness, this thesis establishes a discourse between these elements and representative compositions by Ireland that were composed after his discovery of Machen’s work in 1906. This analysis evinces that a sympathetic understanding of Ireland’s work and character benefits substantially from a dissection of the intricate interaction between his and Machen’s works; between assorted cultural and aesthetic elements of English music, literature, and landscape; between the reception of his works by contemporaneous and contemporary critics; and by contemplating further the aesthetic and philosophical implications of his music for English musicology, musical ontology, and notions of weirdness in art and artists.

Keywords: Arthur Machen
John Ireland
Advisor: Grimley, D
Automated analysis of heterogeneous catalyst materials using deep learning

Heterogeneous catalyst materials play a key role in modern society, as many processes in the chemical and energy industry rely on them. Optimising their performance is directly connected to a large potential of reductions in energy consumption, and thus to a more sustainable future. A fundamental part in the optimisation process is represented by materials characterisation. This is often done using in situ (Scanning) Transmission Electron Microscopy ((S)TEM) imaging in order to obtain a full understanding of the catalyst performance in different environments and temperatures at high resolution. However, the analysis of corresponding dynamical datasets is often time-consuming and requires manual intervention alongside tailored post-processing routines. At the same time, the emergence of direct electron detectors allowing for the acquisition of datasets at kiloHertz frame rates, as well as novel imaging techniques raised data generation rates significantly and created a need for new, reliable and automated data processing techniques.
This work introduces nNPipe as Deep Learning based method for the automated analysis of morphologically diverse heterogeneous catalyst systems. The method is based on two Covolutional Neural Networks (CNNs) that were exclusively trained on computationally generated HRTEM image simulations and allow for rapid and precise analysis of raw 2048 x 2048 experimental HRTEM images. The performance of nNPipe is demonstrated in a realistic automated imaging scenario where statistically significant material properties are inferred accurately. Moreover, time-efficient and reproducible retraining methods based small experimental datasets are described for both, further performance improvements and adaption to new imaging scenarios. In this context, a potentially new pathway for the generation of suitable training datasets obtained by thousands of mostly non-expert annotations is highlighted. Finally, the analytical capacities of the nNPipe method are showcased on time-resolved datasets in two advanced applications scenarios: i) Live image analysis during sample acquisition and ii) Analysis of the particle coalescence of an in situ heated Pd/C catalyst.

Keywords: HRTEM
deep learning
nanoparticle
heterogeneous catalysis
machine learning
electron microscopy
computer vision
image analysis
Advisor: Kim, J
Kirkland, A
Additive manufacturing of ni-based superalloys: effects of composition

Additive manufacturing (AM) is now reaching maturity as a method for processing metal alloys. It promises to bring about multifunctional component design integrating fully digital manufacturing. However, preventing cracking during processing remains a key challenge to overcome. This is of particular importance for the Ni-based superalloys used in high temperature applications such as aeronautics and power generation. In this work the effects of alloy composition on the cracking tendencies and performance of Ni-based superalloys are investigated. This study is motivated by the need to develop a better understanding of how to design new alloys specifically tailored for AM. A set of fifteen different compositions – some heritage and some novel – are studied in order to elucidate composition-microstructure-property relationships in 3D-printed Ni-based superalloys. Quantitative characterisation procedures are here developed to distinguish the two dominant cracking types that occur during AM: solidification and solid-state cracks. Experiments are carried out to explore the effects of alloy composition on the thermophyiscal, thermo-mechanical, and microstructural properties of the alloys and how these relate to the cracking phenomena observed. The magnitude of the ductility- dip (exacerbated by increasing amounts of solid solution strengthening elements) and the solidification path (widened by greater interstitial content) are unambiguously proven to be the critical factors giving rise to solid-state and solidification type cracks respectively. A model for solid-state cracking is proposed, based on an incapacity to relax the thermal stress and withstand the thermal strain arising from differential thermal contraction. This is supported by the development of novel methods for measuring the stress development during constrained cooling using electro-thermal mechanical testing. Stress relaxation by creep was found to be inconsequential during constrained bar cooling given the rapid cooling conditions of AM. This suggests that the development of highly creep resistant yet readily processable alloys is possible. The influence of the (Nb+Ta)/Al ratio is studied to tailor the properties of the novel alloys. This ratio is determined to dictate the trade-off of strength in the athermal regime, creep resistance, oxidation assisted cracking resistance, and oxidation resistance at high temperatures via alumina scale formation. The novel alloys print to γ phase and following sub-solvus heat treatment (with no solutionizing step) generate desirable γ/γ′ microstructures tied to good properties. Further assessment of the high temperature oxidation behaviour of all fifteen alloys provides alloy design guidelines for developing oxidation-resistant alloys for AM. In summary, this work highlights the potential to develop new alloys specifically for AM with properties matching those of the heritage ones designed for investment casting.

