VictorJuiz/thesis huggingface dataset:
New templates for porphyrin nanorings
Keywords: Ferrocene derivatives
Cooperativity
Template-directed syntheses
Porphyrin nanorings
Cyclodextrin derivatives
Self-assembly

New templates based on the structures of cyclodextrin and ferrocene have been developed for porphyrin nanoring syntheses. Flexibility can be taken into account of the molecular template design. The flexibility of butadiyne bonds allow the formation of a 5-porphyrin nanoring, which is the smallest fully-conjugated porphyrin nanoring to date.
Chapter 1 describes the general information of porphyrin, cyclodextrin and ferrocene, which are used as basic structures in the thesis. The polymer chemistry of porphyrins is reviewed as the background knowledge of the work. Meanwhile, chelate cooperativity of supramolecular systems and the corresponding measurement method are introduced.
Chapter 2 presents the chemistry towards 6- and 7-porphyrin nanorings using molecular templates T6&ast; and T7&ast;, which are based on the α- and β-cyclodextrin scaffolds. The cooperativity of respective template-nanoring complexes was investigated by UV-vis titrations. Chapter 3 describes the Vernier-templated syntheses of porphyrin nanorings using T7&ast; and different linear porphyrin oligomers (l-P2, l-P4 and l-P8). Both chapters focus on the influences of spatial preorganization and flexibility to the cooperativity of supramolecular systems.
Chapter 4 introduces the chemistry towards a ferrocene-based five-dentate template T5 which successfully directed the syntheses of 5-porphyrin nanorings. Investigation of the cooperativity in the nanoring-template system is presented. Chapter 5 investigates the cooperativity between T5 and linear porphyrin oligomers in detail; and focuses on the contribution of partially-bound complexes in the measurement of equilibrium constants of the host-guest systems. Both chapters focus on the influences of intramolecular strain to the cooperativity in supramolecular systems.
Chapter 6 provides experimental procedures and characterization data of the known and novel compounds synthesized in the course of completing the thesis.
Genetic basis of rhizoid development in the liverwort Marchantia polymorpha
Keywords: tip growth
rhizoid
evolution
liverwort
root hair
rooting structure
plant development

The evolution of specialised rooting structures was one of the key morphological innovations that allowed the first multicellular plants to colonise land more than 470 million years ago. The first land plants likely resembled modern bryophytes with a rooting structure that consists of filamentous rooting cells called rhizoids, which are morphologically similar to the root hairs of vascular plants. This thesis describes identification of genes required for rhizoid development in a model bryophyte, the liverwort Marchantia polymorpha. The aim was to identify the conserved and novel aspects of the gene regulatory networks for filamentous rooting cell development in land plants. Agrobacterium-mediated T-DNA transformation of haploid M. polymorpha spores was used to generate 150,000 M. polymorpha T-DNA insertion lines, which were screened for defects in rhizoid development. 204 rhizoid defective mutants were isolated which allowed identification of 25 genes required for M. polymorpha rhizoid development. The role of the class I RSL (ROOT HAIR DEFECTIVE SIX-LIKE) genes as positive regulators of root hair and rhizoid differentiation was found to be conserved between liverworts and vascular plants. This suggests that the class I RSL gene mechanism is ancient and originated before the two lineages diverged more than 440 million years ago. Furthermore, the M. polymorpha class I RSL gene MpRSL1 is required for development of gemmae and mucilage papillae, which similarly to rhizoids form from single epidermal cells that elongate to form an outgrowth. Moreover, MpRSL1 is under negative feedback regulation of the FEW RHIZOIDS1 (FRH1) microRNA. Many genes required for rhizoid elongation were similar with those required for root hair elongation, suggesting that these genes are likely to have been part of the genetic network downstream of class I RSL genes in the common ancestor of liverworts and vascular plants.
Order and insecurity under the mara: violence, coping, and community in Guatemala City
Keywords: Legal anthropology
Maras
Street gangs
Insecurity
Guatemala City
Guatemala
Urban violence
Urban ethnography

