VictorJuiz/thesis huggingface dataset:
Aspects of the syntax of prepositions and prepositional phrases in English and Polish

The present thesis focusses on the structure of PP's in English and Polish, and the occurrence of PP's in subject and object positions. The main theoretical references are the X-bar Theory of syntactic categories and the Government Binding framework (GB).
A consideration of English data corroborates Jackendoff's and Emonds' claim that apart from an NP, prepositions can take a PP and an S′ complement or no complement at all, though details of Jackendoff's analysis are revised. Polish prepositions allow the same range of complements, including no complement, although,with a greater variety of complex prepositions and with intransitive prepositions modified by relative and appositive clauses, the P-PP and the P-S′ structures are less common in Polish than in English.
Subject and object PP's have so far received little attention. Like PP objects of prepositions, they are used if the intended meaning cannot be expressed by a suitable NP. The appearance of subject PP's in raising and passive sentences poses a problem for classical Transformational Grammar, though not for a slightly revised version of GB – another category-based framework. The analysis proposed here involves a particular view of the representation of Case, and a revised Case Filter. The Case Filter rules out not merely any lexical NP with no Case but any lexical XP which requires Case but has not been assigned Case. Thus, the properties of being an NP and requiring Case are independent of each other.
It emerges from the investigation (i) that prepositions in English and Polish are more alike than one might expect, given the obvious differences between the two languages; (ii) that prepositions and PP's are like verbs and VP's – as Jackendoff emphasizes – but in some respects they show greater resemblance to other categories; and (iii) that syntactic categories are less important for the distribution of phrases than is commonly assumed, and that the meaning of phrases is of central importance for their distribution.
Advances in fine-grained visual categorization

The objective of this work is to improve performance in fine-grained visual categorization (FGVC). In particular, we are interested in the large-scale classification between hundreds of different flower, bird, dog species. FGVC is challenging due to high intra-class variances caused by deformation, view angle, illumination and occlusion, and low inter-class variance since some categories only differ in detail that only experts notice. Applications include field guides, automatic image annotation, one-click shopping app and 3D reconstruction.
At the start, we discuss the importance of foreground segmentation in FGVC, where we focus on the unsupervised segmentation of image training sets into fore- ground and background in order to improve image classification performance. To this end, we introduce a new scalable, alternation-based algorithm for co-segmentation, Bi-CoS, which is simpler than many of its predecessors, and yet has superior performance on standard benchmark image datasets. Next, we extend BiCos to a new model, Tri- CoS, that adds a class-discriminitiveness term directly into the segmentation objective. The new term aims at removing image regions that, although appearing as foreground, do not contribute to the discrimination between classes.
We also propose a model that combines parts alignment and foreground segmentation into a unified convex framework. The model is called Symbiotic in that part discovery/localization is helped by segmentation and, conversely, the segmentation is helped by the detection (e.g. part layout). The joined system improves over what can be achieved with an analogous system that runs segmentation and part-localization independently.
Finally, we built a new flower dataset consisting of 26,798 high quality images collected by ourselves and 187,559 images gathered from existing datasets. The construction of this dataset follows a strict biological taxonomy. We also evaluate the impact of using the Amazon Mechanical Turk (AMT) service for filtering fine-grained data.

Keywords: computer vision
artificial intelligence
image classification
fine graind visual categorization
Advisor: Zisserman, A
Lempitsky, V
Interconnections, exchanges and influences relating to medicine, warfare and rulership between Egypt and the Aegean during the Middle and Late Bronze Age

