VictorJuiz/thesis huggingface dataset:
Symeon Stylites the Younger and his cult in context: hagiography and society in sixth- to seventh-century Byzantium

This thesis explores the relationship between hagiography and history, with a particular focus on the cult of the little-studied sixth-century Antiochene holy man Symeon Stylites the Younger. It argues that any hagiographic text can only be understood through an appreciation of both its particular historical context and of developments in the genre over time. The first chapter thus addresses the economy, society and culture of the Antiochene area, arguing, against some recent archaeological interpretations, that sixth-century natural and military disasters did have a significant impact on the region. The second chapter turns to the first text associated with Symeon's cult, the sermon collection attributed to the stylite, which reveals how a holy man could construct his own spiritual authority through powerful rhetoric. Starkly polarised in his thought, Symeon eschews the compromises adopted by many clerical preachers, focusing on the opposition of demon and monk, rich and poor, and heaven and hell. The third chapter addresses the Life of Symeon, arguing that it can be read as an extended apology for Symeon's failure to protect the Antiochene from the disasters of the sixth century. The fourth chapter looks at the Life of Martha, Symeon's mother, which contains an original and inclusive vision of holiness, focusing not on asceticism or celibacy but on the redemptive powers of liturgy and the sacraments. The fifth chapter takes a step back, arguing that both Lives reflect broader developments in hagiography in the late sixth and seventh centuries: Symeon's hagiographer's struggle to justify disasters are echoed in other near-contemporary saints' Lives, while Martha's Life resembles in many respects the posthumous miracle collections which flourished in this period and were, in their relatively narrow focus, very suitable for a time of crisis.

Keywords: holy men
earthquakes
Stylite
late antiquity
hagiography
holy women
Byzantium
sermons
Advisor: Booth, P
Ancient mortar production in Ostia, Italy: builders and their choices

The main objective of the research discussed in this thesis was to evaluate the methods and materials used by builders in ancient Ostia to produce mortar for masonry structures. The work was conducted with an eye toward understanding why the ancient builders selected specific materials and employed specific techniques. The research design included scientific investigations of mortar samples from selected structures in Ostia, all dated from brick stamp evidence to the 2nd century CE. The methods employed for this study included thin section petrography, modal analysis via point counting, scanning electron microscopy, X-ray diffraction, and image analysis. Results concluded the samples comprised lime binder and primarily volcanic tuff aggregates derived from the Colli Albani and Monti Sabatini volcanic districts. The selection of these aggregates was integral to mortar performance, as they contained alteration products that would have facilitated pozzolanic reactions during the production phase, greatly improving long term mortar performance and durability. Three distinct types of mortar representing unique mix designs were identified based on the material properties of the mortar samples and the dominant aggregate types. Unique mixes may have been proprietary to specific groups of builders in Ostia, which had been identified by other researchers comparing the architectural features and construction styles of various structures. The results of material analyses showed that the builders from 2nd century Ostia were highly skilled, used sophisticated techniques to produce high quality mortar, and that separate groups of builders employed unique mix designs to achieve similar results.

Keywords: pozzolana
mortar
archaeological science
opus caementicium
petrography
Ostia
concrete
Advisor: Pollard, M
DeLaine, J
Jackson, M
Role of Pcf11 post-translational modifications in gene expression

mRNA export is one of the major steps in the regulation of gene expression as it provides the link between gene transcription in the nucleus and mRNA translation in the cytoplasm. Efficient export of mRNAs requires the formation of mRNPs at the sites of transcription consisting of the mRNA in complex with export and transcription factors. Formation of the mRNPs is tightly coupled with the co-transcriptional processes of capping, splicing and polyadenylation of the transcript.
Our work focuses on the core termination factor Pcf11, a component of the Cleavage Factor II complex in mammals. Pcf11 is an essential protein in yeast and it has been shown to participate in 3' end formation of the transcript (cleavage and polyadenylation) as well as in the release of RNA polymerase II from the DNA.
We discovered the phosphorylation of 2 residues in the CID domain of human Pcf11. The CID domain is responsible for the interaction of the factor with the CTD domain of RNA polymerase II. Furthermore, we identified Wnk1 as the kinase responsible for this phosphorylation. Our experiments show that phosphorylation of Pcf11 CID by Wnk1 disrupts its interaction with RNA polymerase II. Further analysis of Wnk1 and its role in the nucleus revealed that this kinase participates in mRNA export.
We propose a model, where phosphorylation of Pcf11 CID by Wnk1 is required for proper mRNP assembly and release from the site of transcription. Our data identify a new role for Wnk1 in gene expression regulation through mRNA export and new insights into the cross-talk between transcription termination and mRNA export.

