VictorJuiz/thesis huggingface dataset:
A stepwise approach to understanding and effectively mitigating human-wildlife interactions
Keywords: People's livelihood
Red deer
Conflicts in conservation
wildlife management
Elephants

The study of conflicts in conservation (also known as human-wildlife conflicts) is a growing field of research in areas where people and wildlife interact, because of the negative impacts each can have on the other. Addressing conflicts is certainly challenging because of the complexities of considering diverse interests from numerous stakeholders and the specific ecological and socio-economic characteristics of a given study system. No matter how complex the system under study is, the aim is in all cases to find effective and sustainable mitigation strategies for local people, as well as for wildlife conservation and local authorities. In this thesis, I look at two of the preliminary steps required to address conservation conflicts and develop efficient long-lasting management solutions: the gathering of ecological data and the assessment of mitigation strategies in the field. To do this, I use two case studies: crop-foraging by African elephants (Loxodonta africana) in northern Botswana, and selective hunting of the red deer (Cervus elaphus) population on the Isle of Rum in Scotland. In Chapter 2, I built a baseline for the level of conflict in the Okavango Delta Panhandle (Botswana) using temporal trends of crop-foraging by elephants as an index of the level of conflict, and subsequently looked at how this relates to trends in agricultural land allocated in the study area, as well as with trends in human and elephant population size. In Chapter 3, I mapped the distribution of the local population of elephants and assessed its interaction with landscape features and sites where crop-foraging events had been recorded. In both chapters (2 & 3) I found that -in general- the number of elephants was not a determinant of the level of conflict in the study area, but that the spatiotemporal distribution of the species as well as the spatial and temporal scales considered were. In the second half of my thesis, I assessed the effects of two common conflict mitigation methods: the use of deterrents (Chapter 4) and lethal control (Chapter 5). I first evaluated the effectiveness of chilli-briquettes in deterring elephants and secondly, I used a modelling approach to predict the demographic effects of increasing levels of selective hunting in a male red deer population. I found that both mitigation methods showed unexpected results, which would not have been detected had I not tested for them. This thesis highlights the advantages of applying methods that are based on informed decisions in areas of conflict, as well as the value of sharing results in conservation management. My findings contribute towards a better understanding of the negative impacts of human-wildlife interactions, which often lead to conservation conflicts, as well as contributing protocols and methodologies that can be adapted and applied elsewhere.
The north-eastern Aegean 1050-600 BC
Keywords: Aegean Sea Coast (Turkey)
Archaic Period
Early Iron Age
Aegean Islands
Macedonia
Thrace

This thesis aims to construct a historical narrative for the region of the north-eastern Aegean (NEA) during the Early Iron Age (1050-700 BCE) and the early Archaic period (7th century BCE) based primarily on archaeological evidence. Its goals are to investigate the most distinctive material culture elements for the studied period; to explore themes of continuity and connectivity between regions; to trace large- and smaller-scale population movements; to discuss how early communities perceived themselves and each other; and to investigate the social structure and organisation of these communities.
Evidence from settlement sites, funerary contexts, and sanctuaries are presented in the first three chapters in that order. Following that, the final chapter presents the primary, overarching conclusions of the thesis, in four sub-chapters.
Firstly, it is argued that the NEA was characterised by relative cultural continuity from the Late Bronze Age to well within the Archaic period: when new elements were introduced, they were, generally, integrated into earlier paradigms.
Secondly, evidence is provided for an increase in connectivity and maritime traffic peaks during the late 8th century BCE; shortly afterwards, new population groups from the central and southern Aegean arrived in the NEA, and seem to have cohabited relatively peacefully with earlier populations.
Thirdly, it is posited that there is little evidence for overarching NEA regional identities before the 6th century BCE: communities appear to have developed local identities, through association with specific sites and through references to the communal past in cult practice and funerary contexts.
Finally, it is argued that social elites were markedly active in NEA communities of studied period: there is considerable evidence for socially exclusive groups, primarily in funerary and ritual contexts.
The thesis concludes with a short chapter containing the author's closing remarks.
The algebra of entanglement and the geometry of composition
Keywords: PROPs
categorical universal algebra
polygraphs
zw calculus
string diagrams
higher categories
zx calculus
categorical quantum mechanics

