VictorJuiz/thesis huggingface dataset:
The archaeology of middle Byzantie Aphrodisias
Keywords: classical archaeology
Byzantine Asia Minor
Byzantine archaeology
Byzantine coins
funerary archaeology

Aphrodisias is an ancient settlement in the valley of the Morsynos, a tributary of the Maeander in southwest Asia Minor. Excavation at the site has been ongoing since 1961, but to date most research has examined its ancient and late antique remains. The following thesis represents the first detailed study of the site during the seventh through thirteenth centuries, over which period a small Middle Byzantine town adopted and transformed the ancient topography. The thesis integrates material already published with several major new corpora of archaeological evidence, drawing upon archival records, museum depots and targeted fieldwork. These allow for a reconstruction of the fabric of the settlement and the exploration of the relationships that structured the community. The thesis is an exercise in settlement archaeology as social history, and a contribution to the study of the Middle Byzantine Maeander.
The first chapter presents a brief introduction to the study of Middle Byzantine urbanism, and situates the early excavations at Aphrodisias in their twentieth-century intellectual context. The second chapter takes the form of a topographic gazetteer of archaeological evidence for medieval activity and occupation, concluding with a discussion of the shape and extent of the town. The following three chapters then present detailed studies of different categories of evidence, making reference to four descriptive catalogues appended to the thesis. Chapter three addresses the monetary economy of the Morsynos Valley on the basis of 712 coins recorded both at the archaeological site and in the collection of the local museum. The fourth chapter analyses the corpus of marble liturgical sculpture, reconstructing the barriers and canopies that articulated the Middle Byzantine interiors of the town's churches. The fifth and final chapter discusses the three major cemeteries, closing with a short essay on the social context of death and burial. A brief conclusion interrogates the results of the thesis.
Days of revolution: Three essays on the effects of civil war dynamics in Latin America
Keywords: Latin America
Civil War

This doctoral dissertation studies the political effects of civil war dynamics at distinct conflict stages, with an empirical focus in Latin America. Concretely, it aims to address some of the following questions: How do distinct civil war dynamics affect subsequent institutional arrangements? Does exposure to violence from different actors affect civilian preferences towards peace? How do states distribute state power in the aftermath of conflict? Most of these questions have seldomly been treated in the literature of civil war studies. This dissertation aims to expand the debate on the variety of effects of civil war providing four core contributions:promoting the development of an analytical approach that conceptualizes conflict as processes with distinct phases; pushing towards an integrated agenda on political violence; advocating the necessity of engaging in actor dissagregation; and bringing the state back in into the analysis of internal armed conflicts.
In order to do this, this dissertation includes three articles. First, I provide across-national analysis focusing on the inter-relation between insurgent strength, intra-elite competition and coups d’etat, using a novel dataset of insurgencies operating in the region. Second, an article co-authored with Juan Masullo (Leiden University) studying the impact of violence against civilians on preferences towards the implementation of the Peace Agreement between the FARC-EP and the Government in the 2016 Colombian Referendum. And finally, a subnational analysis on the Sendero Luminoso rebellion in Peru (1980-1992), which traces the impact of the spatial distribution of wartime territorial control in the allocation of state capacity measures in the aftermath of conflict. The combination of these projects aim to provide new and important insights to the burgeoning research on civil war, but also to inform policymakers and international organizations about conflict processes and their capacity for intervention or resolution at different stages.
The origins of tolerant and repressive secularism: an analysis of the United States and France in comparative perspectives
Keywords: Turkey
path dependence
types of secularism
state–religion relations
political compromise
secularism
France
political victory
critical junctures
political conflict
periods of secular state-building
Senegal
the United States

In the field of political science, the term “secularism” is commonly understood as a statecraft doctrine that guarantees the separation between religion and state. A careful examination of history discloses that the United States and France are the two founding nations of this principle. Notwithstanding their common foundation of secularism, these two countries exhibit substantive variation in the implementation of this constitutional tenet — notably, in the extent to which they tolerate religious freedom and its expression. My thesis investigates the causal factors as to why the United States practices a tolerant form of secularism, which guarantees freedom of religion; while France exercises a repressive type of secularism, which is concerned with freedom from religion. For this purpose, my research project relies upon a qualitative analysis using comparative–historical methods and within-case process tracing. In essence, I argue that the outcome of the political conflict that occurred between liberal and conservative elites during the periods of secular state-building explains the type of secularism adopted by the country and its persistence in the mid-long run. After providing in-depth and theory-guided narratives of the American and French cases, I explore the external validity of my argument on two shadow cases, namely Senegal and pre-AKP Turkey. These brief studies echo the findings from my main cases by showing that the adaptation and persistence of tolerant secularism in Senegal is the result of a political comprise reached between liberals and conservatives during the country’s process of secular state-building similar to the United States; whereas liberals’ political victory over conservatives in Turkey during a comparable episode resulted in the imposition and persistence of repressive secularism like in France, until the AKP leadership managed to halt it.
Novel machine learning methods for cancer sequencing analysis
Keywords: mutation signature
cancer
whole genome sequencing
genomics
machine learning
copy number alteration
cancer evolution
single cell RNAseq

