VictorJuiz/thesis huggingface dataset:
Molecular characterisation of functionally important regions of Drosophila melanogaster Notch and Serrate

The Notch signalling pathway is conserved in all metazoan species and plays a crucial role in development and tissue maintenance. Canonical Notch signalling requires cell-cell contact to allow the interaction between Drosophila Notch receptor and its ligands, Serrate and Delta. The Notch Abruptex (Ax) region comprises 24-29 of the 36 epidermal growth factor-like (EGF) repeats in the Notch extracellular domain. Mutations in the Ax region give rise to three distinct phenotypes in Drosophila. Notch EGF repeats 11-12 form the ligand binding region (LBR). The recently solved structure of the module at the N-terminal of Notch ligands (MNNL) of a human Notch ligand, Jagged1, revealed that the domain was a calcium-binding C2 domain with Ca2+-dependent lipid binding. This study aimed to investigate the intra- and intermolecular properties of Drosophila Notch Ax region, LBR, and the MNNL of Notch ligand Serrate.
In WT Drosophila Notch EGF23-25, all three EGF domains were found to be Ca2+-binding, and a previously unknown Ca2+ binding consensus sequence was identified. AxN-suppressor mutations D948V and N986I were shown to impair the Ca2+-binding properties of the mutant EGF domain without affecting the neighbouring domains, suggesting a mechanism to explain the signalling phenotype associated with this mutation type.
Notch EGF11-13 showed Ca2+-binding in each EGF domain and binding to ligand-expressing cells. Its C-terminal tag was found to influence the Ca2+-dependent fold of EGF13, suggesting a future strategy for protein expression.
A Serrate fragment MNNL-EGF3 showed Ca2+-dependent lipid binding, which was not observed in a construct lacking MNNL. The lipid binding could be reduced by a substitution D197A in MNNL, suggesting this mutant could be used to probe functional importance of MNNL in model organism studies.
Binding between Serrate and Notch was assessed with a new cell aggregation assay method using flow cytometry, and agreed with previously published studies. Binding to Delta was subsequently measured, which suggested ligand specific differences although Notch residue L504 was important for both Serrate- and Delta-binding.
Collectively these studies establish that Drosophila Notch and its ligand Serrate has similar properties to mammalian homologues, which will facilitate future structural and functional studies.

Keywords: Abruptex
calcium
EGF-domain
Notch
Serrate
MNNL
Advisor: Handford, P
Nomadic geography

Pastoralism on the Mongolian steppe encompasses limited physical resources and evolving anthropogenic influences. Little-studied, the Inner Asian region encounters changing climates, evolving land use practices, and socio-economic transition that impact the natural and human geography. This thesis investigates how bio-physical factors and herder action determine the pastoral environment in the Gobi Desert, Mongolia. Research, focusing on drought, degradation and the extreme winter conditions that define pastoralism in Mongolia, examines pastoralists' perception of and interaction with their environment. This approach highlights steppe ecological and social processes within the global dryland debate.
Fieldwork in Omnogovi and Ovorhangai Province established that drought is endemic in the region. However, drought events were independent of extreme winter conditions and did not exacerbate their impact. Degradation was not found at water points as vegetation cover decreased with distance from water. While remote sensing showed a decline in vegetation cover over time, it did not establish desertification on the steppe.
Changing physical, socio-economic, and political conditions since 1990 continue to impact Mongolian pastoralism. Environmental conditions, particularly water resources and pasture quality, were paramount herder concerns. This research showed that pastoralists are economically motivated, differentiate on multiple dimensions, and value communal land stewardship. On the steppe, traditional mobile livestock practices improve livelihoods and remain an effective management approach. However, the future of pastoralism is uncertain as herders settle, the population ages, and children become educated. Thesis results emphasize the interaction of physical and social environments will define pastoralism's role in the Gobi Desert

Advisor: Thomas, D
Middleton, N
Experimentally simulating high rate deformation of polymers and composites

