VictorJuiz/thesis huggingface dataset:
A study of central exclusive production at LHCb

This thesis presents an analysis of the central exclusive production (CEP) of χc mesons in proton-proton collisions at a centre-of-mass energy of 8 TeV, using data collected with the LHCb detector corresponding to an effective integrated luminosity of 126.3 ± 4.3 pb⁻¹. Candidate χc decays are reconstructed in the K+K- and π+π- final states, where the final state particles have pseudorapidities between 2.5 and 4.5. The products of the cross sections and branching fractions are measured as
σ × 𝓑(χc0 → K+K-) = 28.0 ± 2.8 ± 13.9 pb,
σ × 𝓑(χc0 → π+π-) = 20.3 ± 2.4 ± 8.1 pb,
σ × 𝓑(χc2 → K+K-) &LT; 12.1 pb,
σ × 𝓑(χc2 → π+π-) &LT; 10.5 pb,
where the first uncertainties are statistical and the second systematic, and limits are set at the 95% confidence level. A major source of systematic uncertainty is the determination of the fraction of the selected data which is CEP rather than inelastic backgrounds.
Also described is HERSCHEL, a new subdetector installed at LHCb during the first long shutdown of the LHC. This is a system of forward shower counters which will provide CEP analyses with event-by-event rejection of inelastic backgrounds. The pseudorapidity coverage and detection efficiency of HERSCHEL are determined using Monte Carlo simulations. The pseudorapidity coverage extends to |η| ≥ 10 due to the showering of collision products at the aperture limit. With a photoelectron threshold yield of 0.2 times the yield in the mean minimum bias event, the detection efficiency for single diffractive events is predicted to be 89% in the forward direction and 91% in the backward direction.

Keywords: particle detectors
Particle physics
Large Hadron Collider
Central Exclusive Production
Advisor: Wilkinson, G
‘Communicative sentencing: exploring the perceptions of young offenders in the community’

The purpose of this thesis is to investigate young offenders’ first-hand views of community punishment within the context of the extant literature on communicative theories of sentencing. Fuelled by the traditional marginalisation of young offenders’ views of penal interventions, and drawing upon the qualitative information yielded by fifty semi-structured interviews with 16-18 year old offenders, the study purports to enhance our understanding of the penal messages that punishment communicates to those who experience it. This research initiative is premised on the belief that an empirically-driven research project of this nature can contribute to an improved understanding of the relationship between the youth justice system’s preventive and rehabilitative aims and how offenders themselves perceive the communicative dimensions traditionally attributed to punishment. The Introduction contains the genesis of this investigation and establishes the parameters of the inquiry. Chapter Two analyses the available literature on offenders’ views and argues the case for further research. The third chapter examines the literature on communicative sentencing and anchors the project firmly within the relevant academic debate against which the study’s findings are analysed. Chapter Four contains a detailed account of the methodology employed and prefaces the analysis of findings. While Chapters Five and Six examine the penal messages offenders perceive during sentencing, Chapter Seven explores conceptual issues relating to the communicative functions interviewees ascribed to hard treatment and censure. The next chapter takes cognisance of how offenders conceptualise the penal messages that are transmitted to them during the administration of their sentences. The Conclusion examines the implications of the study’s findings for theory and policy, and proposes a cultural shift from an overly sceptical perspective which does not always afford much value to offenders’ viewpoints, to the creation of a new framework which will allow for greater offender participation.

Keywords: Youth Justice
Offender's Perceptions
Criminology
Youth Justice System
Law
Communicative theories of punishment
Young Offenders
Advisor: Roberts, J
Unnatural amino acids as metal-mediated probes of biological function