Heterogeneity is arguably one of the most important hallmarks of cancer which contributes to its drug resistance property. Cancer heterogeneity is the consequence of an evolutionary process during its development. Understanding cancer evolution will thus benefit the drug development field as well as clinical treatment of cancer.
In this thesis, I developed three novel approaches based on machine learning for the analysis of \correction{cancer evolution} using genomics data.
In the work related to mutation signature, I developed a novel approach using convolution filtering to detect new signatures. I showed that this new approach works better than existing method under certain condition and could be applied to longer nucleotide sequences.
In the work for copy number evolution, I developed a reinforcement learning approach to uncover the evolution history. I showed that this approach could recover the history more accurately than existing methods. It is also the first reinforcement learning approach developed in the field for cancer evolution.
In the work for high dimensional genomic data analysis, I developed an approach which jointly carries out dimension reduction and clustering. I showed that this method could recover the underlying latent structure of genomic sequencing data more accurately than existing methods and this method could be used for scRNA-seq data analysis as well as many other fields.
These novel methods developed could be used for more cancer genomic data to gain better understanding of the cancer evolution process in the future.
Investigating the regulation of ZUP1, a novel deubiquitinating enzyme involved in DNA repair, by coupled monoubiquitination
Keywords: coupled monoubiquitination
ubiquitin binding domain
Lys63 chains
DNA repair
deubiquitinating enzyme
DUB

Ubiquitination, a major post-translational modification, is reversed through the action of a large family of specialised proteases termed deubiquitinating enzymes (DUBs). Due to their involvement in key cellular pathways, such as inflammation, the cell cycle and DNA repair, as well as their potential as targets for therapeutic intervention, DUBs are critical to investigate. ZUP1 is a recently discovered DUB with cleavage specificity for lysine-63 conjugated polyubiquitin chains and has been proposed to have a role in DNA repair and genome stability maintenance via deubiquitination of the Replication Protein A complex. The regulation of DUBs is not well understood, but it has been suggested that ZUP1 undergoes a modification termed coupled monoubiquitination. Coupled monoubiquitination is a process whereby ubiquitin-binding proteins are monoubiquitinated themselves, which effectively abolishes their ubiquitin binding in trans, providing an inhibitory control mechanism. Here, by mutating two of the ubiquitin-binding domains of ZUP1, I show that ZUP1 monoubiquitination is dependent on the integrity of its ubiquitin binding domains, indicating that ZUP1 undergoes coupled monoubiquitination. Moreover, loss of monoubiquitination leads to a reduction in binding to another deubiquitinating enzyme involved in DNA repair, USP11 and its binding partner TCEAL1, an as of yet uncharacterised DNA repair protein. Together, I provide evidence that ZUP1 is regulated by coupled monoubiquitination which sets the foundation to further dissect the functional importance of this regulation in cells and to its enzymatic activity.
Poetry and provisionality in Republic X
Keywords: Republic
Socrates
Plato

This thesis investigates the attitude Socrates has towards his banishment of imitative poetry in Republic X. The standard view is that Socrates is entirely confident in this banishment in the sense that he considers it to be well-justified. Stephen Halliwell (2011) has argued that Socrates thinks that his banishment is not well-justified and that a convincing rebuttal to it is a live possibility, such that he is anxious about his banishment. This thesis develops and defends the view that Socrates oscillates between being confident in and anxious about his banishment of imitative poetry in Republic X. It argues that the standard view rightly detects confidence, but wrongly maintains that Socrates is entirely confident in his banishment. Likewise, it argues that Halliwell rightly detects anxiety, but wrongly maintains that Socrates is never confident in his banishment.
The poetics of subversion and conservatism: popular satire, c.1640 - c.1649
Keywords: satire
Milton, John
Cleveland, John
popular culture
Eikon Basilike
Phillips, John
English Civil Wars