The research presented in this dissertation presents a methodology to experimentally predict and simulate the mechanical behavior of polymers under high strain rate deformation. Specifically, the interplay between the effects of temperature and strain rate on polymer behavior is examined and then used as a tool to help recreate the high rate mechanical response of several different polymers: ranging from rubbers to amorphous polymers to composites. Multiple literature reviews are conducted and presented in this thesis, e.g. experimental mechanics test methods, high rate behavior, time-temperature equivalence, constitutive modeling, and temperature measurement methods.
In accordance with mechanical theory, an experimental and analytical protocol in rate- and temperature- dependence was applied to a range of PVC materials ranging in plasticizer contents. Further to this, these PVC materials were modeled with a rubbery model describing the network stress seen in polymer behavior, and an amorphous polymer model to describe PVC low to high rate responses to deformation. This modeling develops insights in the adiabatic nature of high rate response.
Time-temperature equivalence, and the temperature rise during adiabatic deformation, are studied and exploited in order to implement a proposed experimental method which simulates the high rate deformation of polymeric materials.
The development of an experimental methodology to simulate and predict high rate behavior is presented, applied, and expanded to a range of materials: amorphous polymers (e.g. PVC 20wt% plasticizer, PMMA, PC) and composites (e.g. polymer bonded explosive simulant). The work also presents and highlights the fact that micro to nano-scale imaging may be used in parallel with the simulation method in order to better understand high rate behavior.
Furthermore, in result of the studies conducted in this body of work, several novel techniques were developed, or improved upon, and applied to the current research (e.g. additions to time-temperature equivalence, temperature measurement methods at high, moderate, and low strain rates, and a method for measuring the high rate behavior of soft materials).

Keywords: experimental simulation
composites
modeling
deformation
strain rate
thermodynamics
high rate
polymers
Advisor: Siviour, C
Palaces and elite residences in the Hellenistic East, late fourth to early first century BC: formation and purpose

This thesis investigates the morphology and the purpose of palaces in major and minor kingdoms of the Hellenistic World. Elements of architecture, spatial organisation and decoration are analysed in the attempt to clarify issues of chronology and in order to identify function. The analysis places the material into its social and ideological context by taking into consideration the role of kingship ideologies in the formation of space used by royal courts. Comparison with residences of the elite demonstrates the reception of palaces not only as architectural models, but also as mechanisms of power manifestation.
Macedonia is the starting point of the discussion as the homeland of the first Hellenistic kings. In the light of evidence recovered in the last twenty years and not comparatively studied before, the chapter brings together various chronological phases of the buildings. Questions of definition and on sources of inspiration are clarified further in the following chapters. The third chapter uses textual evidence and finds from the royal district of Alexandria to understand the meaning of palace architecture for the Ptolemies, while the seat of a local official in Transjordania reveals mechanisms of emulation. In chapter four the case of Pergamene palaces and their relationship with residences in the city demonstrates that formation of these royal seats corresponded to ideals of Attalid kingship. Seats of officials in the Seleukid Empire and palaces in Bactria and Kommagene, the subject of the fifth chapter, provide an insight into the position of palace architecture in processes of hybridisation in material culture. The last chapter is a synthesis of patterns of form and function and unifies the conclusions for each separate region. It emerges that shifts in power relations and the structure of the royal court, especially towards the end of the third century BC, were a crucial factor in shaping palace forms. The concluding chapter also provides a view from the West: examples from the late Roman Republic indicate that the role of Hellenistic palaces as models for power display went beyond the limits of royal courts.

Keywords: History of architecture
Antigonids
Hellenistic Middle East
spatial function
Hellenistic architecture
Hellenistic kingship
palaces
Advisor: Smith, R
Estimation of the indirect radiative effects of aerosol on climate using a general circulation model

The indirect effects of anthropogenic aerosols—through their interactions with clouds—are currently one of the most uncertain perturbations to the radiative energy balance at the top of the atmosphere. A crucial link between aerosol and cloud is that aerosols can act as cloud condensation nuclei (CCN). This microphysical process must be parameterised if the large-scale effects are to be represented in a general circulation model (GCM). Theoretical work presented in this thesis highlights the importance of incorporating the kinetic limitations on droplet formation in aerosol activation parameterisations.
HadGEM-UKCA is a GCM, capable of representing the chemical and microphysical aerosol processes required to model CCN accurately. The author has incorporated a Köhler theory based parameterisation of aerosol activation into HadGEM-UKCA, to facilitate quantitative predictions of the indirect aerosol effects.
This thesis presents an estimate of the range of uncertainty in such predictions attributable to the choice of parameterisation of the sub-grid-scale variability of vertical velocity. Results of simulations demonstrate that the use of a characteristic updraught velocity cannot replicate results derived with a distribution of vertical velocities, and is to be discouraged in GCMs.
Consequently, work focuses on the effect of the variance (σw2) of a Gaussian pdf of vertical velocity. Fixed values of σw and a configuration in which σw depends on turbulent kinetic energy are tested. Results from the mid-range fixed σw and TKE-based configurations both compare well with vertical velocity distributions and cloud droplet number concentrations measured in situ. However, the sparse set of available measurements does not provide enough of a constraint to recommend one or the other as the best configuration globally.
The radiative flux perturbation (RFP) due to the total effects of anthropogenic aerosol is estimated at −1.7Wm−2 for the TKE-based configuration. To the extent that it is valid to decouple the individual aerosol effects, the direct effect accounts for approximately −0.6Wm−2 of the total, the cloud albedo effect −0.8Wm−2 and the cloud lifetime effect −0.3Wm−2, indicating that these effects are additive within HadGEM-UKCA. Total aerosol RFP ranges from −1.4Wm−2 from simulations with σw=0.1ms−1, up to −2.0Wm−2 for σw=0.7ms−1. This range of 0.6Wm−2 corresponds to almost a third of the total estimate of −1.9Wm−2, obtained with the mid-range value of σw=0.4ms−1. Reducing the uncertainty in the parameterisation of σw is therefore an important step towards reducing the uncertainty in estimates of the indirect aerosol effects.

