VictorJuiz/thesis huggingface dataset:
Environmental activism, non-governmental organisations and the new generation of civil society in Russia and China

This dissertation analyses the development paradigms of civil society in Russia and China, using the examples of Environmental Non-Governmental Organisations (ENGOs) and youth grassroots movements in Beijing, Moscow, Vladivostok, and Kunming. Civil society in Russia and China have experienced similar path of development over the last thirty years, and in both countries, ENGOs have been supported by Western donors in hopes of democratisation. This factor has created contention with the national governments, and both countries have recently adopted the laws restricting NGO development and limiting the engagement of foreign donors. This dissertation is situated in the context of transition and change of political landscape and examines the impact of these laws on ENGOs and civil society development in Russia and China, as well as on the future of political activism and youth. Qualitative data gathered from semi-structured interviews and participant observation is used to illustrate the effects of these changes on the first generation of ENGOs and their foreign donors, and the impact on the future of civil society - young environmental activists. Despite the consensus on the devastating state of political freedom and activism in Russia and China, this dissertation sheds light on emerging environmental movements and the new forms of activism that may be transforming the landscape for civil society in both countries. Situated in the literature on environmental movements, youth and environmental activism from geography, political science, and area studies, this dissertation challenges dominant discourses on civil society in authoritarian regimes. The results of this study not only contribute to the literature on countries in postcommunist transition but also contribute to our understanding of alternative forms of environmental activism in constrained political environments.

Advisor: Pallot, J
Lora-Wainwright, A
Mountain and sea: settlement and economy in late antique Lycia, Isauria and north central Anatolia

This thesis is an interdisciplinary comparative analysis of the socio-economic developments of three regions in Anatolia: Lycia, Isauria and north central Anatolia in the late antique period (c. AD 330-600s). I present the most up-to-date picture of late antique settlement in these regions by collating recent evidence, particularly amphorae and settlement remains, derived from research conducted in these regions over the past few decades. From this picture, I analyse what the location of settlement and archeological remains within sites may reveal concerning the ways in which settlements participated in local, region and interregional exchange networks.
As these three regions share the common geographic features of bordering major maritime areas and encompassing mountainous interiors, I examine how geography may have impacted the location of settlement and the movement of goods and people. By integrating areas located on opposite Anatolian coastlines, I examine how differing maritime networks may have impacted settlement development. This tripartite comparison attempts to establish northern Anatolia alongside its southern counterpart in the discourse of late antique economy and settlement development.
Alongside this regional analysis, I discuss methodological considerations, such as the ways in which the current state of research and various research methods impact our analysis and interpretation of late antique settlement development. This study reveals that sub-regions within Lycia, Isauria and north central Anatolia developed in diverse ways and that the ways in which each region participated in wider exchange differed. I argue that overarching narratives of development, such as 'prosperity' and 'decline' do not accurately reflect the development of these regions. In sum, this thesis contributes an up-to-date analysis of the settlement development of Lycia, Isauria and north central Anatolia to the wider discourse of late antique regional development, which engages and challenges discourse surrounding the economic development of these regions in Late Antiquity.

Keywords: settlement development
historiography
Lycia
Anatolia
North Central Anatolia
Isauria
Late Antiquity
Advisor: Jacobs, I
Investigation of auto-antibodies targeting TNF-related peptides as possible biomarkers for lethal sepsis

Background: Necroptosis is a programmed form of necrotic cell death. Necroptosis is thought to play an important role mediating the pathogenesis of inflammatory disease. Previously, a 30-mer peptide, P1213, within the most conserved region of TNF was found to be capable of promoting apoptosis. We discovered that autoantibodies targeting the P1213 region of TNF correlated with inflammatory disease, such as rheumatoid arthritis. It has been demonstrated that the autoantibodies convert TNF-related apoptosis into necroptosis when they bind to the apoptosis-inducing P1213 motif.
Objectives: Explore the link between autoantibodies against different regions of the TNF molecule and the clinical outcomes of severe sepsis, using serum samples of patients divided into those who died (lethal sepsis) and those who survived. In addition to explore cellular mechanisms whereby the autoantibodies may promote TNF-mediated necroptosis, and to assess whether the autoantibodies provide a potential biomarker for susceptibility to lethal sepsis.
Results: Through ELISAs and flow cytometry analysis, we found more than half of deceased sepsis patient sera (n=25) were positive for anti-P1213 autoantibodies. We discovered another conserved region, P21, which has the capacity to induce apoptosis similar to P1213. Part of P1213 and P21 are located physically adjacent to each other within the TNF conformational structure.
Conclusion: We have identified the autoantibodies as a potential biomarker to associate mortality in severe sepsis although not all deceased sepsis patients possess the autoantibodies. P1213 and/or P21 oligopeptides could be developed as neutralising ligands for the autoantibodies to protect sepsis patients from mortality.