Conjugation reactions on proteins have been used to access various post-translational modifications, for targeted delivery of drugs, for microscopy, and in studying receptor-ligand interactions. However, the ability to modify native proteins is constrained by the reactive functionalities of naturally occurring amino acids. This has driven research into the incorporation of unnatural amino acids (UAAs) into proteins. Research in this area has been motivated both by the possibility of increasing the breadth of chemical techniques for protein modification by introducing novel 'bio-orthogonal' reactive groups via UAA incorporation, as well as generating well-defined conjugates by the site-selective incorporation of these UAAs into proteins. The objective of this thesis is to both expand the diversity of UAAs for access to new metal-mediated reactions on proteins, as well as to utilise these reactions to reveal functional information about a range of biological systems. A brief introduction into current protein conjugation and UAA incorporation methods will be made in Chapter 1.
In Chapter 2, the genetic incorporation of alkene-bearing UAAs into recombinant proteins expressed in both bacterial and mammalian systems is discussed. This technique is demonstrated to enable Ru-catalysed olefin cross-metathesis (CM) reactions on the resultant proteins. This work builds upon previously established methods to chemically incorporate CM handles onto proteins. The rational design of UAAs, as well as assays and modelling studies to screen them for recognition by the cellular incorporation machinery are discussed in detail. The expression of a range of alkene-tagged recombinant proteins, their complete characterisation, as well as the development of a more general protocol for on-protein CM is elucidated.
In Chapter 3, the utility of UAA incorporation to probe mammalian cell translation systems is examined. Incorporation of an azide-bearing UAA, in addition to heavy stable-isotope labelled amino acids is used to uncover a previously unreported system of protein synthesis in mammalian cell nuclei, along with rapid metabolic degradation of the synthesised peptides. Various orthogonal methods for the detection of this system as well as possible reasons for its conservation are discussed.
In Chapter 4, UAA incorporation and metal-mediated bioconjugation reactions are utilised in the development of a novel and generally applicable proteomics technique. This technique is used to determine quantitative changes in cell proteomes in response to external stimuli, and may be applied to systems to which traditional proteomics techniques cannot, such as ex vivo primary cells.
Finally, in Chapter 5, further applications of UAA incorporation are discussed. Preliminary results are reported in efforts to use UAAs in the vibrational Raman microscopic imaging of biological systems, in generating HIV vaccines, and inducing T-cell stimulation.

Keywords: chemical biology
unnatural amino acids
protein chemistry
proteomics
Advisor: Davis, B
Ethical issues in research ethics governance and their application to the Malaysian context

Evidence available shows that the ethics review process in Malaysia suffers from a range of problems (Kaur, 2011). These problems may be the result of a lack of training given for REC members and relatedly, it may stem from a lack of understanding of the role of RECs. Since Malaysia is striving to promote the country as a research hub for international collaboration, it is important that the ethics review system that is in place is well set up to ensure only ethical research are being approved. The aim of this thesis is to develop three important key elements of a framework that can be used to provide practical guidance for RECs and their governance in Malaysia. These three important elements of the ethics review process are: - the role of RECs, the criteria of REC membership and the acceptability of variation in decisions made between different RECs. These analysis is then applied to the Malaysian context. My initial recommendation is for RECs to adopt the Daniels and Sabin (1997) accountability for reasonableness model to assist with the decision-making process. The adoption of the model helps to clarify the role of RECs and can be used as a basis to develop the criteria for REC membership as well as to provide a better understanding of the acceptability of variation in decisions between different RECs.

Keywords: research ethics
Advisor: Sheehan, M
Epitope dominance studies with serotype O foot-and-mouth disease

Foot-and-mouth disease virus (FMDV) is an economically devastating and highly contagious livestock pathogen. It exists as seven serotypes, comprising numerous antigenically distinct subtypes. The large amount of antigenic heterogeneity has confounded attempts at developing broadly reactive vaccines. In order to overcome this issue the fundamentals of the interactions between the virus and the host humoral immune response must first be understood. Previous work in this area using monoclonal antibody (mAb) escape mutants has identified five antigenic sites for the O serotype and efforts have been made to quantify their relative importance. However, this does not represent a complete picture of serotype O antigenicity. The work conducted in this thesis demonstrates the role of a limited number of dominant substitutions in mediating the antigenic diversity of serotype O Foot-and-Mouth disease virus. Two alternative but complementary methods for identifying epitopes were developed. The first used a mathematical model to analyse newly generated serological and sequence data from 105 viruses, cultured for this purpose (and cross-reacted to 5 reference antisera), in the context of an existing crystallographic structure to identify and quantify the antigenic importance of sites on the surface of the virus. The second approach was purely structural, using existing B cell epitope prediction tools to develop a method for predicting FMDV epitopes using existing crystallographic structures of FMDV. These techniques were validated by the use of reverse genetics, which confirmed the impact on cross reactivity of two predicted novel serotype O antigenic residues, with a further four novel residues identified by looking in depth at the interactions between two genetically close, but antigenically distant viruses. This increased knowledge of the antigenic composition of serotype O FMDV contributes to our understanding of the nature of vaccine efficacy and the breadth of protection, which, in the longer term, will aid in the goal of developing vaccines to better protect livestock from such a highly antigenically variable disease.