Advisor: Stier, P
Grainger, R
Jones, A
Processes of pairbonding

This thesis expands our understanding of the role of several different mating behaviours in the process of forming and maintaining human mating pair-bonds. Chapter 2 investigated within-sex mating strategies and found that their distribution reflects the presence of two phenotypes, one favouring the pursuit of short-term mating and one the establishment of mating pair-bonds, each driven by prenatal testosterone exposure. Chapter 3 investigated the possible functional role of kissing in mating relationships, and found that it was utilised divergently by individuals pursuing different mating strategies, with those interested in short-term mating utilising it to assess the suitability of potential mates at initial relationship stages, and those interested in long-term mating using it to mediate pair-bond attachments. Chapter 4 examined female attitudes towards kissing across the menstrual cycle and found that attitudes varied with cycle phase, mediated by fluctuations in the hormone progesterone. This chapter also investigated the effects of kissing-related information on mate assessment and found that such information influenced mate desirability, even in the presence of typically dominant visual cues. Lastly, Chapter 5 investigated the cognitive effects of established pair-bonds, finding that individuals ‘in love’ with a mating partner show improved empathising abilities, particularly males when it comes to assessing negative emotional states in others.
Using an evolutionary framework, each chapter of this thesis contributes novel insights to our understanding of these diverse behaviours. These results suggest that that future research must take into account within-sex phenotypic differences in order to truly understand human mating strategy decisions, and that different mating strategy phenotypes might adaptively utilise the same courtship behaviours in divergent ways. Furthermore, these results also suggest that pair-bonding in humans may be a relatively recent phenomenon, and that the formation of such pair-bonds can have adaptive cognitive effects for males within such bonded relationships.

Keywords: pair-bonding
love
kissing
mating strategies
romantic relationships
Advisor: Dunbar, R
Refugees and the state in Kenya

The thesis provides an empirical basis for understanding state behaviour towards refugees by focusing on refugees in Kakuma Camp, Kenya. It compares and contrasts the experiences of encamped refugees with the experiences of Kenyans outside the camp, stressing the need to understand the socio-political context within which displacement and protection occurs. The study describes the processes of state formation in Kenya and the evolution of particular understandings of citizenship and membership. It argues that the state in Africa has, inherent within its foundations, exclusionary and discriminatory practices, which affect both citizens and noncitizens. These result in multiple sites of inclusion and exclusion based on membership of a variety of shifting groups, categories and networks. This observation suggests the need to re-evaluate our understanding of the dominant analytical concepts of 'state' as 'protector' and 'citizen' as 'insider' thus far used to address the issue of entitlement to rights, around which the refugee regime has been constructed. The thesis also underscores the importance of breaking out of the 'territorial trap', calling attention to the growing importance of international and transnational actors in defining the actions of the state and the direction of domestic policy. It points out that as refugees are progressively excluded from the realm of the nation-state, they increasingly turn to the international community, represented by international humanitarian actors, for recognition. This contributes to the marginalisation of the state in the management of refugee affairs, which has a negative impact both on the protection of refugee rights and the credibility of the state in the eyes of its citizens. In response to this development, the thesis questions the legitimacy and accountability of international humanitarian actors and emphasises the importance of bringing the state back into the centre of the refugee protection regime.
Greek and related pottery from Al Mina. A case study of production, consumption and distribution of Greek pottery in the Eastern Mediterranean from the 9th to the end of the 7th century BC.