Advisor: Jiang, S
Seymour, L
Investigating the role of factor inhibiting HIF (FIH) in tumourigenesis

The tumour microenvironment (TME) is frequently hypoxic and inflammatory, leading to the activation of the Hypoxia-Inducible Factor (HIF) family of transcription factors. HIF has been shown to exert broad, and sometimes controversial, effects on tumour progression through the induction of over 70 effector genes. Factor Inhibiting HIF (FIH), an oxygen-dependent hydroxylase of HIF, inhibits the transcription of selective HIF target genes, and is hence a potential therapeutic target to fine-tune HIF activity. However, how FIH may affect tumourigenesis has not been comprehensively investigated.
By monitoring the spontaneous tumour formation in mice, it was found that a lack of FIH expression does not profoundly affect the lifespan but accelerates the development of low-grade B cell lymphomas. To investigate whether FIH could suppress tumourigenesis via modulating the TME, syngeneic tumour models were employed on FIH-deficient animals. Reduced FIH expression in the host promotes tumour growth, which is recapitulated by FIH deletion only in the myeloid compartment. Tumours in mice deficient of myeloid FIH exhibit an altered immune profile, reflected by the increased expression of programmed death-ligand 1 (PD-L1) and Arginase 1 (ARG1) in tumour-associated macrophages (TAMs) and a reduced CD4 T cell population. In vitro characterisation of FIH-deficient macrophages reveals that FIH suppresses cell migration to C5a and CCL5, and affects the expression of several inflammatory mediators including PD-L1 and ARG1. Importantly, the transcription of FIH is upregulated in macrophages by tumour cell-conditioned media as well as bacterial infection. Altogether, this study provides the genetic evidence for the role of FIH in tumour suppression, which may result from its influence on the myeloid-mediated immune response. Therefore, FIH represents a new candidate regulator of the TME and can be implicated in other inflammatory conditions such as infection.

Advisor: Lu, X
Ratcliffe, P
Ethno-ornithology and conservation: traditional ecological knowledge (TEK) of birds among the Mushere and the conservation of the Dulu forest in Mushere, Plateau state, Nigeria

This research was aimed at determining the ethno-ornithological knowledge of three Mushere villages close to the Dulu Forest, Nigeria to determine whether this might hold potential for developing a local conservation programme to protect the forest. The conservation objective of the research was aimed at determining the drivers of forest degradation, and possible means of mitigation. Using a mixed method approach, quantitative/qualitative data were collected in two years from different demographics (men, women, children, age differentials, occupation, urbanization). Oral interviews, semi-structured interviews, picture elicitation tasks, free-listing exercises and focus group discussions were employed in the data collection process. The findings revealed a relatively low ethno-ornithological knowledge, and a general indifference (ornitho-apatheia) towards birds. Knowledge transmission was predominantly through oral means while TEK acquisition was mainly through vertical and horizontal methods. While adults perceived birds as not valuable, children generally perceived birds as valuable. Cultural utilization and ecological salience were the main drivers of bird naming and knowledge. However, there was a high valuing of the Dulu forest, with the main drivers of the forest degradation being timber extraction. Overall, I concluded that the indifference of the Mushere towards birds revealed a lack of cultural appreciation of birds, leading to little TEK of birds, insufficient to encourage the use of TEK of birds in the conservation of the Dulu forest, and the use of birds as flagship domain for promoting conservation. However, a sustained approach towards encouraging birding activities could improve the perception of birds. I therefore suggest using an ecosystem approach in the conservation of the Dulu forest. Engaging the locals in dialogue, establishing a leadership structure for the management of the Dulu forest, providing alternative means of livelihoods are suggested as ways of mitigating the degradation of the Dulu forest.

Keywords: Conservation
Ethno-ornithology
Dulu Forest
Cultural transmission
Biodiversity
Traditional ecological knowledge (TEK)
Mushere
Knowledge Acquisition
Ecological salience
Cultural salience
Advisor: Gosler, A
Zeitlyn, D
A reduced tensor product of braided fusion categories over a symmetric fusion category

The main goal of this thesis is to construct a tensor product on the 2-category BFC-A of braided fusion categories containing a symmetric fusion category A. We achieve this by introducing the new notion of Z(A)-crossed braided categories. These are categories enriched over the Drinfeld centre Z(A) of the symmetric fusion category. We show that Z(A) admits an additional symmetric tensor structure, which makes it into a 2-fold monoidal category. ByTannaka duality, A= Rep(G) (or Rep(G; w)) for a finite group G (or finite super-group (G,w)). Under this identication Z(A) = VectG[G], the category of G-equivariant vector bundles over G, and we show that the symmetric tensor product corresponds to (a super version of) to the brewise tensor product. We use the additional symmetric tensor product on Z(A) to define the composition in Z(A)-crossed braided categories, whereas the usual tensor product is used for the monoidal structure. We further require this monoidal structure to be braided for the switch map that uses the braiding in Z(A).
We show that the 2-category Z(A)-XBF is equivalent to both BFC=A and the 2-category of (super)-G-crossed braided categories. Using the former equivalence, the reduced tensor product on BFC-A is dened in terms of the enriched Cartesian product of Z(A)-enriched categories on Z(A)-XBF.
The reduced tensor product obtained in this way has as unit Z(A). It induces a pairing between minimal modular extensions of categories having A as their Mueger centre.