Keywords: foot and mouth
FMDV
in silico
antigenicity
epitope
Advisor: Stuart, DI
Social mobility in Hong Kong

This thesis examines the micro-process of social mobility in modern Hong Kong. It also studies Hong Kong's mobility regime in a conventional macro-comparative fashion. By applying the core model of social fluidity developed in the CASMIN (Comparative Analysis of Social Mobility in Industrial Nations) project to the mobility data collected in the 1989 Hong Kong Social Mobility Survey, I point to several distinctive features of Hong Kong's mobility regime. This exercise also allows me to engage in the ongoing debate concerning the degree of commonality and variation in relative mobility rates across industrial nations. Having made this macrocomparison, I turn to explore the micro-mobility process. Drawing on worklife data collected in the 1991-92 follow-up study, I consider the following issues: (a) typical mobility paths in Hong Kong, (b) how social networks facilitate the job search process, and (c) how career beginning affects subsequent mobility outcome. In this study, I also test and apply a new technique, Optimal Matching Analysis, which compares and classifies complete career sequences. Thus, apart from offering substantive findings on social mobility in Hong Kong, this thesis also seeks to make a technical contribution to the analysis of life course data.
Aspects of the growth and health of the suckling and weanling infant in Ethiopia

This thesis examines inter-relationships between the feeding, health, and growth of infants (aged 0-24 months) in low-income households in Addis Ababa, Ethiopia. Mixed-longitudinal data were collected from a sample of 113 infants and their mothers in Kebele 11, Keftegna 24 from November 1987 to April 1988.
Breastfeeding is the culturally esteemed mode of infant feeding. The culture-specific concept of weaning places the emphasis on the termination of breastfeeding, with little consideration of the quality and quantity of weaning foods. As a result, weaning foods are basic and monotonous. Survival data analysis shows that weaning is commenced at the mean age of 9.2 months, and completed at the median age of 20 months. A probabilistic model is proposed that includes a set of inter-related 'infant-centred', 'mother-centred', and other factors such as the seasonal availability of weaning foods influencing the process of weaning. Culturally-prescribed norms appear to play little or no part in the timing of weaning, in particular, the infant's age is of secondary importance.
Direct observations of suckling behaviour and infant care reveal that 'on demand' breastfeeding was practised, and the mean duration of suckling sessions was 10.96 minutes. The duration of breastfeeding was influenced significantly by maternal body-mass index. Seasonal patterns were detected in the prevalence of fever, coughing, and vomiting in the infants. Associations between morbidity and other data using log-linear models suggest that infant's diarrhoea is closely linked to the level of household hygiene, maternal education, and mother's morale. Infant's ilnesses caused appreciable deficits in weight, but not in stature. Processes of 'catch-up' and 'catch-down' growth are demonstrated by the seasonal effect of diarrhoeal illness on weight. Avenues for further research and policy reform suggested by the findings of this study are discussed.
When work is more than a job: employment among people who inject drugs 

This thesis explores employment among people who inject drugs (IDU). It seeks identify what differentiates IDU who work from those who do not, barriers to labour market participation, and how employment is perceived and experienced by IDU. Using longitudinal data from the Vancouver Injection Drug User Study (VIDUS), it conducts this research through a detailed examination of the implications of missing data, quantitative analyses of transitions into employment and qualitative, in-depth interviews.
Missing data analyses identified differences between those that those that do and do not have missing data, as well as predictors of observation gaps and how individuals end their study participation (either right-hand censorship, attrition, or death). Differences were observed along individual, behavioural and contextual dimensions. Analytical approaches to the relationship between data structure and content gleaned useful information for longitudinal studies with marginalized populations.
Discrete time event history analyses of work transitions revealed complex relationships between drug use, drug-related activities, situational risk factors, and transitions into employment. While most IDU did not make transitions into employment, some did, and while some statistical relationships were expected, others were surprising. Novel findings included mode-specific addiction treatment impacts on employment (methadone vs. non-methadone) and the importance of the broader risk environment over and above even high-intensity substance use.
Finally, qualitative interviews identified heterogeneity in individual motivations toward and experiences of work. Those who maintained concurrent drug use and formal labour market involvement utilized strategies to spatially and temporally separate the two activities. Individual capacities to employ these strategies were facilitated by material, vocational and temporal motivations, and interfered with by health conditions, catastrophic events and institutional relationships that operated as barriers to employment. This study provides insight into what is a known social determinant of health in the general population among injection drug users.

