VictorJuiz/thesis huggingface dataset:
Learning symbolic abstractions from system execution traces
Keywords: formal methods
system abstractions
model learning

This dissertation shows that symbolic abstractions for a system can be inferred from a set of system execution traces using a combination of Boolean satisfiability and program synthesis. In addition, the degree of completeness of an inferred abstraction can be evaluated by employing equivalence checking using simulation relations, that can further be used to iteratively infer an overapproximating system abstraction with provable completeness guarantees.
The first part of this dissertation presents a novel algorithm to infer a symbolic abstraction for a system as a finite state automaton from system execution traces. Given a set of execution traces the algorithm uses Boolean satisfiability to learn a finite state automaton that accepts (at least) all traces in the set. To learn a symbolic system abstraction over large and possibly infinite alphabets, the algorithm uses program synthesis to consolidate trace information into syntactic expressions that serve as transition predicates in the learned model.
The system behaviours admitted by the inferred abstraction are limited to only those manifest in the set of execution traces. The abstraction may therefore only be a partial model of the system and may not admit all system behaviours. The second part of this dissertation presents a novel procedure to evaluate the degree of completeness for an inferred system abstraction. The structure of the abstraction is used to extract a set of conditions that collectively encode a completeness hypothesis. The hypothesis is formulated such that the satisfaction of the hypothesis is sufficient to guarantee that a simulation relation can be constructed between the system and the abstraction. Further, the existence of a simulation relation is sufficient to guarantee that the inferred system abstraction is overapproximating. In addition, counterexamples to the hypothesis can be used to construct new traces and iteratively learn new abstractions, until the completeness hypothesis is satisfied and an overapproximating system abstraction is obtained.
Group four permethylindenyl-phenoxy (PHENI*) complexes for the synthesis of polyolefins
Keywords: ultrahigh molecular weight polyethylene
heterogeneous catalysis
ethylene-α-olefin copolymers
atactic polypropylene
homogeneous catalysis
constrained geometry complexes
post-metallocene catalysts

This thesis discusses the synthesis and characterisation of ansa bridged permethylindenyl phenoxy (PHENI*) complexes and their applications in the synthesis of polyolefins. Efficient homogeneous and slurry phase catalyst systems are developed for the homopolymerisation of ethylene and propylene, and a range of copolymerisations incorporating linear α olefins.
A brief review of polyolefin materials, their synthesis and properties is presented, focussing on how the varied properties makes them suitable for a range of societally relevant applications. Traditional solid state catalysts are contrasted with state of the art molecular catalysts which offer exceptional control over polymer molecular weight and composition, enabling the production of novel materials while maintaining optimal catalytic efficiency. Constrained geometry and phenoxy-imine catalysts are highlighted as examples which offer outstanding performance and tunability for ethylene polymerisation and copolymerisations.
The synthesis and detailed characterisation of PHENI* complexes is developed using a high yielding adaptable procedure from low cost starting materials. A variety of metal centres, ansa bridge substituents, ancillary ligands, and phenoxide substitutions are presented with the influence of steric and electronic factors on structure, bonding, and reactivity explored. Structural trends are identified which help to rationalise the excellent catalytic performance of these complexes. The heterogenisation of PHENI* complexes on a range of solid supports is also discussed.
The homopolymerisation of ethylene and propylene using homogeneous and immobilised PHENI* catalysts was studied, with the effects of the ligand, support, and reaction conditions investigated extensively. Exceptional catalytic activities are reported under mild conditions for the synthesis of substantially disentangled ultra high molecular weight polyethylene, and a novel elastomeric ultra high molecular weight atactic polypropylene.
Supported PHENI* catalysts were finally investigated as a polyolefin platform technology, able to copolymerise a wide range of monomers efficiently. In all cases, random copolymers were produced in a monomer agnostic fashion, with the composition determined simply by the concentration of monomers. This enables a significant degree of predictability and control, enabling the synthesis of designer copolymers through programmed synthesis.
Ecological dynamics of wolves and their ungulate prey in Yellowstone National Park
Keywords: senescence
population demography
community dynamics
dispersal
social living