Drawing on sixteen months of ethnographic fieldwork in a poor and notorious neighbourhood, this dissertation examines how evolving dynamics of urban violence have affected life in a Guatemala City gang territory.
The maras of Guatemala, El Salvador, and Honduras—the gangs that help give these countries some of the world's highest homicide rates—have changed dramatically in their group cultures and criminal economies since they appeared in the 1990s. I trace what I call the mara's predatory turn: the elaboration of an extortion economy, which has had far-reaching consequences for the relationship between gang cliques and their barrios. This transformation has re-shaped the experience of chronic insecurity in the communities that maras operate from: inhabitants report that it is now less manageable, less predictable, and more frightening. They speak of a heightening of danger in their lives brought about by the decline of certain local norms and mechanisms that had previously moderated gang violence and bolstered community resilience.
Local narratives of insecurity and decline illuminate when, how, and why violence disrupts and disorders social life. What many informants emphasized was not a cataclysmic appearance of violence in their lives, but rather a catastrophic breakdown in the mechanisms that had controlled it. In this distressing context, residents struggle to minimize their insecurity and to reclaim or create forms of order. I examine two principal ways that they seek to do so: by working to maintain a moral order based on narratives about the neighbourhood and its values or 'codes', and by looking to external providers of order in the state and its security forces.
Exploring the complex relationships and interactions between inhabitants, gang members, and state forces in this barrio, I contribute to academic debates about local and state responses to insecurity in Latin America and propose modifications to prevailing models of state and criminal 'governance' in marginal urban communities.
Enzymatic synthesis of chemically modified DNA for analytical and diagnostic applications
Keywords: fluorescent labelling
IEDDA
SPAAC
DNA modification

Functionalised nucleotides have found widespread adoption in applications ranging from genome labelling to disease diagnostics. A popular means of introducing these modifications into nucleic acids is via the copper-catalysed azide-alkyne cycloaddition reaction. However, the toxicity of copper limits its use in vivo. Therefore, the copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) and inverse electron demand Diels-Alder (IEDDA) reactions were evaluated as a means of directly and indirectly labelling DNA and RNA. A variety of cyclooctyne, trans-cyclooctene and azide functionalised deoxyuridine triphosphates were synthesised and shown to be incorporated by primer extension, polymerase chain reaction (PCR) and reverse transcription. Bulky cyclooctyne and trans-cyclooctene triphosphates demonstrated moderate incorporation efficiency, while azide nucleotides with smaller functional groups were better substrates. PCR products of ca. 500 base pairs with 100% sequence fidelity can be formed, where all thymidine sites are replaced with azidohexanamidopropargyl deoxyuridine. These modified duplex products were efficiently labelled with fluorophores using the SPAAC and IEDDA reactions, and can be converted to fluorescent single-stranded probes through exonuclease digestion and streptavidin magnetic bead separation of the duplex followed by fluorophore-labelling. To expand the utility of this methodology, a new and simple single-tube dual labelling strategy was demonstrated to give a range of mixed dual coloured probes. Nucleosides bearing azide, trans-cylcooctene modifications and a fluorescent base analogue were evaluated for direct cellular DNA labelling and detection. When cultured adenocarcinoma A549 cells were treated with these nucleosides, then chemically fixed and fluorescently labelled by the SPAAC or IEDDA reaction, cytoplasmic staining without nuclear DNA labelling was observed. To improve the efficiency of fluorescent labelling of genomic DNA in cultured cells, phenyl isopropyl alanine-protected nucleoside monophosphates were prepared in an attempt to directly deliver 5' phosphorylated nucleosides into the cells. Preliminary fluorescence studies indicate bright foci in addition to cytoplasmic staining, the origins of which require further study.
Single-molecule FRET studies in live bacteria
Keywords: Single-molecule fluorescence
Single-molecule FRET
Gene expression

Single-molecule fluorescence and single-molecule Förster resonance energy transfer (FRET) have proven enormously successful in understanding molecular and cellular processes over the last two decades. However, in vivo single-molecule FRET studies are still very difficult, mainly because they require site-specifically labelled biomolecules with photostable organic dyes.
In this work, I established single-molecule FRET studies in live bacteria and applied the developed method to study mechanisms of gene expression and gene regulation. To begin with, I optimised a recently developed internalisation method based on electroporation for the efficient loading of bacterial cells with organic dye-labelled nucleic acids and proteins while maintaining cell viability.
Following these studies, I internalised labelled tRNA molecules, measured their diffusion coefficient, and showed that most tRNA molecules diffuse freely in live bacteria. I also showed that bound tRNA molecules are predominantly at the cell periphery and compete with the endogenous tRNA pool during translation using antibiotic controls and simulations.
Finally, I studied transcription initiation in vivo by internalising promoter DNAs with different FRET labelling schemes reporting on individual steps in transcription initiation. Thus, I observed single-molecule FRET signatures attributed to open complex formation, DNA scrunching during initial transcription, and promoter escape, which were not present in null-promoter DNA and antibiotic controls.
By carefully designing single-molecule FRET assays, I imagine single-molecule FRET studies to become a major tool in understanding protein dynamics, and elucidating mechanistic details of gene regulation processes in living cells.
Records of and controls on temporal variations in activity at arc volcanoes
Keywords: Sollipulli
glaciovolcanism
lava dome
igneous geochemistry
palaeoclimate
entropy
volcano-ice interaction
tephra
detrended fluctuation analysis
palaeoenvironment
hyaloclastite
time-series analysis
eruption
Montserrat
Soufrière Hills
Chile
lithofacies
volcano seismology
Mexico
Andes
Patagonia
Hudson
stratovolcano
volcano monitoring
caldera
Colima