The present thesis provides and examination of the Greek imports from Al Mina dating from the end of the 9th to the end of the 7th centuries BC. Al Mina, located on the Orontes river in the Hatay province of Turkey, was excavated by L. Woolley in 1936 and 1937. In particular the large quantities of Greek imports recovered from the sites triggered a debate about the site’s function and it’s foundation date.
In order to overcome past deficiencies the present thesis provides a detailed record of the Greek pottery recovered from the site. The fragments are analysed stylistically and dated in order to establish a local chronology. Further, a detailed statistical study of the whole assemblage, which comprises about 4800 pieces, reveals evidence for local consumption patterns and further sheds light on the ports external contacts during the 8th and 7th centuries BC. The study also entails a contextual analysis of specific Near Eastern sites in order to set Al Mina in its regional context. Three questions are of major concern in this respect: is it possible to identify the users of Greek pottery in the East in terms of their socio-economic background? Further, is Greek pottery better understood as a commodity or as a gift? Finally, What role does Greek tableware play within the trade with other commodities?
The study illustrates that pottery primarily circulated within the lower social classes. It also highlighted a diverse pattern in which high quality products are circulating besides “mass ware”. This can be understood as a diversification process that was initiated in order to reach a wider range of consumers.

Keywords: trade
Greeks in the East
consumption
Greek pottery
Advisor: Lemos, I
Writing the Indian Ocean in selected fiction by Joseph Conrad, Amitav Ghosh, Abdulrazak Gurnah and Lindsey Collen

Tracked and inscribed across the centuries by traders, pilgrims and imperial competitors, the Indian Ocean is written into literature in English by Joseph Conrad, and later by selected novelists from the region. As this thesis suggests, the Indian Ocean is imagined as a space of littoral interconnections, nomadic cosmopolitanisms, ancient networks of trade and contemporary networks of cooperation and crime. This thesis considers selected fiction written in English from or about the Indian Ocean—from the particular culture around its shores, and about the interconnections among its port cities. It focuses on Conrad, alongside Amitav Ghosh, Abdulrazak Gurnah and Lindsey Collen, whose work in many ways captures the geographical scope of the Indian Ocean: India, East Africa and a mid-point, Mauritius. Conrad’s work is examined as a foundational text for writing of the space, while the later writers, in turn, proleptically suggest a rereading of Conrad’s oeuvre through an oceanic lens. Alongside their diverse interests and emphases, the authors considered in this thesis write the Indian Ocean as a space in and through which to represent and interrogate historical gaps, the ethics and aesthetics of heterogeneity, and alternative geographies. The Indian Ocean allows the authors to write with empire at a distance, to subvert Eurocentric narratives and to explore the space as paradigmatic of widely connected human relations. In turn, they provide a longer imaginative history and an alternative cognitive map to imposed imperial and national boundaries. The fiction in this way brings the Indian Ocean into being, not only its borders and networks, but also its vivid, sensuous, storied world. The authors considered invoke and evoke the Indian Ocean as a representational space—producing imaginative depth that feeds into and shapes wider cultural, including historical, figurations.

Keywords: Lindsey Collen
East Africa
Zanzibar
Mauritius
spatial
Joseph Conrad
Indian Ocean
oceanic
Amitav Ghosh
India
Abdulrazak Gurnah
Advisor: Boehmer, E
New approaches for improving the immunogenicity of modified vaccinia virus Ankara as a recombinant vaccine vector

The CD8&plus; T cell response to a transgenic antigen expressed in Modified Vaccinia virus Ankara (MVA) can be augmented with enhanced transgene expression. This thesis presents different approaches to increase transgene expression in MVA. The transgene used was the sequence of the pb9 murine malaria epitope, fused to Renilla luciferase gene, and then fused to a secretion leader sequence (tPA) at the N terminus. The insertion of Internal Ribosomal Entry Site (IRES) upstream of the transgene, driven by the pB8 promoter and inserted at the B8R locus, or the modification of the pB8 promoter by nucleotide substitution both failed to enhance the transgene expression or immunogenicity. However, utilising endogenous promoters such as the pB8, pE3, and pF11 at their natural loci to drive the transgene resulted in lower transgene expression in vitro, but stronger immune responses to the pb9 epitope in BALB/c mice, as compared to the conventional p7.5 or mH5 promoters. Utilising these promoters at the TK locus (ectopic promoters) revealed similar patterns of transgene expression and immunogenicity, indicating that the improved immunogenicity is linked to promoters despite the low transgene expression measured in vitro. Therefore, the pF11 promoter was further studied to determine its activity in vivo and showed higher transgene expression, as compared to the mH5, which correlated with in vivo immunogenicity. Inactivation of the TK gene in MVAs with endogenous promoters showed reduced in vivo transgene expression and immunogenicity. Finally, in a related attempt to enhance MVA immunogenicity, deleting multiple immunomodulatory genes from the MVA genome did not affect MVA cellular immunogenicity in a range of vaccination regimens, testing either the pb9 epitope or the M. tuberculosis antigen 85A.

Keywords: immunogenicity
Modified Vaccinia virus Ankara
poxvirus
transgene expression
vaccine
viral vector
promoter
Advisor: Gilbert, S
Draper, S