This thesis studies interactions between Egypt and the Aegean during the Middle to Late Bronze Ages, focusing on reciprocal influences in the spheres of healing, warfare, and legitimation of power.
Chapter 1 provides an introduction, starting with an overview of previous research. The next two sections discuss a couple of issues of general significance, namely chronology and the Egyptian terminology for Aegean peoples and locations. The last two sections deal with issues of methodology and explain the aims of this work.
Chapter 2 is devoted to healing practices. Like the two chapters that follow, it begins with a cross-cultural comparison between the Egyptian and Aegean milieus. The basis for the discussion is provided by references to Crete in a couple of Egyptian medical texts. Other potential indications of an exchange of medical lore include containers that might have been used for medical preparations, amulets with healing properties, and possible similarities in practices and medical terminology.
Chapter 3 treats warfare, considering it in its broadest sense as a cultural phenomenon, besides looking for evidence suggesting military interaction or cooperation between Egypt and the Aegean. The material under scrutiny ranges from the decoration of weapons to the exchange of raw materials destined for the production of military equipment. Ideology and iconography also contribute to the discussion.
Chapter 4 explores the possibility of Egyptian influence in the development of the Aegean ideologies of power and the exploitation of foreign contacts as a source of legitimation. The main body of the chapter deals with the role of exotica in the pursuit of prestige. Some potential examples of the adoption of foreign customs and ideas are also discussed.
Chapter 5 summarises the conclusions of the previous chapters concisely and discusses how they may fit within the broader context of the study of Egyptian–Aegean relations. Finally, some possible lines of research for the future are suggested.

Keywords: Egyptian-Aegean relations; intercultural contacts; medicine in antiquity; kingship; warfare in antiquity
Advisor: Baines, J
Bendall, L
Analysis of incomplete and complete contacts in sliding and partial slip

Fretting fatigue is a type of contact fatigue which causes premature failure in a number of engineering assemblies subjected to vibration or other forms of cyclic loading. It is concerned with the nucleation of cracks due to oscillatory micro slip between contacting bodies. Therefore, a detailed knowledge of the interface conditions and the means of quantifying crack nucleation are very important, and will be the ultimate goal of this thesis. The analysis of an incomplete contact (Herzian contact) is considered first followed by various complete contacts. Fretting fatigue tests employing a Hertzian contact are analysed accurately by introducing several modifications needed to the classical formulation. With the total state of stress in a strip established, the crack tip stress intensity factor for a crack growing inward from the trailing edge of the contact is determined by the distributed dislocation technique. The results are then correlated with local solutions for the contact stress field which enable an estimate of the crack nucleation life, and hence a characteristic material property quantifying initiation, to be found. The interfacial contact pressure distribution beneath a complete sliding contact between elastically similar components, in the presence of friction, has been studied in detail, with particular reference to contacts whose edge angles are 60 degree, 90 degree and 120 degree. The possible types of behaviour at the edge of contacts, namely power order singularity, power order bounded and square root bounded, are discussed. A full understanding of the behaviour requires a detailed study of a characteristic equation, and this shows the kinds of pressure distribution to be anticipated, which can vary very markedly. The transition from power order behaviour to local separation and bounded behaviour is examined, and an appropriate asymptotic form developed. The problem of trapezium shaped punches pressed into a frictional, elastically similar half-plane, and subject to sequential normal and shear loading, under partial slip, is studied. Detailed considerations have again been given to the specific cases of 60 degree, 90 degree and 120 degree punches, and maps have been developed showing the initial mix of stick, slip and separation regions, together with the steady state response when the shearing force is cycled. Conditions for full stick are established.

Keywords: asymptotic analysis
complete contacts
incomplete contacts
fretting fatigue
Advisor: Hills, D
Confocal single-molecule fluorescence as a tool for investigating biomolecular dynamics in vitro and in vivo

