VictorJuiz/thesis huggingface dataset:
Electrochemical investigations of H2-producing enzymes
Keywords: hydrogenase
protein film electrochemistry
H2 production

Hydrogenases are a family of enzyme that catalyses the bidirectional interconversion of H+ and H2. There are two major classes of hydrogenases: the [NiFe(Se)]- and [FeFe]-hydrogenases. Both of these benefit from characteristics which would be advantageous to their use in technological devices for H2 evolution and the generation of energy. These features are explored in detail in this thesis, with a particular emphasis placed on defining the conditions that limit the activity of hydrogenases when reducing H+ to produce H2. Electrochemistry can be used as a direct measure of enzymatic activity; thus, Protein Film Electrochemistry, in which the protein is adsorbed directly onto the electrode, has been employed to probe catalysis by hydrogenases.
Various characteristics of hydrogenases were probed. The catalytic bias for H2 production was interrogated and the inhibition of H2 evolution by H2 itself (a major drawback to the use of some hydrogenases in technological devices to produce H2) was quantified for a number of different hydrogenase. Aerobic inactivation of hydrogenases is also a substantial technological limitation; thus, inactivation of both H2 production and H2 oxidation by O2 was studied in detail. This was compared to inhibition of hydrogenases by CO so as to elucidate the mechanism of binding of diatomic molecules and determine the factors limiting inactivation. This allows for a preliminary proposal for the genetic redesigning of hydrogenases for biotechnological purposes to be made. Finally, preliminary investigation of the binding of formaldehyde, potentially at a site integral to proton transfer, opens the field for further research into proton transfer pathways, the structural implications thereof and their importance in catalysis.
Interpersonal affective forecasting
Keywords: focalism
Impact bias
memory
debiasing
Interpersonal affective forecasting
Implicit theories of emotion
Affective forecasting
biased recall

This thesis investigates individual and interpersonal predictions of future affect and explores their relation to implicit theories of emotion, prediction recall, debiasing, and focalism. Studies 1, 2, and 3 assessed affect predictions to upcoming reasoning tests and academic results, and Studies 4, 5, and 6 concerned predictions for self-identified events. The first study investigated the influence of implicit theories of emotion (ITE; Tamir, John, Srivastava, & Gross, 2007) on impact bias and prediction recall manipulating ITE between participant pairs who predicted and reported their affective reactions to feedback on a test of reasoning skills. Neither impact bias nor recalled predictions were affected by the manipulation. Recalled affect predictions differed from original affect predictions, but were not influenced by experienced affect. Study 2 further investigated the effects of target event timing on impact bias and affect prediction recall. The results showed no differences between individual and interpersonal impact biases across conditions. Again, recalled predictions differed from original predictions, and were not influenced by experienced affect. Study 3 investigated the influence of prior information about impact bias on interpersonal affective forecasting involving real-world exam results. The results demonstrated no differences in predictions due to information, however, significantly less unhappiness was predicted for participants’ friends compared to self-predictions. Study 4 examined the effect of different de-biasing information on affective predictions. The results demonstrated no differences in affective predictions by condition and found that participants’ ITE were not associated to affect predictions. Study 5 examined individual and interpersonal affect predictions using a between-subjects design in place of the within-subjects design. The results demonstrated no differences between the affect predictions made for self and for friends, and ITE were not associated with predictions. Study 6 examined the impact bias in interpersonal affective forecasting and the role of focalism. The results demonstrated distinctions between individual and interpersonal affecting forecasting with individual impact bias for positive reactions for negative events and individual and interpersonal reverse impact bias for calm emotional reactions to positive events. Immune neglect was found not to be associated with predictions. Overall, the studies found evidence for similar individual and interpersonal predictions which are resistant to influence.
Essential amino acid depletion by embryonic stem cells as a mechanism of immune privilege
Keywords: mouse embryonic stem cells
immune privilege
transplantation tolerance