String diagrams turn algebraic equations into topological moves that have recurring shapes, involving the sliding of one diagram past another. We individuate, at the root of this fact, the dual nature of polygraphs as presentations of higher algebraic theories, and as combinatorial descriptions of "directed spaces". Operations of polygraphs modelled on operations of topological spaces are used as the foundation of a compositional universal algebra, where sliding moves arise from tensor products of polygraphs. We reconstruct several higher algebraic theories in this framework.
In this regard, the standard formalism of polygraphs has some technical problems. We propose a notion of regular polygraph, barring cell boundaries that are not homeomorphic to a disk of the appropriate dimension. We define a category of non-degenerate shapes, and show how to calculate their tensor products. Then, we introduce a notion of weak unit to recover weakly degenerate boundaries in low dimensions, and prove that the existence of weak units is equivalent to a representability property.
We then turn to applications of diagrammatic algebra to quantum theory. We re-evaluate the category of Hilbert spaces from the perspective of categorical universal algebra, which leads to a bicategorical refinement. Then, we focus on the axiomatics of fragments of quantum theory, and present the ZW calculus, the first complete diagrammatic axiomatisation of the theory of qubits.
The ZW calculus has several advantages over ZX calculi, including a computationally meaningful normal form, and a fragment whose diagrams can be read as setups of fermionic oscillators. Moreover, its generators reflect an operational classification of entangled states of 3 qubits. We conclude with generalisations of the ZW calculus to higher-dimensional systems, including the definition of a universal set of generators in each dimension.
Estimating and comparing the cost-effectiveness of primary prevention policies affecting diet and physical activity in England
Keywords: Public health
Health economics
Cost effectiveness
Health policy
Modelling
Multistate life table
Physical activity
Diet

Health and public health services in England are under increasing financial pressure. At the same time, nearly 40% of the total disease burden is potentially amenable to known causes with two of the leading behavioural risk factors being unhealthy diets and physical inactivity. To better inform decision makers and improve health in England, this thesis aims to develop a cost-effectiveness model that can directly compare diet and physical activity interventions.
Published public health economic models were reviewed and the strengths and weaknesses of the modelling structures were explored. A pre-existing multistate life table model, PRIMEtime, was developed into PRIMEtime Cost Effectiveness (PRIMEtime CE). Disease specific NHS England costs were derived from NHS England Programme Budgeting Data and unrelated disease costs from NHS cost curves. Social care costs were quantified using a Department of Health tool for estimating wider societal costs. Disease specific utility decrements were adopted from a catalogue of EuroQoL five dimensions questionnaire scores. The cost effectiveness of reformulating food to have less salt and of expanding access to leisure centres in England were modelled from an NHS and social care perspective over a 10 year time horizon, including government and industry costs.
Salt reformulation was dominant with an estimated cost per quality adjusted life year (QALY) of -£17,000 (95% uncertainty interval, -£40,000 to £39,000), compared with £727,000 (£514,000 to £1,064,000) for increasing access to leisure centres. Sensitivity analyses and cross validation testing of outcomes demonstrated how cost per QALY estimates were sensitive to the choice of model scope, parameters, and structure.
PRIMEtime CE is a tool for decision makers to compare interventions affecting diet and physical activity, enabling them to make better informed choices about how to spend finite resources. Future work will focus on making the model freely available and expanding its risk factors to enable comparisons of other public health interventions.
An archaeobotanical investigation into the Chalcolithic economy and social organisation of central Anatolia
Keywords: Kuruçay
Crop processing
Canhasan I
Çamlıbel Tarlası
Çatalhöyük West
Agricultural production
Weed Flora
isotopes
Crop husbandry
Consumption

Limited knowledge about the 3000-year period between the Neolithic and the Bronze Age in central Anatolia, Turkey, prevents any understanding of change or continuity in crop production, consumption and crop husbandry techniques. This research aims to address this bias through the examination of archaeobotanical remains from the four central Anatolian Chalcolithic sites of Çatalhöyük West, Çamlıbel Tarlası, Canhasan I and Kuruçay and the consequent investigation of their crop economies. This work draws on multiple methods and techniques to understand the plant-related activities that occurred at the sites.
The four chosen sites bookend the Chalcolithic period (c. 6000-3000 cal BC) and provide the opportunity for exploring the interrelationship between crop choice, crop husbandry, settlement size, surrounding environment and social organisation. Differences in crop species such as hulled barley, glume wheats and pulses, particularly lentil and bitter vetch occur at all four sites with species choice community specific.
Multiple methods are used to disentangle the depositional processes, such as dung burning, that formed the assemblages, providing an indication of the origin of the archaeobotanical material and allowing inferences about the nature of weed seeds found. Crop processing activities are evident at all sites, with the dehusking of glume wheat contributing significantly to the archaeobotanical assemblage. The analysis of stable carbon and nitrogen isotopes of crops coupled with the functional ecology of arable weeds, indicate that crop husbandry techniques/regimes were site specific and were influenced by site size/population as well as environmental conditions. The identification of the crops grown and the methods used to cultivate and process them have implications for understanding the social context of such activities, and the broader socio-economic background of a period preceding the great changes in social structure seen in the Bronze Age.
An analysis of the relationship between monetary policy, business cycles and financial stability
Keywords: Dynamic Stochastic General Equilibrium Model
Mortgage Default
Monetary Policy
Bank Risk-taking
Macroprudential Regulation
Endogenous Default