The thesis deals with the satire produced by the popular print culture in London during the Civil War, examining the satirical texts in the wider context of Renaissance literature as well as in their immediate political and religious setting. The thesis applies the work of historians of popular culture to literary forms of popular expression in order to assess the rôle of the satirical pamphlet in Civil War society and politics. The social function of satire in effecting change in the perception of reality and in public opinion accounts for the deliberate "popular" manner of satirical texts in the 1640s; the satires printed as single-sheet quarto pamphlets exploit the book market and provide a rhetorical vehicle for Parliamentary and Royalist writers. Part I introduces the principal themes examined in the thesis, and provides a methodological framework for the analysis of 1640s popular literature. Furthermore, Part I discusses John Milton's notions of satirical propriety and suggests that Milton's polemical prose has a place among the satires of the 1640s. Part II argues that the ancient understanding of satire as curse provides in the 1640s the basis for the use of anagrams and typographical characters in satirical, formal malediction; the verse satire of John Cleveland (1613-1658) receives particular attention. Part III sets the notion of particular satire in the context of "libel" and the iconological controversy of the seventeenth century: lampoons and "pasquils" are consciously iconoclastic, marring the image of the person attacked. No more clearly is this seen than in the pamphlets responding to Eikon Basilike (1649) which use satire to break the image of the king. Part IV demonstrates the influence of the Greek satirist, Lucian, upon the satire of the 1640s in which heaven and hell feature prominently; Lucian is a particularly interesting example of erudite allusion in popular texts. Part V suggests that the preoccupation with order and disorder is central to the seventeenth century; a study of the function of representations of order, the Ptolemaic model of the cosmos in particular, in satirical and non-satirical texts leads to an examination of the rôle of parody in subverting order. The Appendix consists of a short analysis of A Satyr Against Hypocrites (1655) by Milton's nephew, John Phillips (1631-1706), demonstrating the influence of Milton on popular forms of satirical expression; aspects of satire treated in the thesis coalesce in the examination of Phillips's A Satyr Against Hypocrites.
Engineering transcriptional gene circuits in probiotics and mini SimCells for bacteria therapy
Keywords: minicell
synthetic biology
simcell
bacteria therapy

Numerous bacteria associated with human health (probiotics and pathogens) exhibit inherent properties in terms of targeting, penetrating, proliferating and killing solid tumours through various mechanisms. To rationally redesign these microorganisms into living medicine, there is a lack of genetic software with suitable induction characteristics and compatible cellular chassis with enhanced biosafety, owing to the stringent requirements and controllability during medical practice. Consequently, the development of bacteria therapy lags behind compared to other applications offered by synthetic biology.
The goal of this thesis is to address these two significant challenges to realise the full potential of bacteria therapy. Three different transcriptional control systems were constructed: (1) an aspirin/salicylate responsive regulatory SalR:PSal system (2) a DNA damage responsive Vibrio recA SOS system and (3) a nitric oxide responsive NorR:PNorV system. The system performance was rationally re-designed and optimised based on the detailed molecular mechanism. A universal competitive binding mechanism was found during the tuning process, where the expression level of the regulator played a dominant role in system dynamics and displayed dual activator/repressor features dependent on the state of inducer binding. To enhance the biosafety and usability, these genetic software were characterised and optimised in the cellular context of a probiotic chassis strain, E. coli Nissle 1917 and tested in the non-dividing anucleate E. coli mini SimCells, which are minicells with intact transcriptional/translational machinery. An optimised purification protocol was developed with a final yield of 5 × 10^9 mini SimCells/ml and high purity (total elimination of parent cells). Optimised sensor construct loaded in mini SimCells displayed functional responsive dynamics that (1) are robust against environmental fluctuation, (2) displayed faster response time (<30 mins), and (3) maintained medically relevant sensitivity. These findingsvalidated the programmability of mini SimCells to execute both ơ54 and ơ70 based transcriptional circuits and bypass host interference caused by global resource allocation or external fluctuation.
To conclude, this thesis provides a systematic workflow of designing therapy tailored transcriptional software and its functional deployment in mini SimCells. The circuits allow both external controls using established medical methods such as chemo/radiotherapy, aspirin injection or internal triggering via in-situ disease biomarkers, pave ways for the future pre-clinical development. Furthermore, this thesis demonstrates the potential of mini SimCells and its design guideline as a minimum version of bacteria-bot systems to achieve robust and sensitive performance, making it a preferred choice in clinical practice.
Citizen's Europe: free movement, free markets, and the making of Schengen
Keywords: globalisation
human rights
migration
European Union
Schengen