Keywords: Topological Field Theory
Modular Tensor Categories
Fusion Categories
Advisor: Douglas, C
Device monitoring and device management for smart meters

The utility industries across the world are trying to address challenges such as energy conservation, greenhouse gas emission, demand response management, diversified energy generation and so on. The next generation grid referred to as “Smart Grid” and “Smart Metering” are expected to provide solution to majority of these challenges. Smart metering is simply a culmination of information and communication technologies with traditional utility components – which will deliver intelligent and automated, remote utility meter monitoring and management capabilities [1]. The two main components of Smart metering are, the smart meters and the communications network which will provide the two way communication capability between the utility suppliers and the consumers (Smart meters).
The key aspect of smart metering network is its ability to manage events generated by end devices namely smart meters. An event is any notable condition that happens in the smart metering environment. These events must be reported to both the communication service provider and the utility supplier. An event in general could be a fault in the system such as a device failure or business event such as detection of a threshold condition, over or under voltage detection etc. Both system faults and business related events will occur frequently and it is important that both kinds of events are quickly detected and reported. A fault management system will provide a centralized event monitoring and management capabilities to the network service provider. Like any other larger scale communications network, a smart meter network will also be built with multi vendor devices and technology. Therefore it is essential to build an event monitoring system that is scalable and can support diverse network equipment. The objective of this dissertation is to propose a fault monitoring system model for smart meters.

Advisor: Trigoni, N
Imaging p53 in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) represents 90% of pancreatic cancer cases and is characterised by poor survival rates and resistance to current therapeutic regimes as the majority of patients present with an already advanced disease at the time of diagnosis. Mutations of the TP53 tumour suppressor gene are a frequent event in tumourigenesis and appear in around 75% of pancreatic cancer cases just before the full development of PDAC and metastasis into the surrounding tissues. Molecular imaging tools, such as SPECT, using monoclonal antibodies specific towards tumour associated antigens, could aid the in vivo characterisation of biological processes and provide a non-invasive method for early diagnosis of cancer.
Toward this end, a commercially available mouse monoclonal antibody against total p53 protein (anti-p53 (1C12)) was selected. Anti-p53 (1C12) was first evaluated in vitro regarding its specificity and affinity in cell lines with variable p53 status, derived from a genetically engineered mouse model of PDAC (KPC mice). The subcellular localisation of the p53 protein in the cell lines used was also studied.
Following the selection of the antibody, the anti-p53 (1C12) was conjugated to the cell penetrating peptide TAT to facilitate cellular and nuclear translocation and then to p-SCN-Bn-DTPA to allow labeling with 111In. Further in vitro evaluation was performed on the conjugated antibody, conferring subcellular translocation in fixed cells, unaffected binding affinity, favourable radiochemical yield and purity, and stability of the radioconjugate in serum. Retention of the radioconjugates was also observed and was signicantly different when compared to radiolabeled non-specific IgG1-TAT in cells harbouring mutant p53.
The ability of 111In-BnDTPA-p53 (1C12)-TAT to selectively target endogenously expressed p53 was assessed in vivo using mouse allograft tumour models of the cell lines evaluated in vitro, and in genetically engineered KPC mice. This provided a preliminary ''proof-of-principle" concept for diagnostic detection of PDAC. The knowledge acquired from the current study may be used to develop a first imaging tracer against p53 which could significantly improve the biological evaluation of cancer.

Advisor: Cornelissen, B
Age-period-cohort models

While over-dispersed Poisson age-period-cohort and extended chain-ladder models are used in a number of fields, so far no rigorous statistical theory has been available. We consider models for aggregate data organized in a two-way table with age and cohort as indices, but without measures of exposure. In these models, used for example in actuarial science, demography, economics, epidemiology and sociology, the number of parameters grows with the number of observations. Thus, standard asymptotic theory is invalid. In Chapter 2, we propose a repetitive structure that keeps the dimension of the table fixed while increasing the latent exposure. We pair this with the assumptions of infinitely divisible distributions which include a variety of compound Poisson models and Poisson mixture models. We then show that Poisson quasi-likelihood estimation results in asymptotic t parameter distributions, F inference, and t forecast distributions. In Chapter 3, we build on the asymptotic framework from Chapter 2 and develop tests for model specification. The over-dispersed Poisson model assumes that the over-dispersion is common across the data. A further assumption is that effects do not have breaks, for example age effects do not vary over cohorts. A log-normal age-period-cohort model makes similar assumptions. We show that these assumptions can easily be tested and that similar tests can be used in both models. In Chapter 4, we develop a non-nested test that allows one to evaluate whether the over-dispersed Poisson or log-normal model is the better choice for the data. While the over-dispersed Poisson model imposes a fixed variance to mean ratio, the log-normal models assumes the same for the standard deviation to mean ratio. We leverage this insight to propose a test that has high power to distinguish between the two models. Again, the theory is asymptotic but does not build on a large size of the array and instead makes use of information accumulating within the cells.