Mouse embryonic stem cells (ESCs) are capable of differentiating into any somatic cell type and are known to display fragile immune privilege in vivo and in vitro. The extent to which the depletion of essential amino acids (EAAs) by ESCs contributes to this phenomenon was investigated.
ESCs were found to express various enzymes capable of catabolising EAAs within the culture medium. In particular, depletion of threonine, valine and lysine was found to have significant impact on T cell proliferation and differentiation, biasing their polarisation towards a FoxP3+ T regulatory (Treg) phenotype. Supplementing ESC conditioned medium with these three EAAs alone rescued normal T cell proliferation, whereas artificially limiting their availability was sufficient to induce Treg cell differentiation to a level equivalent to general EAA depletion. The pattern of EAA catabolism by mouse ESC was shared by induced pluripotent stem cells, while mouse melanoma cell lines and human ESCs displayed distinct patterns of EAA depletion.
The cytosolic branched chain aminotransferase enzyme, Bcat1, catalyses the first step of branched chain amino acid catabolism (isoleucine, leucine and valine), and is highly expressed by both mouse and human ESCs. The contribution of this enzyme to the establishment of acquired immune privilege by ESC-derived tissues was, therefore, investigated. ESC lines were derived from mice lacking Bcat1 activity and were characterised. Bcat1−/− ESC lines displayed no difference to their wildtype counterparts (Bcat1LoxP) in terms of in vitro proliferation and their capacity to form teratomas in vivo. Furthermore, the loss of Bcat1 function had little impact on the inhibition of T cell proliferation in culture, ability to induce Treg cell commitment or their ability to prevent rejection by T cell receptor transgenic recipients, suggesting the minimal contribution of Bcat1 to the depletion of EAAs by ESCs.
In conclusion, EAA depletion by mouse ESC may provide a mechanistic explanation for the previously described immune-suppressive capacity of ESC.
Essays on development economics
Keywords: Development
Property Rights
Impact Evaluation
Titling
Economics

This thesis is a collection of essays on the relevance of property right reforms on the wellbeing of poor households in developing countries; specifically titling programmes in urban Peru. The first essay assesses the effects of titling on housing investment. The availability of a unique dataset permits us to trace households' investment behaviour. This allows us to investigate if tenure security induces households to make sizeable investments, the evolution of this effect over time, and whether heterogeneous expectations about future tenure security matter for the estimated impact. Evidence reveals significant effects, especially on large investment; however, the response on this type of investment may take several years to become effective. The second essay contributes to the debate on the sustainability of property rights reforms by emphasising the importance of strong registration systems. Policymakers have focused on the process of granting titles but the conditions needed to maintain the formality of future plot transactions have been left unattended. The analysis exploits an exogenous variation in legislation to examine the impact of a change in the registration process on the registration rate of plot transactions. Evidence suggests a large negative effect, implying that a weak registration system could threaten the reform. The third essay explores the impact of titling on the risk preferences of slum dwellers. The analysis provides evidence that titled dwellers reported lower values of the risk aversion measure than their non-treated counterparts. Results also suggest that tenure security can influence slum dwellers' preference formation process. Evidence shows that beneficiaries who were exposed to tenure security during their youth report on average lower values of the risk aversion indicator than individuals titled at an older age.
Creative sparks: literary responses to electricity, 1830-1880
Keywords: Ainsworth
James Clerk Maxwell
Bulwer-Lytton
Michael Faraday
nineteenth-century
periodicals
Victorian
electricity
elixir vitae
fiction
short stories
Lumley

This thesis examines accounts of electricity in journalism, short stories, novels, poetry and instructional writings, composed between 1830 and 1880 by scientific investigators, popular practitioners and fiction authors. The writings are approached as diverse and often incongruous impressions of electricity, in which the use of figurative and narrative techniques brings into question distinctions between science and literature. It is proposed that the unusual combination of electricity’s historical characterisation as an elixir vitae, intense investigation by contemporary scientists, and close alliance with new technologies offered unique opportunities for imaginative speculation. The thesis contends that engaging with these conflicting characteristics created a synthesis of scientific, social and literary responses that defy epistemological and generic categorisation. Fictionality is approached in chapter two as a central feature of scientific conceptualisation, experiment and discovery, particularly in the work of Michael Faraday and James Clerk Maxwell. In chapters three and four, the landscape of popular non-fiction books and periodicals is mapped, to show the ways in which the period’s publication contexts and forums, reading patterns, and use of literary practices contributed to wider engagement with ideas about electricity. Chapters five and six focus on fiction writings, identifying parallels and divergences between actual electrical science and its fictional portrayal. Short stories are shown to have emphasised associations between electricity, neurosis, deformity and the occult, complicating contemporary scientific optimism and presenting electricity as an alluring yet dangerous phenomenon, which disordered the natural world and man’s relationship with it. These characteristics are identified further in the metaphorical references of several canonical novelists, in the exploitation of electricity, elixirs and power depicted by William Harrison Ainsworth and Edward Bulwer-Lytton, and through a case study of the text and reception of a popular novel about electricity by Benjamin Lumley. The thesis contends that electricity’s anomalous and protean nature produced distinctively hybrid responses that enhance our understanding of contemporary popular writing, its contexts and how it was read.
Abstract satisfaction
Keywords: program analysis
satisfiability
logic
abstract interpretation