This thesis explores the roots of the 1985 Schengen Agreement and the 1990 convention implementing its terms. The central questions are why the Schengen system emerged, first among France, Germany, and the Benelux states, and how it transformed the principle of free movement of persons.
I use delegate lists, draft agreements, diplomatic memoranda, and confidential annexes — archived in state agencies and closed to public view for thirty years — to explore the backroom dealings that produced the accord. I reveal how free movement developed as a guarantee linked to the market but distinct from economic life — a concept that expressed aspirations for European citizens’ rights and that arose within the burgeoning human rights discourse of the postwar era. The account, also drawing on the voices of journalists and judges and unwelcome migrants, sets the development of the Schengen accord, a complex administrative instrument, against the backdrop of global and national events — the end of the Cold War, the fall of the Berlin Wall, cycles of economic recession and recovery, intensifying migration flows, and deepening fear of terrorism. All shaped the boundaries of free movement
I argue that Schengen’s crucial innovation was to classify the bearers of the freedom to cross borders as persons rather than as economic actors. Under the accord, all people who were nationals of EC member states became free to traverse Schengen’s internal borders. This differed from the 1957 Treaty of Rome, which predicated cross-border mobility on economic pursuits. Shorn of that condition, Schengen reinforced distinctions based on nationality in seeking to pair liberty with security, giving rise to new mechanisms of surveillance and crime control that produced an outcry from non-Europeans in the Schengen space.
The thesis contributes to greater understanding of globalisation and the integration of Europe; security and transnational sovereignty; and citizenship and individual rights.
Epic, idealism, and romanticism
Keywords: epic
romanticism
idealism

My opening argument is that Romantic aesthetics is grounded in a metaphysics for which epic is a fitting form. This metaphysics presents an ontological picture that endorses a substance monism that either claims mind to be this substance or includes mind as part of some neutral substance. I then argue for what I call ‘metaphysical Hegelianism about epic’, which is the view that epic’s ‘inner form’, to borrow Georg Lukács’s term, is characterised by concern with the limitation of the freedom of individuals by objective reality. Epic is characteristically concerned with two types of limitation particularly: limitation of the will, and limitation of freedom by the presence of other minds. The first of these leads to artistic consideration of the kinds of experience associated with apprehension of questions surrounding free will and determinism. The second leads to artistic consideration of the place of the individual agent in relation to the community. To show the epic’s preoccupation with mind-emphasising ontologies and normative models of agency, examples are given from the four main epics I discuss: The Prelude (1798-9, 1805, and 1850 texts), Sordello (first published 1840), Aurora Leigh (first published 1856), and Leaves of Grass (first published 1855). I then ask why epic consideration of these problems can be valuable. With reference to Romantic epistemology, I argue that art can provide knowledge that goes beyond what is possible for propositionally-based knowledge. Consequently, artworks must be experienced for the kinds of unparaphrasable knowledge they contain to be accessed. I suggest that a central function of the scholarship and criticism of art is to assist the experiencer in this experiencing. Finally, I discuss two different ways in which the word ‘epic’ is sometimes used: to describe the epic form; and to describe the experience of individual works in the epic form that satisfy certain conditions.
Imagining reality: Ritual visualization in Jīva Gosvāmī's Bhakti-Sandarbha
Keywords: Gauḍīya
imagination
visualisation
Vaiṣṇavism
ritual
Jiva
religion India

In Bhakti-sandarbha, the fifth volume of his seminal treatise, Ṣaṭ-sandarbha, the sixteenth century Indian religious thinker Jīva Gosvāmī presents a brief and tradition-specific description of a set of widely practiced meditation rituals that are preparatory to the worship of the representative-image of a deity, or mūrti. Whereas many traditions other than his own Gauḍīya Vaiṣṇavism regard the visualizations in these rituals imaginative, his descriptions couch their imaginative content in a paradox, namely: the imaginal of the deity visualized as part of this ritual enactment is not imaginative. Moreover, the prospect for reconciling this paradox is compounded by Jīva’s further classifying the mental-image as a non-visually manifest reality. Seeking clarity on the role of imagination in generating or capturing this reality, this thesis initially looks to the feasibility of various relationships between the mental-image and the non-imaginative object, such as those of representation and mediation. However, it turns out that these do not satisfactorily resolve the paradox. Eventually it is found that the paradoxical notion of reality in the imaginative rituals can be reconciled through addressing it in terms of the relationship between the imaginer and the imaginal. The exploration of this relationship takes this thesis beyond the analysis of mental-images and objects to the author’s appeal to an ancient dramaturgic and poetic theory which his tradition had mapped onto its theology. This theory analogically defines the reality accessed through imagination in the terms of a real participation of audience and actors in a play. For Jīva, real participation occurs in an imaginatively enacted cosmic play, the object of which is the deity’s original but ordinarily unseen theatre of activities. Although this is the described experience of those who no longer are required to perform rituals, it is nevertheless prefigured in Jīva’s articulations of ritual visualization and, hence, impact his expression of reality as accessed by imagination in the rituals.