A core challenge for ecologists is to understand how biotic and abiotic processes influence demography and the dynamics of populations through time. I explore how ageing, social processes, and population conditions drive demography, movement, and community dynamics in a restored population of wolves Canis lupus in Yellowstone National Park, USA. I combine the analysis of empirical data for multiple species with models designed to simulate the dynamics of the system in which they live and interact, focussing on social and demographic processes in wolves.
I assess the utility of movement data for identifying functional senescence—declines in biological functions with age—in wild populations. I use long-term GPS data to describe movement across lifespans, identifying elevated rates of movement in older individuals and a pronounced annual cycle in movement rates.
I show that the fundamental demographic rates of survival and recruitment depend on attributes of individual wolves and their social groups, as well as effects of competition and population. Despite evidence that demographic performance is positively related to group size, packs are consistently small in Yellowstone. This apparent contradiction may derive from an inequality in fitness between breeding and non-breeding individuals in socially reproductive groups. To test this, I construct a group and age structured model simulating Yellowstone’s high-density wolf population, and find that by constraining group size, dispersal imparts a substantial regulatory effect on the population. This work forms a foundation for future work to understand the environmental and social basis for dispersal in a large carnivore.
Finally, to examine whether the reintroduction of wolves led to the changes in Yellowstone’s community structure observed in the past three decades, I use a novel approach to model community dynamics by parameterising for direct species interactions. I find that widespread and complex indirect effects emerge across the community and show that wolf predation has cascading effects that lead to the gradual recovery of vegetation.
This thesis provides new insights into the social and environmental basis of demography in an ecologically important carnivore and details the role of predator restoration in shaping community dynamics.
Gas-phase infrared spectroscopy of metal-containing clusters and complexes
Keywords: infrared
metal
IR-MPD
spectroscopy
DFT
photodissociation
complexes
clusters

Metal-containing clusters and complexes may represent active sites in heterogeneous catalysts, where catalytic transformations take place, thus offering an elegant approach in studying the fundamental interactions in a simplified way. In this thesis, infrared-(multiple) photodissociation spectroscopy is used to study metal-containing clusters and complexes with atmospherically relevant adsorbates to learn about their reactivity, structural binding motifs, and the degree of activation of adsorbed moieties. Complementary density functional theory calculations help in the assignment of experimentally observed phenomena.
Each chapter describes a different system that presents unique and sometimes unexpected results. N2O binding to Pt+n proves to be size-dependent; small clusters form molecular N2O adsorption products whereas larger ones react to produce PtO+, and similar chemistry is observed upon infrared excitation. Examining N2O binding to Au+n and Co+n reveals inertness of gold clusters whereas cobalt species prove to be similar in their reactivity to platinum. Size-selective cooperative binding effects are discovered for AunO2CO− species both from mass spectrometry and spectroscopy. Infrared action spectra of Co(NO)+n and Rh(NO)+n complexes disclose spectral differences in the number and position of the bands as well as similarities in the NO binding motifs to these metal centres. Rh(CO)n(N2O)+m system proves to be different than Au(CO)n(N2O)+m studied by the Mackenzie group previously, and these observations are explained in terms of different electronic structures, relative binding energies, and coordination numbers. Isotopic study of Au(CO)n(N2O)+m using 13CO reveals a band in the infrared spectrum of the Au(12CO)2(N2O)+ complex that is an overlap between individual 12C≡O and N2O N=N vibrational bands.
The reform of the British civil service: life cycle, family, and class in the treasury, c.1847-1914
Keywords: state
nineteenth century
life cycle
Britain
civil service
class
family

This thesis examines the reform of the British Civil Service and its impact on society by providing the first systematic exploration of developments in the Treasury department between 1847 and 1914. It covers some of the most significant changes in the modern history of the British state in terms of appointments, promotions, pensions, and the development of a new idea of profession in the Civil Service from youth to old age. It reveals the interconnections between the aristocracy and the professions over the nineteenth century, and the Treasury’s key role in the professionalization of government administration.
Existing scholarship on the Civil Service has provided the foundations of our understanding of reforms and public departments. However, few scholars have studied these processes from a social history perspective, exploring how reforms impacted the lives of civil servants, or how social structures shaped the new Civil Service profession. By analysing the Civil Service through the lenses of life cycle, family, and class, this study offers a new dimension to our understanding of the professionalization of the British state and society. Reforms evolved in ways that reflected and were influenced by changing attitudes to class, public office, life course, and family. Between 1847–1914, new Civil Service employment and career structures common to clerks from the aristocracy, middle classes, and working classes were developed, yet considerable disparities between the different levels of the Civil Service persisted. The professionalization of the British state played out in private as well as in public spheres, where family formations, intergenerational support, social connections, educational institutions, and voluntary associations meshed with the structures of the Civil Service in various forms in the late nineteenth century. By analysing the reform of the Civil Service from a social and cultural perspective and through thus far untapped sources, this thesis explores an important shift in British administrative, political, and social history.
The impact of military duties in the early 19th century on urban commoners in Russia: recruit and militia levies and billeting in the communes of St. Petersburg province
Keywords: urban communes
the Russian North-West
the Russian Empire
militia of 1806-1807
military duties
increased demands
merchants
the Napoleonic Wars
district towns
meshchane
19th century
zemskoe opolchenie of 1812
town councils
urban self-government
St. Petersburg province
18th century