This dissertation shows that satisfiability procedures are abstract interpreters. This insight provides a unified view of program analysis and satisfiability solving and enables technology transfer between the two fields. The framework underlying these developments provides systematic recipes that show how intuition from satisfiability solvers can be lifted to program analyzers, how approximation techniques from program analyzers can be integrated into satisfiability procedures and how program analyzers and satisfiability solvers can be combined. Based on this work, we have developed new tools for checking program correctness and for solving satisfiability of quantifier-free first-order formulas. These tools outperform existing approaches.
We introduce abstract satisfaction, an algebraic framework for applying abstract interpre- tation to obtain sound, but potentially incomplete satisfiability procedures. The framework allows the operation of satisfiability procedures to be understood in terms of fixed point computations involving deduction and abduction transformers on lattices. It also enables satisfiability solving and program correctness to be viewed as the same algebraic problem.
Using abstract satisfaction, we show that a number of satisfiability procedures can be understood as abstract interpreters, including Boolean constraint propagation, the dpll and cdcl algorithms, St ̊almarck’s procedure, the dpll(t) framework and solvers based on congruence closure and the Bellman-Ford algorithm. Our work leads to a novel understand- ing of satisfiability architectures as refinement procedures for abstract analyses and allows us to relate these procedures to independent developments in program analysis. We use this perspective to develop Abstract Conflict-Driven Clause Learning (acdcl), a rigorous, lattice-based generalization of cdcl, the central algorithm of modern satisfiability research. The acdcl framework provides a solution to the open problem of lifting cdcl to new prob- lem domains and can be instantiated over many lattices that occur in practice. We provide soundness and completeness arguments for acdcl that apply to all such instantiations.
We evaluate the effectiveness of acdcl by investigating two practical instantiations: fp-acdcl, a satisfiability procedure for the first-order theory of floating point arithmetic, and cdfpl, an interval-based program analyzer that uses cdcl-style learning to improve the precision of a program analysis. fp-acdcl is faster than competing approaches in 80% of our benchmarks and it is faster by more than an order of magnitude in 60% of the benchmarks. Out of 33 safe programs, cdfpl proves 16 more programs correct than a mature interval analysis tool and can conclusively determine the presence of errors in 24 unsafe benchmarks. Compared to bounded model checking, cdfpl is on average at least 260 times faster on our benchmark set.
Static and dynamic performance of Ti foams 
Keywords: Foams
Titanium
Voronoi
engineered materials design
strain rate
finite element
multiscale
cellular materials
virtual foam
stochastic geometry
materials design

Titanium (Ti) foams of different densities 1622-4100 Kgm-3 made by a powder sintering technique were studied as to their structural and mechanical properties. The foams were tested under static and dynamic loading. The material was tested quasi statically and dynamically under strain rates in the range of 0.001-2500 s-1 and under different loading modes. It was found that strain rate sensitivity is more pronounced in lower density foams. Experiments were complimented by virtual testing. Based on the Voronoi tessellations a computational method was developed to generate stochastic foam geometries. Statistical control was applied to produce geometries with the microstructural characteristics of the tested material. The generated structures were numerically tested under different loading modes and strain rates. Voronoi polyhedrals were used to form the porosity network of the open cell foams. The virtually generated foams replicated the geometrical features of the experimentally tested material. Meshes for finite element simulations were produced. Existing material models were used for the parent material behaviour (sintered Ti) and calibrated to experiments. The virtual foam geometries of different densities were numerically tested quasi statically under uniaxial, biaxial and triaxial loading modes in order to investigate their macroscopic behaviour. Dynamic loading was also applied for compression. Strain rate sensitive and insensitive models were used for the parent material model in order to examine the influence of geometry and material strain rate sensitivity under high rates of deformation. It was found that inertial effects can enhance the strain rate sensitivity for low density foams and numerical predictions for the generated foam geometries were in very good agreement with experimental results. Power laws were established in scaling material properties with density. The study includes: 1. Information on the material behaviour and data for macroscopically modelling this type of foams for a range of densities and under different strain rates. 2. A proposed method for virtually generating foam geometries at a microscopic scale and examine the effect of geometrical characteristics on the macroscopic behaviour of foams.
Educational planning for situations of instability: standardization and advocacy in humanitarian aid practice 
Keywords: policy
education
humanitarian assistance
planning
advocacy
INEE

