VictorJuiz/thesis huggingface dataset:
Compositional distributional semantics with compact closed categories and Frobenius algebras
Keywords: distributional models
computational linguistics
compositionality
category theory
vector space models
mathematics of language
categorical quantum mechanics
semantics

The provision of compositionality in distributional models of meaning, where a word is represented as a vector of co-occurrence counts with every other word in the vocabulary, offers a solution to the fact that no text corpus, regardless of its size, is capable of providing reliable co-occurrence statistics for anything but very short text constituents. The purpose of a compositional distributional model is to provide a function that composes the vectors for the words within a sentence, in order to create a vectorial representation that re ects its meaning. Using the abstract mathematical framework of category theory, Coecke, Sadrzadeh and Clark showed that this function can directly depend on the grammatical structure of the sentence, providing an elegant mathematical counterpart of the formal semantics view. The framework is general and compositional but stays abstract to a large extent.
This thesis contributes to ongoing research related to the above categorical model in three ways: Firstly, I propose a concrete instantiation of the abstract framework based on Frobenius algebras (joint work with Sadrzadeh). The theory improves shortcomings of previous proposals, extends the coverage of the language, and is supported by experimental work that improves existing results. The proposed framework describes a new class of compositional models thatfind intuitive interpretations for a number of linguistic phenomena.
Secondly, I propose and evaluate in practice a new compositional methodology which explicitly deals with the different levels of lexical ambiguity (joint work with Pulman). A concrete algorithm is presented, based on the separation of vector disambiguation from composition in an explicit prior step. Extensive experimental work shows that the proposed methodology indeed results in more accurate composite representations for the framework of Coecke et al. in particular and every other class of compositional models in general.
As a last contribution, I formalize the explicit treatment of lexical ambiguity in the context of the categorical framework by resorting to categorical quantum mechanics (joint work with Coecke). In the proposed extension, the concept of a distributional vector is replaced with that of a density matrix, which compactly represents a probability distribution over the potential different meanings of the specific word. Composition takes the form of quantum measurements, leading to interesting analogies between quantum physics and linguistics.
Electronic structure of open-shell transition metal complexes
Keywords: Zintl ions
redox non-innocence
xenophilic metal clusters
CuNiR
broken-symmetry
MO theory
DFT

This thesis presents electronic structure calculations on problems related to the bonding in inorganic coordination compounds and clusters. A wide range of molecules with the ability to exist in different structural forms or electronic states has been selected and density functional theory is systematically applied in order to gain detailed insight into their characteristics and reactivity at the electronic level. First, we address the question of redox non-innocent behaviour of bipyridine in a series of 1st row transition metal complexes. Complexes of the type [M(2,2'-bipyridine)(mes)₂]0 (M = Cr, Mn, Fe, Co, Ni; mes = 2,4,6-Me₃C6H₂) and their one-electron reduced forms have been explored. The results clearly show that the anions are best described as complexes of the monoanionic bipyridine radical (Sbpy = 1/2), giving a rationale for the observed structural changes within the ligand. Likewise, we have identified dianionic bipyridine in both the complexes [Zn2(4,4'-bpy)(mes)₄]²− and [Fe(2,2'-bpy)₂]²−. In no case have we found evidence for significant metal-to-ligand backbonding. The subject of redox-noninnocence is further revisited in a comparative study of the two complexes [M(o-Clpap)₃] (M = Cr, Mo; o-Clpap = 2-[(2-chloro-phenyl)azo]-pyridine), and their associated electron transfer series. The results indicate that all electron transfer processes are primarily ligand-based, although in the case of the Mo analogue these are coupled to substantial electron density changes at the metal. The ability of pap to form radical anions finds a contrasting case in the di- nuclear Rh complex [Rh₂(μ-p-Clpap)₂ (cod)Cl₂], where the two ligand bridges act as acceptors of strong dπ∗ backbonding from a formally Rh–I centre. We then direct our attention to the endohedral Zintl clusters [Fe@Ge10]³− and [Mn@Pb12]³−, which reveal peculiar topologies. We have probed the electronic factors that influence their geometric preferences, and propose a model based on the shift of electron density from the endo- hedral metal to the cage to account for the observed geometries. Subsequently, we reassess the electronic structure of the xenophilic clusters Mn₂(thf)₄(Fe(CO)₄)₂ and [Mn(Mn(thf)₂)₃(Mn(CO)₄)₃]–. We conclude that these are best viewed as exchange coupled MnII centres bridged by closed- shell carbonylate fragments. In the closing chapter the reduction of NO₂– to NO by the complex [Cu(tct)(NO₂)]+ (tct = cis,cis-1,3,5-tris(cinnamylideneamino)cyclohexane) is studied, a process that mimics the enzyme-catalysed reaction. Two viable pathways for the reaction have been traced and key inter-mediates identified. Both direct release of NO or via decomposition of a Cu-NO complex are kinetically and thermodynamically feasible.
Structural studies on determinants of receptor/ligand binding in the tumour necrosis factor and T cell receptor protein families
Keywords: T-Cell Receptor
X-ray crystallography
TNF