The thesis sheds light on key policy issues emerging from the recent Global Financial Crisis. The first chapter studies whether expansionary monetary policy contributes to bank risk-taking, in the case of Asia. I rely on panel data analysis covering 432 banks in 9 Asian countries over the year 2000-2011. The ratio of risky assets to total assets serves as a risk-taking indicator. The results support the existence of the bank risk-taking channel, which is more pronounced for banks listed on the stock market. I also report new findings with respect to how banks take more risk following monetary expansion. Importantly, evidence of excessive leverage is not found. The second chapter constructs a model for analyzing bank risk-taking. I embed firm heterogeneity, endogenous default risk and capital adequacy regulation into both RBC and NK DSGE models. A subset of the firms can partially default on their loans obligation but subject to non-pecuniary default penalty. With those financial frictions in place, I find that standard macroeconomic shocks can induce banks to engage in higher risk-taking. The chapter then explores the effectiveness of several macro-prudential tools in mitigating risk-taking. I find countercyclical capital buffers and risky to total asset ratio targeting to be effective. The third chapter emphasises the spillover effects of shocks originating in the housing and financial market on the real economy. I embed endogenous mortgage default into a New Keynesian model that features housing and the banking sector. The latter faces capital regulation. We study two key shocks, namely shocks to the variance of idiosyncratic housing shock and shocks to the penalty on capital regulation. Both are instrumental in causing a surge in mortgage default and loans risk premium, which constrains bank lending activity. The chapter later introduces three macroprudential measures to explore whether they improve economic stability and welfare.
Chemical probes for histone lysine demethylases
Keywords: Epigenetics
Chemical Probes
Lysine Demethylases

The primary objective of this DPhil research project was to develop selective and cell-active inhibitors of the histone lysine demethylase KDM2A, which could potentially lead to the discovery of a novel chemical probe. Chapter one of this thesis introduces the role of histone lysine demethylases (KDMs) in the epigenetic regulation of gene expression and discusses the value of chemical probes as tools to study these enzymes. Chapter two describes the synthesis of a library of indoline-based KDM2A inhibitors using a modular synthetic approach to explore key structure-activity relationships and a chiral counterion-mediated strategy to synthesize lead candidates enantioselectively. Chapter three discusses investigations into the cellular activity of lead compounds and explores strategies to address limitations associated with cytotoxicity and promiscuity. Chapter four describes the application of a variety of experimental techniques to identify the mode of target inhibition. Finally, chapter five focuses on the development of an enantioselective C-acylation reaction to access spirocyclic fragments asymmetrically.
Social norms and learning in games
Keywords: Social norms
Learning

Duelling
The norm of duelling endured for hundreds of years in Europe. In the United Kingdom it disappeared abruptly in the mid-nineteenth century, whereas in France it declined slowly. I present a simple model of social norms that explains these phenomena. The model predicts that the evolution of norms is characterised by tipping, whereby norms can shift suddenly due to shocks, and by a ratchet effect, whereby changes in parameters can cause norms to decline gradually. I show that the model can be supported by an equilibrium of a repeated game, with no special assumptions about preferences.
Community enforcement using modal actions
I prove two folk theorems for repeated games with random matching. A large group of players is rematched at random each period, so that players who deviate must be sanctioned by third parties. Previous analyses have either relied on strong assumptions about information transmission, or have been limited to equilibria that are not robust to noise or in which players are indifferent. I use a simple construction based on modal actions to obtain results for strict and robust equilibria.
Learning repeated-game strategies
The literature on boundedly rational learning has tended to focus on stagegame actions. I present a stochastic learning rule for repeated-game strategies. Players form beliefs about their opponent’s strategy based on past actions and best-respond. Occasionally, they make mistakes and experiment, and I show that the equilibrium selected depends on exactly how players make mistakes. Simple specifications of the learning rule yield intuitive selection results: the maxmin, or Rawlsian, outcome; the Nash bargaining solution; the maximum of the sum of payoffs; and a generalisation of risk dominance.
The genetic regulation of Kranz anatomy in maize
Keywords: Kranz
Gene duplication
IDD genes
Scarecrow/ shortroot genes
Rice
Maize