Many attributes of volcanic activity, whether physical, geochemical/petrological, or geophysical, change over timescales from minutes to millions of years. Understanding the nature of these variations and their controls is essential both for hazard assessment and to understand volcanic and magmatic processes. Arc volcanism entails a relatively broad range of eruption styles and magma compositions, and thus wide-ranging hazards and a variety of eruption records. Despite their significance, records of activity for many arc volcanoes are inadequately characterised, so any temporal variability is poorly constrained. In this thesis, I investigate temporal variations in different styles of activity (dome-forming, Plinian-style, and effusive/glaciovolcanic) on a range of timescales (days–years, millennia, and hundreds of ky, respectively), from diverse records (seismicity, tephra deposits, and effusive eruption products), at four arc volcanoes. I analyse seismic time-series from Soufrière Hills Volcano (Montserrat) and Volcán de Colima (Mexico) using two statistical techniques, identifying temporal variation in the extent of long-range correlations and randomness in these data, which has potential to inform real-time monitoring and constrain eruptive processes. I also present new composition data for and review previous studies of tephra deposits from Volcán Hudson (Chile), revising its explosive eruption history and finding previously unrecognised shifts in the magma composition erupted through the Holocene. I also describe and analyse sequences of lithofacies from effusive eruptions of a range of magma compositions from Volcán Sollipulli (Chile), inferring varying extents of interaction with ice during their emplacement, and so changes in eruption style through time. These case studies highlight the importance of detailed characterisation of temporally varying records of volcanic activity, and some of the limitations of and uncertainties in these records and their interpretation.
Caesar’s Castor: the cult of the Dioscuri in Rome from the mid-Republic to the early Principate
Keywords: Castor, Pollux, Dioscuri, Religion, Politics

This thesis examines the development of the cult of the Dioscuri in Rome from the mid-Republic to the end of the Julio-Claudian dynasty. This was a period of great political and social upheaval and of religious change. Through a detailed examination of the cult of the Dioscuri, I trace how the cult developed and adapted in conjunction with religious, political and cultural changes within Roman society. I furthermore examine how the cult changed and explore the reasons why those changes occurred at that time and in that place.
Chapter One surveys the two temples of Castor and Pollux in Rome, focusing in particular on their temple in the Roman Forum. Using archaeological and literary evidence, I argue that this temple was a central stage for many of the pivotal events and speeches of the late Republic. Chapter Two examines the epiphanies of the Dioscuri, most commonly associated with battles and their aftermath, although later appearing to commemorate the deaths of prominent individuals such as Julius Caesar and Drusus the Elder. I examine how the epiphanic tradition of the Dioscuri changed over time and ask why it was these gods in particular who rode to aid Rome. Chapter Three turns to exploring the relationships Castor and Pollux were said to possess with groups in Roman society, in particular horsemen, boxers and sailors. I examine how these relationships were formed and publicised and how they benefitted both the mortals and the gods. Chapter Four explores how a different aspect of the Dioscuri became prominent in the imperial period: their fraternal harmony. Castor and Pollux were linked to and compared with pairs of potential imperial successors. I explore the purposes of this comparison and how apt it was for the different pairings.
Throughout this thesis, I examine some of the most prominent aspects of the cult of the Dioscuri in Rome within the wider context of history, culture and politics, arguing that the cult was a fully integrated part of Roman society as a whole.
The purpose of the Book of Numbers in relation to the rest of the Pentateuch and post-exilic Judaism
Keywords: Pentateuch

A mosquito once landed in a nudist colony. "How very excellent," he was heard to remark, "But just where do I begin?" This is the dilemma faced by any critic dealing with tne Pentateuch. If he examines the whole, then he is open to the charge that he has carried his conclusions about one book over into his consideration of the others. On the other hand, when he treats one book by itself, he is always in danger of a certain off-balance. This thesis falls into the letter class of investigation; it is therefore admitted that there are a certain number of loose ends, although every attempt will be made to see Numbers in the context of the Pentateuch as a whole. Nonetheless it is apparent that it is legitimate to consider a book of the Pentateuch by itself. For example, Genesis, although written as part of a series in its present form, can be dealt with as a book having meaning in itself. The theory that the present division of the Pentateuch into five books is a result of a mechanical process after the work was completed is not axiomatic. To the contrary it will be argued that the Book of Numbers is a book in the same sense that Genesis is a book, namely a part of a series, but with a specific theme and purpose of its own.
The reign of Emperor John II Komnenos, 1087-1143
Keywords: John II Komnenos
Anatolian Castles
Komnenoi
12th Century
Byzantine
Komnenian
Crusader States
Balkan Castles