This thesis examines the role and relationship of standardization and advocacy in humanitarian aid planning processes within the emergent field of education and instability. Standardization refers to the aid industry’s increasing emphasis on establishing ‘universal’ principles and normative frameworks. Advocacy refers to transnational-policy-network activities that move forward the global standardization agenda. The study focuses on the purposes and practices of knowledge creation by an education-and-instability ‘epistemic community’: the Inter-Agency Network for Education in Emergencies (INEE).
Drawing on global-level interviews with key figures, participant observations, and documentary analysis, the research explores how this epistemic community promotes its core tenets: that education is an inherent human right and that educational provision should be a frontline humanitarian response on par with food distribution and shelter construction. The thesis analyzes the consensus-making process that resulted in the publication of the 2004 INEE Minimum Standards handbook, the then-epitome of the epistemic community’s knowledge.
Next, the thesis examines the local application and adaptation of such global standardization processes in post-conflict Uganda. The case study presents the relationships among international and local ‘development partner’ institutions concerned with educational planning as a complex and contradictory story of power dynamics and knowledge circulation. These ‘partnerships’ are characterized by a shared quest for adherence to the knowledge encapsulated within standardized global frameworks and their normative principles. For Ugandan institutions, fluency in this discourse is a powerful tool to appropriate for their own ends. For international institutions, the knowledge is at once a technical resource and a means to bring ever more stakeholders into the wider epistemic community concerned with humanitarian aid.
I argue that, through judicious use of standardization and advocacy mechanisms, INEE seeks to legitimize the education sector’s existence within the humanitarian aid industry and expand support for (or ‘conversion’ to) the education-and-instability epistemic community’s core beliefs.
Automatic verification of competitive stochastic systems
Keywords: stochastic games
probabilistic logic
Markov chains

In this thesis we present a framework for automatic formal analysis of competitive stochastic systems, such as sensor networks, decentralised resource management schemes or distributed user-centric environments. We model such systems as stochastic multi-player games, which are turn-based models where an action in each state is chosen by one of the players or according to a probability distribution. The specifications, such as “sensors 1 and 2 can collaborate to detect the target with probability 1, no matter what other sensors in the network do” or “the controller can ensure that the energy used is less than 75 mJ, and the algorithm terminates with probability at least 0.5'', are provided as temporal logic formulae. We introduce a branching-time temporal logic rPATL and its multi-objective extension to specify such probabilistic and reward-based properties of stochastic multi-player games. We also provide algorithms for these logics that can either verify such properties against the model, providing a yes/no answer, or perform strategy synthesis by constructing the strategy for the players that satisfies the specification. We conduct a detailed complexity analysis of the model checking problem for rPATL and its multi-objective extension and provide efficient algorithms for verification and strategy synthesis. We also implement the proposed techniques in the PRISM-games tool and apply them to the analysis of several case studies of competitive stochastic systems.
Development of magnetic bond-order potentials for Mn and Fe-Mn
Keywords: DFT
Materials Modelling
Iron
Manganese
BOP
High Manganese Steels
Density Functional Theory

While group VII 4d Tc and 5d Re have hexagonally close-packed (hcp) ground states, 3d Mn adopts the complex chi-phase which exhibits non-collinear magnetism. Density functional theory (DFT) calculations have shown that without magnetism the chi-phase remains the ground state of Mn implying that magnetism is not the critical factor, as is commonly believed, in driving the anomalous stability of the chi-phase over hcp. Using a tight-binding (TB) model it is found that while harder potentials stabilise close-packed hcp, a softer potential stabilises the more open chi-phase. By analogy with the structural trend from open to close-packed phases down the group IV elements, the anomalous stability of the chi-phase in Mn is shown to be due to 3d valent Mn lacking d states in the core which leads to an effectively softer atomic repulsion between the atoms than in 4d Tc and 5d Re.
Subsequently an analytic Bond-Order Potential (BOP) is developed to investigate the structural and magnetic properties of elemental Mn at 0 K. It is derived within BOP theory directly from a new short-ranged orthogonal d-valent TB model of Mn, the parameters of which are fitted to reproduce the DFT binding energy curves of the five experimentally observed phases of Mn, alpha, beta, gamma, delta, and epsilon-Mn. Not only does the BOP reproduce qualitatively DFT binding energy curves of the five different structure types, it also predicts the complex collinear antiferromagnetic (AFM) ordering in alpha-Mn, the ferrimagnetic (FiM) ordering in beta-Mn and the AFM ordering in the other phases that are found by DFT. A BOP expansion including 14 moments is sufficiently converged to reproduce most of the properties of the TB model with the exception of the elastic shear constants which require further moments.
Magnetic analytic BOPs are also developed for Fe and Fe-Mn. The Fe model correctly reproduces trends in the structural stabilities of the common metallic structures except that AFM hcp is overstabilised. Reproduction of the elastic constants with a 9-moment BOP is reasonable although as is found for the Mn BOP the elastic shear constants require more moments to converge. Vacancy formation energies are close to those determined by experiment and DFT and the relative stabilities of self-interstitial atom (SIA) defects in ferromagnetic bcc Fe are correctly reproduced. The SIA formation energies are found to be better than those calculated with existing BOP models.
The Fe-Mn TB and BOP models were challenging to fit and nonmagnetic face-centred cubic (fcc) structures are overstabilised. Furthermore within BOP an incorrect magnetic solution is predicted for one fcc structure resulting in poor reproduction of the DFT stacking fault energies. Refitting the bond integrals might help to better reproduce the nonmagnetic hcp-fcc energy differences while an environment-dependent Stoner parameter could help provide the flexibility needed to correctly capture the magnetic energy differences.