Confocal single-molecule fluorescence is a powerful tool for monitoring conformational dynamics, and has provided new insight into the enzymatic activities of complex biological molecules such as DNA and RNA polymerases. Though useful, such studies are typically qualitative in nature, and performed almost exclusively in highly purified, in vitro settings. In this work, I focus on improving the methodology of confocal single-molecule fluorescence in two broad ways: (i) by enabling the quantitative identification of molecular dynamics in proteins and nucleic acids in vitro, and (ii) developing the tools needed to perform these analyses in vivo.
Toward the first goal, and together with several colleagues, I have developed three novel methods for the quantitative identification of dynamics in biomolecules: (i) Burst Variance Analysis (BVA), which unambiguously identifies dynamics in single-molecule FRET experiments; (ii) Dynamic Probability Density Analysis (PDA), which hypothesis-tests specific kinetic models against smFRET data and extracts rate information; and (iii) a novel molecular counting method useful for studying single-molecule thermodynamics. We validated these methods against Monte Carlo simulations and experimental DNA controls, and demonstrated their practical application in vitro by analyzing the “fingers-closing” conformational change in E.coli DNA Polymerase I; these studies identified unexpected conformational flexibility which may be important to the fidelity of DNA synthesis.
To enable similar studies in the context of a living cell, we generated a nuclease-resistant DNA analogue of the Green Fluorescent Protein, or “Green Fluorescent DNA,” and developed an electroporation method to efficiently transfer it into the cytoplasm of E.coli. We demonstrate in vivo confocal detection of smFRET from this construct, which is both bright and photostable in the cellular milieu. In combination with PDA, BVA and our novel molecular counting method, this Green Fluorescent DNA should enable the characterization of DNA and protein-DNA dynamics in living cells, at the single-molecule level. I conclude by discussing the ways in which these methods may be useful in investigating the dynamics of processes such as transcription, translation and recombination, both in vitro and in vivo.

Keywords: DNA structure
single molecule fluorescence in vivo
DNA polymerase
FRET
Single molecule fluorescence
confocal fluorescence
Advisor: Kapanidis, A
Duchenne muscular dystrophy: RNA-based therapeutics and microRNA biology

Duchenne muscular dystrophy (DMD) is a progressive muscle wasting disorder caused by absence of functional dystrophin protein. This thesis describes investigations into the role of small non-coding RNAs in both DMD pathology, and as potential therapeutic molecules.
MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression and are implicated in wide-ranging cellular processes and pathological conditions. This study has compared differential miRNA expression in proximal and distal limb muscles, diaphragm, heart and serum in the mdx dystrophic mouse model relative to wild-type controls. Global transcriptome analysis revealed muscle-specific patterns of differential miRNA expression as well as commonalities between tissues, including previously identified dystromirs. miR-1, miR-133a and miR-206 were found to be highly abundant in mdx serum, suggesting that these miRNAs are promising disease biomarkers. Indeed, the relative serum levels of these miRNAs were normalised in response to peptide-PMO mediated dystrophin restoration therapy. This study has revealed further complexity in the miRNA transcriptome of the mdx mouse, an understanding of which will be valuable for the development of novel DMD therapeutics and for monitoring their efficacy.
Myostatin is a secreted growth factor that negatively regulates muscle mass and is therefore a potential pharmacological target for the treatment of muscle wasting disorders such as DMD. This study describes a novel myostatin inhibition approach in which small interfering RNAs (siRNAs) complementary to a promoter-associated transcript induce transcriptional gene silencing (TGS) in cultured myotubes. Silencing was sensitive to treatment with the histone deacetylase inhibitor Trichostatin A, and the silent state chromatin mark H3K9me2 was enriched at the myostatin promoter following siRNA transfection, suggesting epigenetic remodelling underlies the silencing effect. These observations suggest that long-term epigenetic silencing may be feasible for myostatin and that TGS is a promising novel therapeutic strategy for the treatment of muscle wasting disorders.
The work in this thesis therefore demonstrates the potential of small RNAs as therapeutic agents and as disease biomarkers in the context of DMD.

