VictorJuiz/thesis huggingface dataset:
Social networks, collaborations and high-tech cluster formation in an emerging country: the case of biotechnology in Chile

Geographic clusters of firms have been extensively studied in different bodies of literature, but little attention has been paid to the process of cluster formation and its determinants. While focusing on the effects of clusters on innovations and on the productivity of firms, the literature has neglected the agency of entrepreneurs in cluster emergence.
This thesis aims to contribute to the literature on clusters by studying the role of personal networks and firm networks in three aspects of the emergence of clusters: 1) the early stages of formation; 2) the creation of business relations between firms; and 3) the creation of knowledge among clustered firms.
The analysis was conducted using the biotechnology sector in four geographic regions of Chile as a case study. Data on firms was collected using in-depth interviews and a survey. The analysis of the data was carried out using content analysis, multilevel estimations and econometric analysis.
The results reveal three main findings. First, the personal and business relations of entrepreneurs can determine the location decisions of firms. Second, personal relations are positively associated with the emergence of formal business relations between firms. Third, the number of personal and business connections a firm has positively affects its production of knowledge, measured as patent applications and scientific journals.
These findings suggest that social networks within a cluster shape its emergence and development. The results also show that the different types of networks coexisting in a cluster – personal networks, business networks and research networks, among others – affect one another and determine the development of clusters.
The implications of this research may be helpful for policy-makers, professional associations and cluster managers. Activities to foster personal interaction between members of a cluster and other key actors – universities, incubators, venture capital firms, government agencies, etc. – may generate collaborations between firms that would not otherwise emerge.

Keywords: biotechnology
cluster emergence
social networks
emerging country
high-tech entrepreneurship
Advisor: Fu, X
An international history of unemployment through the League of Nations and the International Labour Organization, 1931-1937

Late in 1931, the International Labour Organization (ILO) estimated that worldwide unemployment had reached 20-25 million. The ILO was also mindful that the consequences of unemployment were borne by dependents and concluded that the number of people directly affected by unemployment was therefore probably in the region of 50-60 million. The thesis revisits this old theme of the ‘Hungry Thirties’ but considers it in a new and different way. Most histories of unemployment during the Great Depression have been presented in national terms but this study examines unemployment from an international perspective by utilizing the League of Nations and ILO as sites through which to explore how debates about unemployment and how to respond to it were being internationalized. Utilizing the vast archives of the League of Nations and ILO, the thesis focuses on a series of interconnected themes – public works and economic policy, migration, housing, and nutrition – themes that the League and ILO identified as being the ‘fallout’ from unemployment. It builds on recent research of the League and ILO that has revealed more complex histories of these two international organizations and that has recognized that the ‘technical’ agencies were core functions that consumed significant resources of personnel and money. Crucially, this work not only continued during the 1930s but thrived even as the political atmosphere darkened; it is, therefore, a history that offers another side to the autarky and nationalism of the 1930s. The thesis also connects the technical agencies of the League of Nations to the ILO and, in contrast to the customary treatment of the interaction of these two organizations that emphasizes inter-agency tension, it identifies how the collaboration was an important step in the rediscovery of the fundamental connection between economy and society by linking economic policy to social and physical welfare.

Keywords: nutrition
1930s
housing
migration
economic policy
Advisor: Clavin, P
Development of computational methodologies for antibody design

Antibodies are proteins of the adapative immune system. Structural diversity in an antibody's two variable domains, VH and VL, allow it to bind almost any molecule with high affinity and specificity. This thesis focuses on characterising such variations to develop computational tools for antibody design, with a particular interest toward engineering antibodies as therapeutics.
First, we describe a method to predict the binding affinities of antibody–antigen interactions. Using the contacts at the antibody–antigen interface, we show promising results, but the performance is too poor for extensive design applications. Since several factors can influence antibody binding, we investigate VH–VL pairing, one of the largest sources of antibody structural variation. Based on our data, we describe a structure–based mechanism to describe VH–VL pairing. In particular, the high conservation of contacts at the VH–VLinterface in over 6000 antibody sequences provides support for random VH–VL pairing.
Following this analysis, we introduce our antibody modelling pipeline, ABodyBuilder. We demonstrate that ABodyBuilder can rapidly build accurate models, and is useful for mapping the antibody structural landscape from sequence. Furthermore, ABodyBuilder calculates the model's expected accuracy in order to help the decision–making process for users during antibody design. To complement ABodyBuilder's current setup, an antibody–specific rotamer library and side chain prediction algorithm are described. Although the maximum achievable accuracy is near 100%, the actual accuracy is closer to 80%, suggesting that the algorithm needs further refinement before full integration into the ABodyBuilder pipeline.
Finally, we discuss how the tools presented in the thesis can be improved, and applied to other problems in computational antibody design. We also present an overview on the potential avenues for expanding the work herein.