Advisor: Proudfoot, NJ
Textural and petrological studies of anatexis and melt transfer in the Himalayan Orogen

Mineral textures, preserved in the metamorphosed sedimentary sequences that are exposed in orogenic hinterlands, are crucial to understanding the architecture and evolution of collisional mountain belts. In this thesis the textural record of anatexis and melt transfer in the Himalayan metamorphic core is decoded and the controls that these processes exert on the tectonic evolution of the Himalaya are explored. The problem is divided into two parts, corresponding to variations in protolith lithostratigraphy: melt source – the pelitic region where melt was first generated, and melt sink – the psammitic region where melt accumulated and crystallised. Dehydration melting of muscovite has long been recognized as a critical reaction for the generation of anatectic melt in the Himalaya, but a textural understanding of how this reaction progresses is limited by the inherent difficulties in identifying specific reaction products. Using samples collected from the Langtang area in central Nepal, a mechanistic model for muscovite dehydration melting was constructed, and a set of textural criteria were developed, which were used to distinguish peritectic K-feldspar from K-feldspar grains formed during melt crystallisation. Melt is transferred from the source to the sink in two stages: firstly along a pervasive network of mineral grain boundaries, and secondly via a channelised network of sills and dykes in the melt sink where it solidified as leucogranite. Variation in the primary mineral assemblage and appearance of leucogranite bodies reflect the degree of interaction that occurred between the melt and metasedimentary country rock, rather than a change in primary melt composition. The modal proportion of K-feldspar in the melt source requires vapour-absent conditions during muscovite dehydration melting and leucogranite formation, indicating that the generation of large volumes of granitic melts in orogenic belts is not necessarily contingent on an external source of fluids. The crystallisation of hydrous minerals in leucogranite consumes &LT;15.5 % of water released by the breakdown of muscovite. These results indicate that anatexis efficiently dehydrates the middle crust and suggests that the continents have limited potential to store water over geological time.

Keywords: Petrology
Muscovite dehydration melting
Anatexis
Advisor: Waters, D
Searle, M
St-Onge, M
Conditional many-body dynamics and quantum control of ultracold fermions and bosons in optical lattices coupled to quantized light

We study the atom-light interaction in the fully quantum regime, with the focus on off-resonant light scattering into a cavity from ultracold atoms trapped in an optical lattice. Because of the global coupling between the atoms and the light modes, observing the photons leaking from the cavity allows the quantum nondemolition (QND) measurement of quantum correlations of the atomic ensemble, distinguishing between different quantum states. Moreover, the detection of the photons perturbs the quantum state of the atoms via the so-called measurement backaction. This effect constitutes an unusual additional dynamical source in a many-body strongly correlated system and it is able to efficiently compete with its intrinsic short-range dynamics. This competition becomes possible due to the ability to change the spatial profile of a global measurement at a microscopic scale comparable to the lattice period, without the need of single site addressing. We demonstrate nontrivial dynamical effects such as large-scale multimode oscillations, breakup and protection of strongly interacting fermion pairs. We show that measurement backaction can be exploited for realizing quantum states with spatial modulations of the density and magnetization, thus overcoming usual requirement for a strong interatomic interactions. We propose detection schemes for implementing antiferromagnetic states and density waves and we demonstrate that such long-range correlations cannot be realized with local addressing. Finally, we describe how to stabilize these emerging phases with the aid of quantum feedback. Such a quantum optical approach introduces into many-body physics novel processes, objects, and methods of quantum engineering, including the design of many-body entangled environments for open systems and it is easily extendable to other systems promising for quantum technologies.

Keywords: Quantum measurement
Ultracold atomic gases
Measurement backaction
Conditional dynamics
Advisor: Mekhov, I
From teacher-regulation to self-regulation in early childhood: an analysis of Tools of the Mind’s curricular effects

The aim of my DPhil is to identify educational practices predictive of students' self-regulation development during early childhood. Specifically, I will analyze the Tools of the Mind preschool curriculum (Tools), which emphasizes students’ self-regulation cultivation as its paramount aim.
Since its development in 1993, Tools has spread to schools in the United States, Canada, and South America. In the face of Tools' proliferation, two questions emerge: does Tools significantly improve children's self-regulation skills? And, if so, then which of its effective elements could be applied across various educational contexts?
This dissertation contains two studies. In the first, I will systematically review extant Tools research and then execute a multilevel meta-analysis of the quantitative results. Study one serves three purposes: 1) to identify all studies in the existing Tools evidence base, 2) to estimate an aggregate curricular effect, and 3) to determine how that effect varies across contexts and student characteristics. Thus, study one will assess whether Tools, at the curricular level, improves students’ self-regulation.
By contrast, study two will involve more granular analyses of the discrete learning activities that collectively comprise Tools. Specifically, study two will analyze child-level self-regulation and teacher-level Tools implementation data for 1145 preschool children in 80 classrooms across six American school districts. I will employ multilevel structural equation models to assess which Tools activities are associated with students’ self-regulation growth, which are associated with decline, and which exhibit no association at all.
Ultimately, this dissertation features the first Tools meta-analysis as well as the first analysis of specific Tools instructional activities. It is hoped that these analyses will identify educational practices predictive of self-regulation development both within and beyond the Tools curricular context.