Advisor: Nielsen, B
Role of PDE2A in cAMP/PKA signaling compartmentalization

Background and Aims : cAMP/PKA signaling is compartmentalized within the cell, with tight spatial and temporal control of signal propagation underpinning specificity of response. The cAMP-degrading enzymes, phosphodiesterases (PDEs), are key regulators of this process. They are situated in specific subcellular domains within which they control local cAMP levels. Several components of the cAMP/PKA cascade have been identified in different mitochondrial compartments, including isoform 2 of PDE2A and multiple A-kinase anchoring proteins, suggesting the presence of multiple cAMP/PKA signaling domains within the organelle. The aims of this project were to examine the role of PDE2A in cAMP/PKA signaling compartmentalization and its biological function, with a particular focus on its role at the mitochondria.
Methods : Real-time PCR and fluorescence imaging were used to assess PDE2A expression and localization in different cell lines and tissues. Co-immunoprecipitation (Co-IP) was used to validate PDE2A2 interactors. Co-IP, electron microscopy and live-cell imaging were used to explore the role of PDE2A2 at the mitochondria. Fluorescence Resonance Energy Transfer (FRET) was used to investigate the involvement of PDE2A on endoplasmic reticulum (ER) Ca2+ handling and local cAMP/PKA dynamics.
Results : PDE2A2 localizes to the outer mitochondria membrane and intermembrane space and it interacts with several mitochondria and ER proteins, including components of the MINOS (mitochondrial inner membrane organizing system) complex and Caveolins. Functionally, PDE2A2 is involved in mitochondria degradation by mitophagy while PDE2A1 seems to be involved in the regulation of Ca2+ release from the ER. Phosphatases are responsible for the differential PKA dynamics between cytosol and ER.
Conclusions : PDE2A isoforms localize to different compartments and are involved in distinct cellular functions. The data presented in this thesis demonstrate that PDE2A2 activity at the mitochondria controls mitochondria clearance by mitophagy. This mechanism is dysregulated in multiple pathological conditions, making PDE2A2 a potential therapeutic target.

Advisor: Zaccolo, M
Investigating the variability of virulence in natural populations of Staphylococcus aureus using whole genome sequencing

Invasive Staphylococcus aureus disease is an important cause of morbidity and mortality, but is much rarer than asymptomatic carriage. The contribution of the bacterial genome to S. aureus infection is incompletely understood, and molecular epidemiology provides conflicting evidence. This thesis aims to improve our understanding of this contribution using the resolution afforded by whole-genome sequencing.
In a systematic study of S. aureus evolution in 105 hosts during invasive S. aureus disease, I demonstrate extensive within-host diversity, with evidence for varying selective pressures and within-host adaptation. Evidence for adaptation is strongest in genes under control of transcriptional regulatory systems, including Repressor of surface proteins (Rsp) (p=10–6.4) – a recently discovered global virulence regulator – and the Accessory gene regulator (Agr) (p=10–5.6), which are enriched for protein-altering variants 3.6- and 2.9-fold respectively. The development of invasive disease is associated with subtle changes in the transcriptional regulation of Staphylococcus aureus arising within hosts.
Applying recently developed tools for bacterial genome-wide association studies (GWAS), I present GWAS investigating for S. aureus genomic associations with two disease phenotypes: bacteraemia and pyomyositis. A study of S. aureus bacteraemia and carriage in 2001 isolates from the United Kingdom shows bacteraemia is not strongly bacterially determined: no lineages, genes or variants were significantly associated with bacteraemia.
In a study of 518 isolates from pyomyositis and carriage in Cambodian children, the presence of Panton-Valentine leukocidin (PVL) genes increases the odds of pyomyositis 130-fold (p=10–18), and variation in these genes and an adjacent promoter region are sufficient to explain over 99.9% of the heritability of pyomyositis. These results establish staphylococcal pyomyositis, like tetanus and diphtheria, as a disease depending critically on expression of a toxin.
Microbial genomics offers unparalleled opportunities to understand infections, and here I demonstrate insights generated through pathogen evolution within hosts and bacterial GWAS.

Advisor: Crook, D
Wilson, D