Advisor: Deane, C
The judgment of love: an investigation of salvific judgment in Christian eschatology

My study offers a constructive exploration of divine judgment as salvific rather than destructive which I describe aphoristically as iudicandus est salvandus ('to be judged is to be saved'). My provocation to Christian eschatology is that human beings are not saved from judgment, but are saved within it.
In chapter 1, I introduce the context of the study and propose the concept of salvific judgment. In chapter 2, I engage in an exploration of the symbols and problems of judgment through a reappraisal of De novissimis ('concerning the last things'), the last section found in traditional works of dogmatics. This is followed, in chapter 3, by a critical engagement with the soteriological optimism posited by four twentieth- and twenty-first century theologians: Sergei Bulgakov, Hans Urs von Balthasar, J.A.T. Robinson, and Marilyn McCord Adams. In chapter 4, I explore four versions of the purpose of judgment: (1) as retributive with a dual outcome, engaging the work of Paul O'Callaghan; (2) as retributive and universalist, in conversation with Sergei Bulgakov; (3) as non-retributive, rectifying, and universalist, exploring the oeuvre of Jürgen Moltmann; and (4) as non-retributive, constitutive of personhood, and quasi-universalist, investigating the eschatological thought of Markus Mühling.
In chapter 5, I propose to approach divine judgment as the event of absolute recognition. I posit that it is within the eschatic recognition of God, the self, and the other that transformation and glorification occur in a way that avoids a dual outcome of salvation and damnation. I then explore the problems concerning eternal life ('heaven') in the received tradition and propose that life in the eschatic realm of God is not eternal stasis, but the semper novum. I also explore this understanding of eternal life as it relates to the communion of saints.
I conclude by arguing that we may approach divine judgment with faith, hope, and love – not only for ourselves, but for the human race as a whole.

Keywords: Christian
Universalism
Heaven
Salvation
Death
Hell
Purgatory
Judgment
Advisor: Jeanrond, W
"Narrative dandyism": the theology of creation in the French decadent-dandyist novel 1845-1907

This thesis explores how selected "decadent-dandyist" writers of late 19th century France at once exemplify and subvert the self's act of shaping and imprinting its own selfhood upon the world: a model in which an autonomous, discrete artist-self freely creates, and in which both reader/audience and artistic "subjects" are treated as raw canvas and denied agency of their own. Storytellers like Barbey D'Aurevilly, Villiers de l'Isle-Adam, J. K. Huysmans, and Remy de Gourmont create not only hyper-artificial, cloistered, "auto-telic" (to use Charles Taylor's term) textual worlds (e.g. Huysmans' theïbade raffinée) but also hyper-artificial selves: presenting themselves and their often autobiographical protagonists as dandy-artists for whom artistic creation is an extension of self-creation.
Central to this thesis is the 19th century figure of the dandy – he who, to quote D'Aurevilly, "[causes] surprise in others, and [has] the proud satisfaction of never showing any oneself." Appropriating the divine power of self-fashioning, the dandy transforms the chaos of existence into a clear narrative over which he alone exerts control, denying that he himself is subject to the control of the world.
In my thesis, I first explore the cultural and economic roots of this understanding of the autonomous dandyist-artist in the light of wider tensions in 19th century Paris. I then explore selected "decadent-dandyist" texts through close reading, focusing on the theological implications of our authors’ treatment of narrative, character, setting, and language: showing how our writers cast doubt on both the possibility and morality "autonomous" creation on theological grounds. Finally, I ask how constructive theologians might learn from our authors’ condemnation of "dandyist" storytelling to create a new Christian aesthetics for the novel: proposing elements of an alternate, "kenotic" novel, in which self-projection gives way to "self-giving", a model based not on power and ego but rather on love.