Protein-protein recognition plays a central role in the surveillance of self and non-self in the mammalian immune system and ultimately in cellular survival within the organism. Two systems of fundamental importance to the immune system are the Tumour Necrosis Factor (TNF) and the T cell receptor (TCR) families.
High-throughput methods developed within the Oxford Protein Production Facility have been successfully applied to the production of members of the TNF receptor and ligand superfamilies for structural characterisation. The TNF receptor DR6 was successfully refolded from E.coli inclusion bodies using a rapid-dilution technique and yielded diffraction quality crystals. Data collected from these crystals will be used to obtain an x-ray crystallographic model of DR6. Vascular Endothelial Growth Inhibitor (VEGI) was produced as a soluble recombinant protein in E.coli, and formed a number of poorly diffracting crystals, it is hoped that further trials and optimization of conditions will lead to improved data quality. Lymphotoxin β receptor was produced in a Eukaryotic system. This has shed light on the complications posed by signal peptide cleavage and glycosylation on the production of protein for crystallization trials.
TNF superfamily proteins are ideal targets for the design of novel therapeutic agents due to their involvement in a number of disease pathologies. Various methods of molecular docking and small molecule design were applied to the search for potential inhibitors of receptor binding for the TNF ligand proteins TRAIL and BAFF. A number of potential drug leads were identified from the National Cancer Institute drug database.
The Natural Killer (NK) T cell restricted TCRs recognise CD1d-presented glycolipid. Determination of the crystal structures of the invariant NK TCR and the NK restricted TCRs 5E and 5B shows that these proteins adopt the canonical structures of class I MHC restricted TCRs. This suggests that the binding of CD1d-glycolipid by these receptors will conform to the same model of binding seen for the class I MHC restricted TCRs.
An autonomy-based foundation for legal protection against discrimination
Keywords: antidiscrimination
equality
discrimination
autonomy
dignity
Expressive theory

The impressive growth of antidiscrimination law in liberal democracies in the past few decades belies the inadequacy of the normative bases on which it has been sought to be justified. Popular ideals such as rationality, equality and dignity have been unsuccessful in providing a coherent liberal framework for the fundamental aspects of the practice of antidiscrimination law. In this thesis, I have argued that a unified normative framework comprising autonomy and dignity-as-autonomy does a markedly better job of justifying the most fundamental aspects of these laws. The ideal of personal autonomy is understood here as a principle that seeks to guarantee an adequate range of valuable options to individuals. Dignity-as-autonomy is understood to be an expressive norm, which forbids certain persons from expressing contempt for the autonomy of another. These ideals have different forms: autonomy is a non-action-regarding principle, while dignity-as-autonomy is action-regarding. They are also distinct substantively: it is often possible to violate one of them without affecting the other. When these ideals make incompatible demands, I argue that those made by autonomy should prevail. Mandating positive action and reasonable accommodation on the one hand, and prohibiting indirect discrimination and harassment on the other, are essential features of a model of antidiscrimination law based on this framework. Further, under this framework, antidiscrimination law is not vulnerable to objections such as ‘levelling down’ and responds well to claims of discrimination on ‘intersectional grounds’. Furthermore, it is not essential to find an ‘appropriate comparator’ in order to prove discrimination. This model also explains when, and under what conditions, can some forms of discrimination be ‘justified’. Finally, on an autonomy-based model, antidiscrimination law is only one of several complementary tools that should be employed to protect and promote personal autonomy.
Studies on optical characterisation of carbon nanotube suspensions
Keywords: excitons
carbon nanotubes
photoluminescence spectroscopy

This thesis reports studies done on single-walled carbon nanotubes (SWNTs) using optical spectroscopy as the primary investigative technique. It focuses on advances in sample preparation which have been made possible through improvements to the method of photo-luminescence excitation (PLE) mapping of nanotubes.
An introduction to the field and some theoretical models are presented initially to provide a background to the experimental chapters which follow. A description of the standard procedure for sample preparation in aqueous surfactants is then followed by a detailed introduction to PLE mapping, including modeling of SWNT spectra. The next chapter discusses improvements to the sample preparation method by using organic polymer solutions instead of aqueous surfactants for suspending the nanotubes. The results show reductions in the distribution of SWNT species which are solubilised, leading to significant improvements in the resolution of the optical absorbance spectra and an increased photoluminescence yield.
Two experiments which were performed on the novel polymer-SWNT systems are then described. The first shows (via PLE mapping) that energy is transfered to the SWNTs when the polymer is photo-excited. The possible mechanisms behind this, as well as the implications for using carbon nanotubes as an additive in polymer photovoltaics, are discussed. The second experiment details a recent magneto-PL study of SWNTs embedded in films produced from the polymer solutions. Here, the improved optical signatures and absence of strain at low temperatures have revealed a previously unseen high field intensity dependence. The behavior has been explained by the magnetic field induced mixing of the excitonic states.
Essays in development economics
Keywords: economics
natural disasters
infrastructure
intra-household allocation
local labour markets
children
transport
construction