Keywords: DMD
microRNA
epigenetics
Advisor: Wood, M
Stability tests of opto-electronic systems for use in the SLHC

The Large Hadron Collider (LHC) located at CERN is the world’s most powerful particle accelerator, with plans to collide protons at a center of mass energy of 14 TeV. These proton-proton collisions occur within particle detectors located around the circumference of the accelerator. After approximately 10 years of running at this energy, the LHC accelerator will be upgraded to the super-LHC and it will be necessary to upgrade the constituent particle detectors, in particular the CMS and ATLAS detector experiments. The innermost layers of these detectors will have experienced a very high radiation environment over an extended period of time and will have reached the maximum radiation dose for which they were designed. Upgrades to the accelerator will increase the radiation dose rate and total dose experienced by the detectors, which will demand both increased radiation-hardness of detector components and improved detector performance to handle the increased data rate driven by accelerator upgrades.
This thesis presents results of tests performed as a part of the research and development of the LHC upgrade. In particular, we report on the optical fibres to be used in the readout systems of the inner detectors. Fibres were tested for performance variability in high radiation and temperature-variant environments.

Keywords: SLHC
radiation
fibre optics
temperature
Advisor: Huffman, T
The use of functionalised lithium amides in the total synthesis of alkaloids

This thesis is concerned with the application of the conjugate addition of functionalised lithium amides in the asymmetric syntheses of (−)-morphine and all members of the homalium alkaloids. Chapter 1 introduces the conjugate addition reaction as an important bond forming reaction, and explores its utility in the asymmetric synthesis of a variety of natural products. The conjugate addition of secondary lithium amides derived from α-methylbenzylamine is discussed, along with its application to the asymmetric synthesis of alkaloids.
Chapter 2 describes two distinct attempts towards the asymmetric synthesis of (−)-morphine, both reliant upon the lithium amide conjugate addition and an intramolecular Diels-Alder reaction to set the five required stereogenic centres. The use of the novel and highly functionalised reagent lithium (R)-N-[2′-(7-methoxybenzofuran-3-yl)ethyl]-N-(α-methylbenzyl)amide and its derivatives is reported.
Chapter 3 focuses on the use of the novel reagent lithium (R)-N-(3-chloroprop-1-yl)-N-(α-methylbenzyl)amide and its derivatives in the asymmetric synthesis of two of the homalium alkaloids, (−)-(S,S)-homaline and (−)-(R,R)-hopromine, culminating in the most efficient syntheses of these alkaloids to date. Further, a sample of the (4′R,4′′S)-diastereoisomer of hopromine was synthesised, serving to confirm the proposed absolute configuration within natural (−)-(R,R)-hopromine.
Chapter 4 extends the methodology developed in chapter 3 to the asymmetric synthesis of all possible diastereoisomers of the remaining homalium alkaloids, (−)-hopromalinol and (−)-hoprominol. These syntheses were used to propose the absolute configurations within these alkaloids, and therefore represented the first asymmetric syntheses of natural (−)-(4′S,4″R,2‴R)-hopromalinol and (−)-(R,R,R)-hoprominol.
Chapter 5 contains full experimental procedures and characterisation data for all compounds synthesised in Chapters 2, 3 and 4.

Keywords: hoprominol
conjugate addition
hopromalinol
lithium amide
asymmetric synthesis
hopromine
morphine
homalium alkaloids
alkaloids
homaline
Advisor: Davies, S
Allele specific gene expression in the major histocompatibility complex