Despite ruling over arguably the most powerful Christian nation in the period, in a time when European and middle-eastern history entered a new phase of interaction due to the Crusades, John’s reign has received little scholarly attention. The only major monograph is Chalandon's Les Comnènes from 1912, since which a number of new sources have come to light, together with numerous studies on his contemporaries. Despite the impression that sources are lacking for his reign, in fact there are over 50,000 words of court letters and poetry that allow us to take the political pulse of the Komnenian court. When incorporated with the extra information found in Syriac, Arabic, Russian, Hungarian and many other texts, archaeological remains, sigillographic and numismatic evidence, John’s reign is in fact very well covered, and ripe for analysis. Between fieldwork in Turkey, Serbia and Kosovo and translations of these previously unused texts, this thesis contains new material on top of over a century of updated methodologies and research since Chalandon.
As such, this thesis will reevaluate assumptions concerning John and his reign, including rewriting the narrative itself, which has previously been distorted due to the agendas of the few sources used. Through the reconstruction of this narrative John's empire can be reexamined, and how it operated in the changed world of the twelfth century determined. The empire found itself in a more multi-polar power dynamic, and tackled this by operating more as an empire than it had as a larger polity as in the previous century: incorporating other peoples as clients and emphasing the rhetoric of imperial piety and legitimacy of the Roman empire. Equally, all of John’s actions on the frontiers were fuel for the political theatre that was Constantinople, and this dynamic shaped his actions and resulted in the empire that Manuel inherited.
Religion and ethnic identity: Gurung experiences of belonging in the UK
Keywords: diaspora
migration
Gurungs
Nepal
Nepali diaspora
Belonging

This thesis seeks to identify the place and significance of religion in constructions of ethnic identity and experiences of belonging among Gurungs in the UK. It assesses both the vision of Gurung ethnic identity put forward by ethnic organizations, which is itself much disputed, and the extent to which this vision either reflects or shapes religion 'on the ground'. It argues that debates and controversies surrounding Gurung religious identity are influenced by ethnic politics in Nepal, by social changes and modernist ideas about the superiority of world religions over local traditions, by the pervasive discourse regarding exclusivity in religion, as well as by historical, but highly contested, status differences within Gurung society. It also suggests that those debates are complicated by divergent conceptions of 'religion', and of how 'religion' relates to 'culture'.
When considering religion 'on the ground', the thesis assesses the extent to which Buddhism and Bon are practised as an expression of Gurung culture, thus reinforcing a sense of belonging within the Gurung community, and the extent to which particular religious traditions strengthen a broader Nepali identity or universal orientation, whereby religious belonging outweighs ethnic loyalties. It concludes that both orientations are in evidence and, in general, are considered mutually reinforcing. However, from the perspective of Christian Gurungs and followers of Sai Baba - paths often considered foreign to Gurung culture - a tension is more evident. For many Nepalis, however, religious identity is complex and multiple. Many include elements of different religious traditions in their regular practice and there is a whole range of customs, values, attitudes and understandings of religion which are shared by Nepalis but which are understood to belong to no particular religion, or to all. I suggest that it is as much through these aspects of religion, as through commitment to the vision of Gurung religious identity officially promoted, that a sense of commonality and belonging is created within the diaspora.
Quantitative imaging of cerebral oxygen metabolism using MRI
Keywords: ASL
brain
arterial spin labeling
positron emission tomography

Magnetic resonance imaging (MRI) is a non-invasive medical imaging technique that is sensitive to the level of oxygen in the blood. Calibrated MRI is capable of producing maps of absolute oxygen metabolism by using gas challenges to independently manipulate blood flow and blood oxygen content. In this thesis, several aspects of the signal model are investigated. It is confirmed that the commonly used Davis model is reassuringly insensitive to field strength, provided sufficient signal-to-noise (SNR) can be obtained. The effect in varying the experimental parameter of echo time is explored, and the results are shown to match the theory more closely when intravascular signal contribution is reduced by crusher gradients.
A direct comparison was performed between resting oxidative metabolism as measured by calibrated MRI and the gold standard method of positron emission tomography (PET). Good correlation was observed for resting blood flow, but no correlation was found for oxygen extraction fraction (OEF) or absolute cerebral metabolic rate of oxygen consumption (CMRO2). A follow-up study was performed to further investigate some methodological aspects of the calibrated MRI procedure, including the application of background tissue suppression, different gas delivery methods, the effects of using measured respiratory timecourses as part of image analysis, and the impact of physiological noise correction.
The limiting factor in the quality of data obtained for calibrated MRI is the SNR of the arterial spin labelling (ASL) method, which is used to quantify blood flow to the brain. The alternative method of intravoxel incoherent motion (IVIM) was investigated, which is hypothesised to be sensitive to cerebral blood volume and perfusion without the signal limitations of ASL. However IVIM was shown to be primarily sensitive to the presence of cerebrospinal fluid within the brain, and thus is not a suitable alternative to ASL when quantification is of interest.