The C4 photosynthetic pathway acts to concentrate CO2 around the enzyme Ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), ensuring that it catalyses a carboxylation rather than oxygenation reaction, which in turn suppresses photorespiration. In nearly all cases C4 photosynthesis is underpinned by characteristic Kranz anatomy, with concentric wreaths of bundle sheath (BS) and mesophyll (M) cells surrounding closely spaced veins. The increased yields associated with the C4 pathway have lead to the suggestion that C3 crops such as rice should be engineered to undertake C4 photosynthesis, however, this goal is currently held back by a lack of understanding about how the development of Kranz anatomy is regulated.
Recently, a number of candidate Kranz regulators have been identified in an RNA-seq study that compared leaf development in maize foliar (Kranz) and husk (non-Kranz) leaves. However, this study did not consider the impact of a recent whole genome duplication in the maize lineage on the gene expression patterns analysed. Therefore, in this thesis maize homeolog gene-pair divergence during early leaf development was assessed. This revealed that expression divergence of homeolog gene-pairs is a significant evolutionary phenomenon.
Functional validation of a subset of Kranz candidates revealed that a Zmscr1-1; Zmscr1h-1 double mutant exhibited defects in Kranz patterning, including increased formation of extra BS cells and veins with no separating M cells. Furthermore, Zmnkd1; Zmnkd2 double mutants exhibited a subtle increase in extra BS cell formation. Taken together, this indicates that both ZmSCR1/ZmSCR1h and ZmNKD1/ZmNKD2 function redundantly during Kranz development. No evidence was obtained that two additional genes, ZmSHR2 and ZmRVN1, play a role in Kranz development, and expression of candidate Kranz regulators in rice did not alter leaf anatomy. Together, this work has confirmed roles for a number of genes in Kranz regulation, and has provided insight into the complex regulation underpinning Kranz development in maize.
Remnant in koinonia: towards an Adventist version of communio ecclesiology
Keywords: communio ecclesiology
ecclesiology
identity
remnant
theology
communion
community
adventism
fellowship
adventist
seventh-day adventism
church
Holy Spirit

In the last two decades, Seventh-day Adventist scholars have been attempting to articulate a balanced and distinct ecclesiology, aimed at helping the denomination to retain its global unity, maintain its relevance and enable a more fruitful and meaningful interaction with others. No comprehensive account of the church has been developed yet, however.
This thesis is intended to facilitate a more rounded and systematically articulated concept of church from an Adventist perspective. Part I presents a thumbnail history of the denomination and considers the advantages and limitations of its standard claim to be the 'remnant', awaiting a pre-millennial parousia. Part II engages with the ideas of some of the ablest communio ecclesiologists of the twentieth and twenty-first centuries and considers their ecclesiological system, built around the concept of koinonia, while Part III examines ways in which their theoretical framework can assist the Adventist community to deal with practical ecclesial issues.
Four major proposals are made for deepening Adventist understanding of the nature of church. Whereas the formal structure of communio framework can help Adventists move beyond one-sided, single-metaphor communal self-descriptions, the idea of the church as essentially a koinonia of believers in God can supplement their predominantly functionalist portrayal of the church as herald or messenger. Thirdly, the Adventist notion of truth can be enriched by viewing the community of believers not only as a messenger, but also as an organic part of divine revelation. This makes ecclesiology central to the theological enterprise, intrinsic to the grounding of theological claims and the interpretation of biblical texts. Finally, the development of a richer interpretation of the Spirit’s activity in the church is seen as one of the key prerequisites for a fuller, more nuanced account of the church’s participation in the life of the triune God. The highlighting of these four aspects, hitherto neglected or underdeveloped in Adventism, and the presentation of tentative solutions to its ongoing ecclesiological problems, form the principal contribution of this monograph.
Hindu-Muslim violence in Gujarat, 2002: political logic, spatial configuration, and communal cooperation
Keywords: conflict
India
Gujarat
Hindu-Muslim
ethnic violence

This thesis uses a mixed methods approach to investigate the different levels of Hindu-Muslim violence in Gujarat (western India) in 2002 when at least a thousand Muslims were killed. An original dataset of killings is compiled to analyse macrospatial variation in the violence across towns and rural areas of Gujarat. Data collected from 21 months of ethnographic fieldwork in Ahmedabad city is used to investigate microspatial variation across three neighbourhoods with varying levels of violence.
Macrospatial analysis discusses the link between political authority and its capacity to instigate ethnic violence as a response to electoral calculations and identifies the mechanisms by which violence against Muslims was orchestrated by the Hindu nationalist Bharatiya Janata Party (BJP). Ethnographic findings demonstrate the importance of ecological strategies adopted by attackers and targets during the course of attack and urge a re-examination of the intuitive association of spatial proximity with greater interethnic contact. Findings also reveal methods of enforcement used by legitimate and illegitimate institutions of a peaceful slum neighbourhood in resolving commitment problems of cooperation. Finally, the thesis examines the aftermath of the violence, more specifically a political phenomenon of Muslims of Gujarat supporting the BJP nine years after the brutal violence.
Methodologically, the main contribution of this thesis is in bridging the quantitative and ethnographic traditions in the sociology of ethnic violence to make possible the linking, and disentangling, of macrolevel risk factors associated with violence from microlevel factors. Findings of the thesis hopefully provide a better understanding of ethnic violence in multi-ethnic democracies and a roadmap of policy-making for India as it continues to struggle with ethnic strife.