This thesis examines the impact of increased military duties on the social and political evolution of urban commoners of the Russian Northwest in the early 19th century. The impact of increased recruit and militia levies and billeting duty in the 1800s-1820s is examined in relation to the communes of three district capitals: Novaia Ladoga, Sofia-Tsarskoe Selo, and Gdov. The focus is on the practices, actions, and motivations of individuals, communes of merchants and meshchane, and town councils.
These increased duties led to the modernization of social relationships and political culture.
Increased conscription revealed the limits of the communal process of nomination for service: with the first mass militia levy announced in 1806, communes failed to supply enough soldiers on time. The government had therefore to revise the system of nomination. The practice of nomination for dissolute behaviour was put on a stable legal footing and family recruit groups were introduced, reducing conflict, delays, and disputes within communes.
Local merchant elites were crucial to the performance of military duties: the richest families controlled the town council, organizing fundraising during the recruit and especially the militia levies of 1806-07 and 1812. The merchants themselves made additional contributions. But those in district towns were heavily impacted by the upheavals of war, the growth of taxation, and other financial demands: the local elites significantly contracted from 1807, and especially after 1812.
Relationships between councils and the Chief of Police and Civil Governor were likewise crucial to the performance of military duties. Effective cooperation with urban police on the ground helped in the supply of recruits, money, and equipment during levies. The Governor played a role as mediator whenever disputes and conflicts arose between commoners and police or army officers, most of which were solved by negotiation: commoners and councils were not as powerless as often imagined.
Following the war, there was a growing demand for the equalization of duties and tax burdens among commoners in the 1820s; dissatisfaction with officialdom grew, which manifested itself in cholera riots, e.g., in Staraia Rusa in 1831.
Characterisation of allergic reactivity to fungi in a Zimbabwean population
Keywords: allergic reactivity
epidemiology
disease
fungi
Zimbabwe

While fungal diseases are a growing global problem, there remains a paucity of epidemiological data in most developing countries. Hence, this thesis aimed to investigate the epidemiology, immunology, and aetiology of fungal allergic diseases in Zimbabwe.
This study demonstrated that the burden of fungal diseases in Zimbabwe is high (14%), with tinea capitis being the most prevalent condition. The country's background sensitivity to fungal allergens and the effect of host-related factors was unknown. Therefore, this thesis further investigated the prevalence of fungal sensitisation and reactivity among Zimbabwean children and how the gut mycobiome composition affected these, whilst considering the effects of host age, gender, and Schistosoma haematobium infection status. The prevalence of fungal sensitisation to ≥1 fungal species was 96%, and the metagenomic analysis of the gut mycobiome showed that the mycobiome comprised <1% of the sequenced gut microbiome. There was no association between the mycobiome and fungal reactivity, or the host factors studied. Interestingly, an increase in Aspergillus, Tricholoma, and Periglandula abundance was associated with schistosome infection.
Due to the high prevalence of fungal sensitisation, this thesis further identified and characterised fungal proteins that were immunoreactive against serum samples from fungal-sensitised children. Furthermore, the utility of a specific Aspergillus fumigatus allergen (Asp f 2) peptide in the differential diagnosis of fungal allergy was evaluated. As a result, novel immunogens from fungi were discovered, potentially increasing the number of known fungal allergens. The Asp f 2 peptide was demonstrated to be an inadequate indicator for diagnosing fungal allergy in the population.
Taken together, the findings of this thesis add to the ongoing global discussions about the burden of fungal diseases. Furthermore, it provides novel data on several important aspects of fungal allergy that must be evaluated and validated since they may have implications for the care of allergic individuals.
Gerda Walther: mysticism, philosophy, art
Keywords: social ontology
mysticism
modernism
phenomenology