The Major Histocompatibility Complex (MHC) is a highly polymorphic region of the genome located on chromosome 6p21 in which genetic diversity has been associated with susceptibility to many autoimmune, infectious and other common diseases. Despite strong associations between disease and variation in the MHC that have been identified initially from serological testing and more recently by genome-wide association studies, functional insights into how specific variants may be altering disease susceptibility remain poorly understood in most cases. It is predicted that gene expression will play a significant role in the modulation of disease susceptibility and so further understanding of allele specific gene expression in the MHC will be necessary to help define the function of disease associated variants in this region.
This thesis aimed to define allele specific gene expression in the MHC by characterising specific candidate genes together locus-wide approaches in order to try and resolve functional variants. Gene expression was analysed in both lymphoblastoid cell lines (LCLs) and primary human peripheral blood mononuclear cells (PBMCs). Data is presented validating a novel haplotype-specific MHC microarray and fine mapping putative local, likely cis-acting, regulatory variants. This was done by expression quantitative trait mapping for two cohorts of healthy volunteers. A transcription factor ZFP57, encoded in the MHC, was found to show significant differential allelic expression relating to specific single nucleotide polymorphisms (SNPs) and possession of HLA-type. This provided new insights into reported disease associations, notably HIV-1 infection and cancer. The function of ZFP57 was further investigated in terms of genome-wide DNA binding sites by ChIP-seq together with its binding co-factor KAP1.
Allele-specific gene expression was also demonstrated for several classical HLA genes including the HLA-C and HLA-DQ genes, fine mapping specific putative regulatory variants. This provided new insights into disease association, notably variants of HLA-DQB1 and susceptibility to leprosy. The applicability and sensitivity of the technique of RNA sequencing (mRNA-seq) for allele-specific quantification of gene expression was investigated for different allelic ratios of RNA from LCLs homozygous for sequence across the MHC. Significant challenges were identified in successful application of this technique to MHC genes while high levels of accuracy were observed dependent on read depth in non-MHC genes.
This thesis provides new insights into the extent and nature of allele-specific gene expression in the MHC, experimental approaches that can be used and insights gained into disease susceptibility for this important genomic region.

Keywords: eQTL
human genetics
allele-specific
gene expression
MHC
Advisor: Knight, JC
Magnetic field effects in chemical systems

Magnetic fields influence the rate and/or yield of chemical reactions that proceed via spin correlated radical pair intermediates. The field of spin chemistry centres around the study of such magnetic field effects (MFEs). This thesis is particularly concerned with the effects of the weak magnetic fields B₀ ~ 1mT relevant in the ongoing debates on the mechanism by which animals sense the geomagnetic field and on the putative health effects of environmental electromagnetic fields. Relatively few previous studies have dealt with such weak magnetic fields. This thesis presents several new theoretical tools and applies them to interpret experimental measurements. Chapter 1 surveys the development and theory of spin chemistry. Chapter 2 introduces the use of Tikhonov and Maximum Entropy Regularisation methods as a new means of analysing MARY field effect data. These are applied to recover details of the diffusive motion of reacting pyrene and N,N-dimethylaniline radicals. Chapter 3 gives a fresh derivation and appraisal of an approximate, semiclassical approach to MFEs. Monte Carlo calculations allow the elucidation of several "rules of thumb" for interpreting MFE data. Chapter 4 discusses recent optically-detected zero-field EPR measurements, adapting the gamma-COMPUTE algorithm from solid state NMR for their interpretation. Chapter 5 explores the role of RF polarisation in producing MFEs. The breakdown in weak fields of the familiar rotating frame approximation is analysed. Chapter 6 reviews current knowledge and landmark experiments in the area of animal magnetoreception. The origins of the sensitivity of European robins Erithacus rubecula to the Earth’s magnetic field are given particular attention. In Chapter 7, Schulten and Ritz’s hypothesis that avian magnetoreception is founded on a radical pair mechanism (RPM) reaction is appraised through calculations in model systems. Chapter 8 introduces quantitative methods of analysing anisotropic magnetic field effects using spherical harmonics. Chapter 9 considers recent observations that European robins may sometimes be disoriented by minuscule RF fields. These are shown to be consistent with magnetoreception via a radical pair with no (effective) magnetic nuclei in one of the radicals.

Keywords: MARY
ODEPR
electron spin resonance
regularization
anisotropic
RF
MFE
zero-field EPR
Wiltschko
electron paramagnetic resonance
magnetoreception
Maximum Entropy
Tikhonov
semiclassical
magnetic
MARY-B0
RPM
ESR
Erithacus rubecula
MARY-nu
magnetic field effect
polarization
Ritz
Advisor: Hore, P
Timmel, C