Advisor: Malmberg, L
Evangelou, M
Novel halogenation and pallado-biology strategies for biological probes

Post-translational modifications (PTMs), which biochemically modify proteins to generate diversity and control functionality, are important in the field of chemical biology research. However, typical bioconjugation methods involving nucleophilic addition of cysteine and lysine residues are limited by their lack of site-specificity. In this thesis, we have demonstrated the site-selective chemical modification of a variety of proteins through protein halogenation and subsequent pallado-biology strategies.
The "Tag-and-Modify" approach, developed previously in our group and involving the creation of a protein tag for further manipulation, is a useful tool for site-selective chemical modification. Here, we envisioned extending its utility to a novel concept of [18F]-radiolabelling of proteins involving direct electrophilic fluorination, thus forming a C-F bond at a specific modification site and leading to the generation of protein species applicable for in vivo [18F]-PET imaging and diagnosis. We also explored several alternative methods for the installation of C-Br/C-I bonds onto a protein of interest. Our first attempts involved the biosynthetic incorporation of a synthetic bromotryptophan into the protein, however these processes were unsuccessful. As a workaround, we found IPy2BF4, an iodinating agent, to be very effective as a direct method for the site-specific installation of C-I bonds on tyrosine/histidine residues of proteins. We subsequently demonstrated novel and efficient palladium-catalysed cross-couplings of the resultant iodinated tyrosine/histidine moieties, leading to the creation of new C-C bonds. This approach was compatible with a wide range of functionally diverse boronic acids, using a water-soluble and phosphine-ligand-free Pd-complex catalyst under fully aqueous conditions.
Our novel, successful method for C-C bond formation onto proteins is potentially applicable to the initial investigation of challenging in vivo Pd cross-coupling of thyroglobulin, based on our achievement of protein labelling under ex vivo conditions. In summary, we are able to create new chemical tools for the site-selective/site-specific chemical modification of proteins, enabling their use as biological probes.

Keywords: Protein modification
Advisor: Davis, B
Interstitial modification of palladium for partial hydrogenation reactions

Heterogeneous catalysis is a key industrial process involved in the synthesis of nearly all chemicals currently produced. The environmental impact of these processes is huge so improvements must be made to current catalysts. Should a new material provide better yields at lower energy cost the benefits to both the industry and the planet are significant. There are many ways to change the behaviour of a catalyst, the addition of dopants, the selective blocking of active sites, and changing the strength of the support interaction to name a few. One technique that has become increasingly investigated is interstitial modification, the insertion of a light element into a metal lattice to change the metal’s catalytic properties.
The work presented in this thesis devises greener synthetic routes to the known Pd-interstitialB/C catalyst and investigates potential routes to a novel interstitial material, Pd-interstitialLi/C. Initially, successful verification of interstitial modification comes from the characteristic increase in palladium lattice parameter from 3.89 to 4.00 Å and the blocking of the β-hydride formation. Initial catalytic screening determines the synthetic route which yields the most active catalyst which subsequently undergoes thorough characterisation. The wealth of evidence generated confirms the interstitial location of lithium within the palladium lattice, as well as adding to the current understanding of the Pd-interstitialB/C material. EELS analysis on Pd-interstitialB is the closest to direct observation of boron within the palladium lattice to date. PDF on Pd-interstitialLi shows 13.7 % of the palladium octahedral interstitial sites are occupied by lithium. This is the first report of interstitial lithium within palladium to date. The effect of the interstitial modification on catalytic hydrogenation by two elements that have opposite effects on the surface electronics of the host palladium gives intriguing results.
The effect on catalysis varies depending on the conditions investigated. This bank of hydrogenation data allows an informed choice as to which interstitial material would be best suited to the gas or liquid phase catalytic hydrogenation under investigation.