This thesis examines the work of Gerda Walther, a philosopher and mystic whose work had until very recently been almost entirely neglected. A member of the Freiburg and Munich circles of phenomenologists, Walther worked in her main published texts (Ein Beitrag zur Ontologie der sozialen Gemeinschaften (1922) and Zur Phänomenologie der Mystik (1923)) to balance the competing impulses arising out of a radically atheistic Marxist upbringing, her study of philosophy, and the onset of what she describes as mystical and telepathic experiences. Walther’s work, seen more or less as failed interventions into conventional phenomenological discourse by several of her contemporaries, has been recently reassessed by philosophers, and presented as more successful than previously thought. I undertake a reorientation of emerging scholarship on Walther in terms of a meditative-mystical tradition, and in terms of German modernist writing: examining the overlooked conditions and cultural contexts that show their workings in Walther’s texts. I argue that Walther does indeed ‘fail’ to fit the mould of an early phenomenologist, and that this ironically staged failure forms the interest of her work.
My thesis is the first study of Walther to be grounded in a language-based reading of her texts, and which takes a wider cultural approach to her work. I employ a methodology of critical close reading to make explicit the compelling implicit textual processes of Walther’s work. Throughout her work, peculiar accounts of personal experiences masquerade as the result of abstracted philosophical reflections; and artistic approaches to religious experience and social life are presented as having as much of a hold on those topics as philosophy does. Walther is asking what it means for a text to be philosophical, mystical or artistic, with work that occupies an intersection of generic traditions, and blurs these distinctions in productive and problematic ways. The set of problems she presents contributes to a new vision of the philosophical and cultural landscape in early twentieth-century Germany. I introduce Walther’s work into areas of scholarship in which she is virtually unknown, but to which she ought to be of most interest: discussions of the margins of modernist cultural life and writing; and philosophical scholarship which questions the grounds of its investigations.
Structural studies of bacterial biofilm matrix fibres
Keywords: cryo-EM
cryo-ET
biofilm matrix fibres

Many bacteria live in multicellular communities called biofilms. Within the biofilm, cells are embedded in a self-secreted extracellular biofilm matrix, which provides numerous benefits to bacteria inside. Biofilms also form during human infection, where the matrix provides protection against antibiotic treatment and the immune system. A major component of the biofilm matrix are protein fibres, which provide stability to the biofilm and scaffold its formation. Little is known about the structure of the biofilm matrix in general, and matrix fibres specifically. Here, structural and functional studies on biofilm matrix fibres are presented. An electron cryomicroscopy (cryo-EM) structure of the biofilm-promoting archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa was solved, showing a zig-zag subunit architecture, where the majority of inter-subunit interactions are mediated by an N-terminal donor strand that extends into the following subunit and completes its Ig-like fold. Electron cryotomography (cryo-ET) imaging shows that the CupE pilus can adopt significant curvature in situ, which may aid in promoting cohesion between cells. Structural studies on the biofilm matrix fibre Fap from P. aeruginosa are presented, supporting previous work showing the fibres are amyloid. Moreover, a cryo-EM fibre structure of the major protein component of the Bacillus subtilis biofilm matrix, TasA, was solved. The structure shows that TasA fibres are not, like previously proposed, amyloid but instead polymerise through a donor strand, similar to Chaperone-Usher pili, but employing a different, previously undescribed assembly machinery. Finally, a compressed sensing algorithm is trialled for reconstruction of cryo-ET data of biological specimens, leading to improved direct visualisation and subtomogram averaging of macromolecules from small datasets, which may aid future studies in visualising the biofilm matrix in situ. Together, these findings will advance our structural understanding of biofilms.
Making books without end: anthology and generative rereading in the wisdom tradition
Keywords: Ecclesiastes
proverbs
ethical reading
Qohelet
wisdom literature
Hebrew Bible
Biblical interpretation

This dissertation explores the literary features of biblical wisdom sayings, examining their function and effect both as individual sayings and contextualised in discourse and anthology. The first introductory chapter situates wisdom as an expression of tradition, addressing the shared poetic features and clear moral order of wisdom sayings. These features of poetic simplicity are unlocked in the following chapters through a variety of comparative analogies. The second chapter reexamines the way that the sayings make claims about human experience, rejecting models that view proverbs as maxims describing the factual workings of a well-ordered world in favour of a model built on narrative order and expectation. This draws on comparative materials from Classical and Romantic era folk traditions to situate the patterns of wisdom sayings in a broader context of making sense of the world. The third chapter uses miniatures to problematise interpretations of wisdom’s moral simplicity, arguing that the poetics of brevity creates idealised patterns designed to provoke self-reflection and transformation in the reader. The fourth chapter examines the proverb as a fragment of a larger discourse, arguing that the decontextualised proverb inspires the imaginative reconstruction of possible meanings, applications, and interpretations as part of the process of constructing a traditional worldview. The fifth chapter uses these new models to develop a new method for reading the wisdom anthologies as neither an elaborate literary structure nor a haphazard heap of sayings, but as a collection that by its very nature invites creative interpretation through the resonance generated by the broad juxtaposition of sayings. The final chapter returns to the unifying theme of the dissertation, examining how wisdom preserves a past tradition in a nostalgic mode, using memory, idealism, and repetition to construct in the reader a sense of shared identity and belonging.