Keywords: metallurgy
superalloys
3D Printing
cracking
additive manufacturing
alloy design
Leonidas of Tarentum, Fifty-nine epigrams: text, translation, and commentary

The present thesis is an edition with translation and commentary of 59 epigrams of the Hellenistic poet Leonidas of Tarentum. It starts with an Introduction which, after briefly tracing the history of the scholarly work on Leonidas, considers general aspects pertaining to his life, his work, and his poems. The transmission of text is outlined (medieval transmission, papyri, epigraphic evidence, quotations). Leonidas is then placed in his historical and cultural context and his potential links with historical figures and poets of the Hellenistic age are treated, as well as his reception in Antiquity. Lastly, his language and style are outlined, followed by observations on the metre of his poems. There follows the text, translation and commentaries of selected epigrams. These are chosen from three macro-categories (dedicatory, sepulchral and ‘miscellaneous’ epigrams) and are arranged according to their theme. Some general observations precede specific groups of epigrams. The commentary deals with all relevant aspects of the poems, such as text, interpretation, 'Realien', and matters of style, metre and diction.

Keywords: epigram
Hellenistic Literature
Leonidas of Tarentum
Hellenistic Epigram
Hellenistic Poetry
The knowledge of afterthoughts: a comparative reading of the poetry of Caproni and Sereni

The present work explores the idea that one of the forms of knowledge literature produces can be understood in terms of afterthought. It focuses on the retrospective attempts to understand that characterise two poetic collections both published in Italy in 1965, Vittorio Sereni’s Gli strumenti umani and Giorgio Caproni’s Congedo del viaggiatore cerimonioso & altre prosopopee. Sereni often laments the long years it takes him to write a poem, the despair he feels, and the shame that follows for caring so much about poetry. This fluctuation between hope and guilt, meaning and non-sense, far from being just a biographical detail, becomes what life and literature seem to have in common, and what his poetry sets out to investigate by using the resources of the ‘parlato-scritto’ (to use Giovanni Nencioni’s term) to create a cohesive and yet open structure. Caproni’s poems combine everyday discourses and poetic form to scrutinise the little we can reach, express, and communicate. The possibility of pointing at reality through deictics, or of connecting words thanks to rhyme, is carefully analysed to verify whether a residue of sense can be found in the structures we rely on to make sense of our lives despite their apparent emptiness. Sereni’s and Caproni’s ideas and texts are studied through a broad set of comparisons, as one of the ways in which the claim that literature can know is explored in this thesis is by using literary works to understand each other. This methodology is outlined through the figure of the critic-reader and aims at exploring a possible response that critical works may offer to the afterthoughts of literature, considering the hypothesis that we may know something better after having read a text in thinking back to certain passages that struck us, comparing them to other ones from that or other books, and to what we have learnt through our experiences.

Keywords: comparative literature
contemporary Italian poetry
knowledge
literature
Totalism

Totalism in population axiology is the view that one population is better than another if and only if it contains greater total wellbeing. This thesis defends Totalism. I begin, in Chapter 1, by arguing for the principle of Anonymity, according to which any two populations with the same anonymous distribution of wellbeing are equally good. Chapter 2 argues against Prioritarian population axiologies on the basis that they imply the desirability of welfare diffusion: the implausible claim that it can be better for there to be less total wellbeing spread thinly between a larger total number of people. Chapter 3 argues against the popular intuition that adding good lives within a certain range cannot result in a better population. Chapters 4 and 5 provide new evidence for the unavoidability of the Repugnant Conclusion, the controversial implication of Totalism which holds that a smaller population of excellent lives can be worse than a much larger population of mediocre lives (and which is traditionally considered to be a damning objection to Totalism). Chapter 6 argues for a version of Totalism applicable to prudence in fission cases: cases where an individual “splits” into two or more successors, while retaining what matters in survival. Finally, Chapter 7 ties things together and summarises several direct arguments for Totalism. With the exception of Chapter 7, which makes extensive use of results and notation from earlier parts of the thesis, each chapter is entirely self-standing and can be read independently of the others.