This thesis comprises three stand-alone chapters:
The first chapter is on the effect of natural disasters on labor markets. Using data from the Indonesia Family Life Survey, the Desinventar database, the US Geological Survey and district level employment indicators, we explore how a large earthquake in Indonesia affected local labor markets, in particular the evolution of wages and employment across sectors. We find that wage growth in the agriculture sector is significantly higher in earthquake affected areas. We propose two mechanisms for this result and show evidence for both mechanisms.
vThe second chapter investigates the intra-household allocation of leisure and consumption among siblings. Children are often treated as passive members in the household and their preferences over consumption and leisure are rarely modeled. This chapter considers children as agents with their own preferences over leisure and consumption and builds a theoretical and empirical model for children's time and consumption allocations in a household. We test the predictions of the model with data from Ethiopia, India, Peru and Vietnam. The results suggest that differences in siblings' relative time and consumption allocations are driven by their relative preferences over leisure and consumption rather than differences in parents' relative altruism.
The third chapter examines the cost of transport infrastructure in developing countries. To our knowledge, this is the first study that analyzes drivers of unit costs of construction of transport infrastructure using a large data set of 3,322 unit costs of road work activities in low and middle income countries. We find a large dispersion in unit costs for comparable work activities. Unit costs are significantly higher in conflict and corrupt countries, and these effects are robust to controlling for a country's public investment capacity and business environment. Finally, higher unit costs are significantly negatively correlated with infrastructure provision.
Neural degeneration and plasticity following damage to the post-chiasmal visual pathway
Keywords: stroke
hemianopia
magnetic resonance imaging
vision

Hemianopia is a disorder where a patient loses vision in one half of their visual field, following damage to the post-chiasmal visual pathway. If the hemianopia does not spontaneously resolve within the first few months, the prognosis for recovery is poor, with very few patients recovering vision in the affected area of the visual field. The reasons for this are unclear, although it is likely that both degeneration and plasticity in the visual system have an impact on patient outcome. The goal of this research is to investigate the changes that occur in hemianopia, and how these differ for lesions at different locations in the visual pathway and with differing underlying pathologies.
Patients with hemianopia arising from different causes were recruited, including 17 with a hemianopia acquired in adulthood, 9 with congenital hemianopia, and 6 patients with hemianopia due to posterior cortical atrophy (PCA). Structural, functional, and diffusion-weighted MRI data were acquired for each patient, in order to examine changes in the structural and function of the visual pathways. Analyses focused on either atrophy, or plasticity and residual function. Atrophy was assessed in acquired and congenital hemianopia by quantifying transneuronal degeneration in the optic tract, which was present in all patients with long-term lesions. Degeneration was also assessed more generally in PCA, who have substantial loss of white and grey matter in posterior brain regions. Investigation of plasticity and residual function focused on the motion processing area (MT), quantifying the level of functional activity in MT, and assessing whether subcortical pathways from the pulvinar to MT exist in hemianopia. A wide degree of variation existed between patients in the extent to which motion processing was preserved, which had no clear link to lesion location, however was related to the size of the lesion.
Synthesis and use of new chiral DABCO derivatives for asymmetric fluorination
Keywords: Synthetic organic chemistry