Keywords: theology of creation
decadence
theology and literature
Advisor: Zachhuber, J
McGuinness, P
Between the courts of Lahore and Windsor: Anglo-Indian relations and the re-making of royalty in the nineteenth century

This thesis examines the political and social worldview of British and Indian royalty during the nineteenth century. Rather than viewing them as mere 'ornamental' figureheads, it seeks to highlight and scrutinise the ideas held by monarchs (sovereign or deposed) about empire and the role of royalty, as well as considering how their attempts at implementing such ideas can complicate existing narratives about the relative influence and authority of this group.
Above all, this thesis breaks new ground by adopting a transnational approach in its study of such royal ideas and endeavours. Ruling dynasties, monarchs and courts have long been part of an interconnected, if rarefied, world encompassing Europe and Asia, though this is not adequately reflected in the historiography on the nineteenth century. This is despite the ironic fact that in that century, many royal houses were brought closer together than ever before, through the impact of growing global empires, and advancing communications and transportation networks. The first direct meetings between British and Indian royalty took place during this period, in the early 1850s, and are closely examined here.
Based on a core case-study of the longstanding relationship between the Punjabi and British dynasties of Maharajah Ranjit Singh and Queen Victoria, and using a wide variety of textual and material sources, this thesis captures royal perspectives of their status and role in an evolving world, alongside considering how British and Indian royalty directly or indirectly influenced one another. This study effectively de-centres the British imperial official as the primary agent in Anglo-Indian elite encounters, and goes further to demonstrate that whether in the case of the connections between royal personages, or in the ties between ‘monarchy, nation and empire’, the capability for royal agency to shape the nature of such relationships evolved over time and was a consistently contested matter.

Keywords: Queen Victoria
empire
Duleep Singh
royal
Sikh
Britain
Jind Kaur
monarchy
Raj
Ranjit Singh
imperialism
court
dynasty
Punjab
Advisor: Devji, F
The genomic epidemiology of Campylobacter from the Republic of South Africa

As the leading cause of bacterial gastroenteritis, Campylobacter represents a significant public health burden; however, our knowledge of its epidemiology in low- and middle-income countries remains limited. Recent studies have demonstrated the power of whole-genome sequencing (WGS) for public health microbiology. The primary aim of this thesis was to exploit WGS to improve our understanding of the epidemiology of Campylobacter from the Republic of South Africa, a middle-income country.
In the first half of this thesis, in silico approaches were developed to evaluate diagnostic assays and methods of species identification. Large-scale analyses of publicly available WGS data identified a robust real-time PCR assay for the detection of Campylobacter jejuni and Campylobacter coli, the primary causes of human campylobacteriosis. Evaluation of in silico speciation methods demonstrated that the atpA gene and ribosomal multilocus sequence typing can be used to identify Campylobacter from WGS data.
The second half of this thesis extended concepts developed in the first half to investigate the epidemiology of Campylobacter from animals and humans from South Africa. Isolates from a study of Campylobacter from free-range broiler carcasses belonged to the agriculture-associated ST-828 lineage, but were atypically homogenous and differed at only 46/1,513 (3%) loci, providing novel insights into clonal infections in chickens. Analyses of human disease isolates collected in Cape Town in 1991, 2011, and 2012 confirmed that the local epidemiology of Campylobacter is distinct from that of high-income countries: in addition to major agriculture-associated C. jejuni and C. coli lineages, a putative novel C. jejuni subsp. jejuni/C. jejuni subsp. doylei hybrid clade and genetically diverse C. jejuni subsp. doylei and C. upsaliensis isolates were identified.
This work delivers further evidence of the utility of WGS for clinical microbiology, presents approaches that address general problems in Campylobacter diagnostics and public health microbiology, and provides insights into the epidemiology of this important group of pathogens in South Africa.

Keywords: Genomics
Campylobacter
South Africa
Molecular epidemiology
Advisor: Maiden, M
Controlling the electrospinning of nanofibrous polymer scaffolds for neuronal tissue engineering

The use of nanofibrous scaffolds for tissue engineering applications is emerging as an important area of research in the field of regenerative medicine. Due to their close morphological similarity to the extracellular matrix (ECM) these types of scaffolds could be ideal candidates for synthetic, ECM-like substitutes. The main aim of this thesis is to understand and tailor the physical and morphological properties of nanofibrous scaffolds through control of the processing conditions and the incorporation of multi-walled carbon nanotubes and finally their application as substrates for neuronal cell growth.
Nanofibrous scaffolds from polycaprolactone, poly(methyl methacrylate) and gelatin were produced using a self-made electrospinning kit. Advanced experimental design was employed to understand the impact of the processing parameters on the morphology of these scaffolds. The crystalline structure of polycaprolactone scaffolds was measured as a function of the fibre morphology and the processing conditions. It was found that the mechanical properties were strongly dependant on both of these factors which allows for the production of scaffolds with similar fibre structures but markedly different mechanical properties. Carbon nanotubes were successfully incorporated into polycaprolactone and gelatin nanofibres to form composite scaffolds. The targeted functionalization – polycaprolactone was chemically grafted onto carbon nanotubes to macht the polycaprolactone matrix – of carbon nanotubes to the polymer matrix was found to be superior to a more common approach to nanotube functionalization in its reinforcement properties on the electrospun scaffolds. Finally the performance of polycaprolactone scaffolds with bespoke fibre morphologies and different levels of carbon nanotube reinforcements as substrates for human neuronal cell growth was explored in a pilot study. Initial results indicate that the addition of carbon nanotubes greatly enhance neuronal cell growth on scaffolds as determined by an increased cell proliferation and neuronal cell cell differentiation.