Keywords: repugnant conclusion
fission
population axiology
total utilitarianism
prioritarianism
population ethics
procreation asymmetry
totalism
impossibility theorems
Advisor: Thomas, T
Greaves, H
'Putting your heart on the screen': an ethnography of young filmmakers in Israel


Putting Your Heart on the Screen explores a new generation of Israeli filmmakers whose approach to filmmaking is defined by their conviction that they both must and can only make films about their own painful experiences—what they call their ‘heart’ (lev). It introduces a new approach to the complex subjective processes at play within film production via its focus on the intersections between this new genre of personal films and the subjectivities and lived experiences of the filmmakers who make them. The thesis draws primarily on 14 months of fieldwork conducted in Israel (2018–2019) that involved observing and participating in the everyday working and learning practices of young filmmakers. The thesis identifies and interrogates the influences that shaped the form and content of their work, developed their ways of knowing, and crystallized their conceptions of what types of film are worth making.
The thesis argues that the widespread desire among the young filmmakers to make ‘personal films’ emerged from a regime of truth that has become dominant at the expense of other forms of truth telling—a regime in which the truth that the creative subject seeks to uncover and represent is her own ‘wounded heart.’ ‘The heart’ is analysed as a historically particular form of truth that lies at the centre of a complex discursive apparatus consisting of ethical practices, affective orientations, aesthetic forms, spatial components, and economic relations, all of which come to inform the creative practice of filmmaking. In this way, the thesis ethnographically demonstrates how larger cultural formations shape subjectivity, thereby contributing to scholarly understandings of the effects of identity politics in the form of personal, painful, and subjective experiences, at the microscale of how people think of themselves and others.

Keywords: affect
neoliberalism
filmmaking
ethics
film
university
media
ethnography
film production
subjectivity
cultural production
anthropology
education
schooling
Israel
Advisor: Dzenovska, D
Adaptive robust control with statistical learning

In stochastic control problems the agent chooses the optimal strategy to maximise or minimise the performance criterion. The performance criterion can be either the expectation of a reward function for the standard control problem or the non-linear expectation for the robust control problem. In parameterised stochastic control problems, the agent needs to know the value of the model parameters in the stochastic system to specify the optimal strategy correctly. However, it is hardly the case that the agent knows the values of the model parameters.
In this thesis, we aim to study a robust stochastic control problem where the agent does not know the values of the parameters of the underlying process. Therefore, we frame the stochastic control problem where we assume that the agent does not know the values of the model parameters. However, the agent uses the observable processes to estimate the values of the model parameters while simultaneously solving the stochastic control problem in a robust framework.
There are two key components in this new stochastic control problem. The first component is the parameter estimation part where the agent uses the realisation of the underlying process to estimate the unknown parameters in the stochastic system. We particularly focus on online parameter estimation. The online estimator is an important ingredient for our stochastic control problem because this type of estimator allows the agent to obtain the optimal strategy in feedback form. The second component is the stochastic control part which is the question of how to design a time-consistent stochastic control problem that allows the agent to also estimate the parameters and optimise her strategy simultaneously. In this thesis, we address each component of the problem above in the continuous-time setting and then the utility maximisation problem under this framework is studied carefully.

Keywords: stochastic control
model uncertainty
algorithmic trading
statistical learning
stochastic gradient descent
Advisor: Cartea, A
πολὺν γέλων: laughter, humour & Greek tragedy

This DPhil builds upon the relatively limited prior research into laughter and humour in Greek tragedy. Recent and long-standing social theories of laughter are introduced to account for the textual instances of γέλως ‘laughter’ vocabulary in extant tragedy, clarifying its associations and consequences in the dramatic context. As laughter and humour are not one and the same, cognitive theories of humour are also employed to elucidate scholars’ perceptions of comic elements and even jokes in tragedy. Humour is traditionally associated with tragedy’s sister genre, Old Comedy, and so common comedic tropes appearing in tragic contexts are identified and analysed as potential sources of audience amusement. Euripides’ reciprocal parodic engagement with Aristophanic paracomedy is assessed, and this framework is extended further to address Euripides’ apparent parody of Sophoclean and Aeschylean tragedy too. Performance theory, and particularly that of theatre clowning, is introduced to account for certain characters’ rather idiosyncratic relationships to laughter and humour. An analysis of laughter and humour disputes the various aesthetic, ethical and affective arguments against comic interpretations of tragedy, simultaneously challenging inherited interpretations of humour that are perhaps grounded more in the cultural prejudices of receiving cultures than in the ancient texts themselves.

Keywords: Sophocles
parody
Aristophanes
laughter
clown
old comedy
joke theory
Aeschylus
humour
tragedy
comedy
play theory
Euripides
Greek tragedy
Advisor: Scullion, S