Keywords: Interstitial boron
Interstitial lithium
Electronic modification
Catalytic hydrogenation
Catalyst modification
Heterogeneous catalysis
Advisor: Tsang, E
“When reason is against a man, a man will be against reason”:  Hobbes, deism, and politics

This thesis explores the relationship between Thomas Hobbes and English deism. It seeks to show that Hobbes's work had a significant influence upon subsequent deists, namely, Charles Blount, John Toland, Matthew Tindal, and Anthony Collins. The thesis shows that these deists were influenced by certain distinctively Hobbesian anticlerical ideas, such as his biblical criticism, his materialism and determinism, his scepticism towards present revelation, and more. The deists, who were motivated by a similar form of anticlericalism, found in Hobbes a particularly resourceful ally. Furthermore, this thesis explores how some of Hobbes's political ideas influenced the deists: particularly his concerns regarding the dangerous role that priestly interests played in society and the instability that they generated.
This thesis thus argues that Hobbes can be seen as a major influence upon English deism. Secondly, it offers an examination of Hobbes's concepts of God and reason. It shows that whilst Hobbes’s accounts of God and reason were multilayered and at times perhaps underdeveloped, they contained significant elements that anticipated the later positions of the deists. Finally, this thesis argues that for Hobbes, the rational potential of humankind, implanted by God, could be cultivated and fulfilled once peace and security are guaranteed. Thus, this thesis attempts to recover some of the more utopian aspects of Hobbes's thought. It concludes that both Hobbes and the deists were part of a project of enlightenment, but one which was not aimed against religion as such. They attempted to liberate natural reason from the darkness of corrupt clerics and their false doctrines: this was an anticlerical enlightenment that was partly initiated by Hobbes and developed significantly by the deists.

Keywords: English Deism
Thomas Hobbes
Advisor: Parkin, J
Philp, M
Engaging Eckhartian mysticism in a secular context: a hermeneutical study in post-Kantian thought

The aim of this thesis is to define, develop, and defend an interpretation and application of the mystical ontology of Meister Eckhart. Briefly, mystical ontology should be understood as a distinctive theology insofar as it presents God’s being, the being of the world, and the individual’s being as an essentially unified whole. My research focus for this thesis will then be to situate Eckhart’s theology within current debates on mysticism and amidst the post-Kantian philosophical turn toward ontology. The cumulative effort of this thesis will reach its height when I apply my conclusions on the mystical nature of being that can be found in Eckhart’s medieval writings and transcriptions in order to address the modern, theological problem of secularity. This effort will be implemented with the objective of creating a space for dialogue between Christian theology and the generally secularized culture that, in part, defines the present age. In so doing, this thesis will demonstrate the philosophical and cultural relevance of this particular understanding of the nature of being when treating modern problems in theology. The guiding question for this thesis will be the following: what insights can Meister Eckhart’s thought offer to theologians today in addressing the problem of secularity? My overall thesis will then be: the mystical ontology of Meister Eckhart can be interpreted and applied in a manner that successfully opens a space for constructive dialogue between secular culture and the presence of God in the world. Overall, this thesis should be read as a scholarly project on Eckhartian theology and its applicability toward productively treating the problem of secularity. All of my conclusions will be derived as a result of having been situated and argued for amidst current debates on relevant topics, as well as in relation to other major works that are indispensable for such a project. To be clear, my aim will not be to appropriate Eckhart’s work and to assimilate it to a post-Kantian perspective. Rather, I will look to Eckhart for his clear and definitive theological statements. I will then interpret those statements and apply them in a manner that efficaciously engages specific principles of secularity in demarcating a common ground for dialogue.

Keywords: Post-Kantian
Hermeneutics
Meister Eckhart
Mystical Theology
Advisor: Edwards, M
Drosophila melanogaster as a model to study ciliogenesis

Cilia are microtubule-based extensions of the cell membrane that extend from a mature centriole. Primary (non-motile) cilia are present on most human cells and have important roles in signalling pathways. At the base of the cilium is a selective barrier known as the transition zone (TZ). Defects in the TZ are associated with human congenital diseases such as Meckel-Gruber syndrome (MKS) and Nephronophthisis (NPHP). The TZ is formed by three protein complexes, the MKS, NPHP and Cep290 modules, although the fruit fly Drosophila melanogaster appears to lack the core components of the NPHP module. Results presented in this thesis shows that MKS proteins are spatially separated from Cep290 at the TZ in Drosophila spermatocyte cilia. The TZ of the spermatocyte cilia is perturbed in flies mutant for MKS1 (MKS1Δ1) and fails to recruit key TZ proteins, although Cep290 and Chibby are recruited normally. Male fertility, however, is unaffected. Similarly, while there are substantial abnormalities in microtubule and membrane organisation in developing MKS1Δ1 mutant cilia, defects in mature MKS1Δ1 mutant cilia are limited to subtle changes in IFT and a membrane surrounded volume within the cilium. The function of sensory neurons is not negatively affected by the MKS1Δ1 mutation. Evidently, given enough developmental time, ciliary defects can be largely rescued in flies and the localisation of MKS module proteins to the cilia or flagella is not essential for viability or fertility in Drosophila.

Advisor: Raff, J