Advisor: Dobson, P
Watt, A
Characterising the role of microglia in the early stages of brain metastasis

Brain metastasis is a common complication of breast cancer patients with poor survival. Histological analysis of autopsy samples from patients with brain metastases suggests that microglia, rather than lymphocytes, are the major immune population activated around the metastatic foci. Microglia and macrophages are versatile immune cells with the ability to polarise to different functional phenotypes depending on the microenvironment they reside in. Clinical and preclinical data report both tumourigenic and cytotoxic effects of microglia and macrophages in the tumour microenvironment. However the role and phenotype of microglia during the early stages of metastatic growth in the brain has not yet been fully determined. The aim of this thesis, therefore, was to determine the temporal and spatial profile of microglial activation in a mouse model of brain metastasis, and to assess the effect of M2 (anti-inflammatory) microglial depletion on tumour growth.
Iba1, a specific marker for microglia, was robustly expressed around 4T1 metastatic foci. Quantitatively, microglial activation positively correlated with tumour volume over a 28 day study. Moreover, populations of classically (M1) and alternatively (M2) activated microglia were identified by co-localisation of Iba1 with inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX2), or mannose receptor 1 (MRC1) and arginase 1 (Arg1), respectively. M1 and M2 microglia were found within the tumour microenvironment as well as adjacent to the 4T1 foci. Temporally, MRC1+ M2 microglia maintained their levels across the time-course, as did iNOS+ M1 cells. In vivo depletion of MRC1+ microglia using mannosylated clodronate liposomes at an early stage significantly reduced intracranial tumour burden in the metastatic brain. Moreover, increased levels of apoptosis, indicated by cleaved caspase 3 expression, were associated with 4T1 tumour foci in the animals injected with clodronate liposomes compared to those injected with control liposomes.
A genetic mouse model of deficient M2 polarisation of myeloid cells was also employed as an alternative approach to further validate the aforementioned findings. However, there was no significant decrease in intracranial metastasis burden in the specific model, possibly due to inefficient microglial targeting.
Our findings suggest that microglia are effectors of the inflammatory response in the early stages of brain metastasis. We have shown that M1 and M2 phenotypes co-exist within the tumour microenvironment and that targeting the anti-inflammatory M2 microglial population could be of therapeutic benefit. Further research will provide insights into the M2 molecular signatures that sustain metastatic outgrowth in the brain with the aim of therapeutic intervention.

Advisor: Sibson, N
Design of an application process for research grants

We use a version of a Bayesian Stackelberg game to model a one-stage application process for research grants. A research council wants to allocate research grants to researchers in an environment of imperfect information. The information asymmetry stems from the fact that selection should ideally be based on the quality of the researcher's project. However, neither the researcher nor the research council know the quality but each agent receives a separate signal that is informative about it. We show that the application process always yields a better expected quality of research projects and that, despite the costs it imposes on each agent, the equilibrium of the game can be a welfare improvement over a random allocation of the research grants.

Keywords: Microeconomics
Imperfect Information
Asymmetric Information
Mechanism Design
Advisor: Jewitt, I
Forest structure and biomass in a mixed forest-oil palm landscape in Borneo

The research focusses on differentiating between the AGB and forest stand parameters of riparian and non-riparian zones of a mixed land use type in Malaysian Borneo comprising of lowland forests, logged forests and oil palm plantations. Detailed field surveys were carried out to collect forest mensuration data.Field work was complemented by extensive remote sensing analysis. Fourier analysis and grey level co-occurrence based texture analysis techniques were applied on SPOT 5 data for both differentiating and predicting the AGB values for different forest types. It was found Fourier based methods could both differentiate and predict the biomass of different land use types without undergoing saturation. The research establishes thresholds for disturbances these forests zones can undergo before their AGB values decline. The research also determined that AGB value is much higher for riparian margins than for surrounding oil palm plantations. Hence the retention of riparian margins can yield significant carbon storage benefits.

Keywords: Borneo
plantation
Advisor: Malhi, Y
Bhagwat, S