In this thesis, the synthesis, reactivity and enantioselectivity of novel chiral Selectfluor Analogues were investigated.
Chapter 1: Discussed is a general introduction to Selectfluor as an achiral electrophilic fluorinating reagent and its role as an oxidant in a wide variety of transformations and summarises the aims and objectives of the project.
Chapter 2: The synthesis of chiral 2-monosubstituted, 2,3-disusbstituted and 2,5-disubstituted DABCO derivatives is described. We selected two strategies to prepare these chiral analogues of DABCO. Strategy A takes advantage of a large range of commercially available natural and unnatural amino acids. 2,3-Disubstituted DABCO motifs were prepared via a protocol of Sharpless in strategy B. Eleven chiral DABCO systems have been synthesized, six of which are novel compounds.
Chapter 3 describes the synthesis of novel chiral non-racemic Selectfluor analogues using F₂. Mono-fluorinated chiral DABCOs were found to be unstable at low temperature, however, quaternized derivatives of these chiral reagents induced stability1. The fluorination proved challenging with chiral DABCO derivatives having sterically demanding substituents.
Moreover, we have developed a practical and general process for the synthesis of novel chiral non-racemic Selectfluor using N-fluoropentachloropyridinium triflate 221. This methodology alleviates the need to handle F₂ gas.
In Chapter 4: An investigation into how chiral Selectfluor analogues compare to N-F derived cinchona alkaloids in term of reactivity and enantioselectivity. The reactivity of the chiral Selectfluor analogues was challenged with both activated and less activated substrates. The novel chiral Selectfluor analogues showed superior reactivity than the cinchona alkaloids. Moderate to excellent yields of the desired products were obtained for all of the substrates studied.
Computational studies of cell-penetrating peptides interactions with complex membranes models
Keywords: bilayer
MD
CPP
molecular dynamics
membrane
cell-penetrating peptides
CG
coarse grain

Membrane active peptides with the ability to cross the plasma membrane represent a promising class of therapeutic compounds. However, translocation efficacy and membrane toxicity of these peptides appear correlated and a better understanding of their mechanisms of action is needed to achieve the desired effect. Here, a range of coarse grain molecular dynamics simulations have been performed to systematically investigate the interactions of such cell-penetrating peptides (CPPs) with biologically relevant membranes. Challenges associated to the development of a suitable asymmetric mammalian membrane model demonstrated the importance of lipid species distribution on the bilayer mechanical properties, as well as the effect of coarse graining on its electrostatic properties. However, simulations successfully discriminated between two CPPs, penetratin and transportan, and were consistent with the experimental data available for these. The results obtained suggest that the ability of transportan peptides to aggregate into flexible, dynamic, transmembrane bundles is responsible for their relative membrane toxicity. The stability and structure of these aggregates, as well as the extent of the bilayer perturbations they induced, were shown to depend on the membrane composition and asymmetry, thus providing a molecular basis to explain how the toxicity of CPPs is modulated by membranes. In particular, bilayer destabilisation was enhanced by the presence of anionic lipids and hampered by that of cholesterol. Transportan aggregates were also observed to trigger lipid flip-flops above a certain size and a new pathway for such events, not relying on the formation of water defects, was characterised.
Charge transfer processes of atomic hydrogen Rydberg states near surfaces
Keywords: nanoparticles
molecular beam
charge-transfer
Rydberg
surface interaction
atomic hydrogen

When approaching a metal surface, the electronic structure of Rydberg atoms or molecules is perturbed by the surface potential and at close enough distances resonant ionisation of the Rydberg electron into the conduction band of the surface can occur. It is possible to interfere in this process and steer the ionisation distance by making use of the polarisability of the Rydberg orbital in the presence of electric fields. The resulting ions from the surface can extracted via electric fields and subsequently detected via well established ion detection schemes. The question of how this charge-transfer process is affected by different properties of the surface (both electronic and structural) represents the main aspect of the work presented in this thesis.
At first, the charge transfer of atomic hydrogen Rydberg atoms with a flat gold metal surface is investigated. While such a surface might appear homogeneous, stray fields are present in its vicinity due to local variations in the surface work function. The surface ionisation process as a function of applied electric field is therefore measured experimentally and the results are compared with classical Monte-Carlo simulations (which include stray field effects). This way the possibility to utilize Rydberg states as a probe of the magnitude of such stray fields is demonstrated. To investigate the effect the surface structure can have on the ionisation process, the interaction of Rydberg atoms with surfaces covered by nanoparticles is investigated. Surface ionisation is measured at a 5 nm nanoparticle monolayer surface and it is shown that population transfer between surface- and vacuum-oriented Rydberg states occurs. In addition, results are presented, which suggest a dependence of the ionisation process on the relative size of Rydberg orbital and nanoparticle. Furthermore, charge transfer between a Rydberg state and discrete electronic states at the surface vacuum interface are investigated by performing experiments with a Cu(100) band-gap semiconductor surface. By analysing surface ionisation as a function of collisional velocity ionisation rates can be determined and are subsequently compared with theoretical predictions. The potential of identifying resonant ionisation is thereby demonstrated. Last, a new method to produce 2s atomic hydrogen via mixing of the 2s and 2p state in an electric field is proposed and first experimental results are presented, thus demonstrating viability of the idea.
The experiments presented in this thesis represent the most in depth analysis of the charge-transfer process between atomic hydrogen Rydberg states and a range of different surfaces to date. As such, they demonstrate the potential of utilizing the unique properties of Rydberg states and their applicability as surface probes. In addition, these results pave the way for further experiments involving thin films or the phenomenon of quantum reflectivity.