Keywords: employment
longitudinal analysis
substance use
HIV/AIDS
social determinants of health
missing data
Advisor: Gershuny, J
Ribbon braids and related operads

This thesis consists of two parts, both being concerned with operads related to the ribbon braid groups. In the first part, we define a notion of semidirect product for operads and use it to study the framed $n$-discs operad (the semidirect product $f\mathcal{D}_n=\mathcal{D}_n\rtimes SO(n)$ of the little $n$-discs operad with the special orthogonal group). This enables us to deduce properties of $f\mathcal{D}_n$ from the corresponding properties for $\mathcal{D}_n$. We prove an equivariant recognition principle saying that algebras over the framed $n$-discs operad are $n$-fold loop spaces on $SO(n)$-spaces. We also study the operations induced on homology, showing that an $H(f\mathcal{D}_n)$-algebra is a higher dimensional Batalin-Vilkovisky algebra with some additional operators when $n$ is even. Contrastingly, for $n$ odd, we show that the Gerstenhaber structure coming from the little $n$-discs does not give rise to a Batalin-Vilkovisky structure. We give a general construction of operads from families of groups. We then show that the operad obtained from the ribbon braid groups is equivalent to the framed 2-discs operad. It follows that the classifying spaces of ribbon braided monoidal categories are double loop spaces on $S^1$-spaces. The second part of this thesis is concerned with infinite loop space structures on the stable mapping class group. Two such structures were discovered by Tillmann. We show that they are equivalent, constructing a map between the spectra of deloops. We first construct an `almost map', i.e a map between simplicial spaces for which one of the simplicial identities is satisfied only up to homotopy. We show that there are higher homotopies and deduce the existence of a rectification. We then show that the rectification gives an equivalence of spectra.
Probing the deformation of ductile polycrystals by synchrotron x-ray micro-diffraction

Microscopic beams of penetrating synchrotron radiation provide a unique tool for the analysis of material structure and deformation. This thesis describes my contributions to the development of new synchrotron X-ray micro-beam diffraction experimental techniques and data interpretation, and the use of experimental results for the validation of material deformation models.
To study deeply buried material volumes in thick samples, the micro-beam Laue technique was extended to higher photon energies. Through-thickness resolution was achieved either by a wire scanning approach similar to Differential Aperture X-ray Microscopy (DAXM), or by applying tomographic reconstruction principles to grain-specific Laue pattern intensity. Both techniques gave promising first results.
For reliable micro-beam Laue diffraction measurements of elastic strains in individual grains of a polycrystal, understanding of the error sources is vital. A novel simulation-based error analysis framework allowed the assessment of individual contributions to the total measurement error. This provides a rational basis for the further improvement of experimental setups.
For direct comparison of experimental measurements and dislocation dynamics simulations, diffraction post-processing of dislocation models in two and three dimensions was developed. Simulated diffraction patterns of two-dimensional dislocation cell/wall type structures captured correctly some of the features observed experimentally in reciprocal space maps of a large-grained, lightly deformed aluminium alloy sample. Crystal lattice rotations computed from three-dimensional dislocation dynamics simulations of a Frank-Read source showed anisotropic orientation spread similar to that observed in micro-beam Laue experiments.
For the experimental study of crystal lattice distortion, a novel technique was proposed that combines micro-beam Laue diffraction with scanning white-beam topography. Diffraction topography allows the study of lattice rotation at scales smaller than the scanning beam size. The new technique makes it possible to apply classical topography methods to deformed samples.

Keywords: Nickel
Micro-beam Laue diffraction
X-ray diffraction
Dislocation dynamics
Synchrotron techniques
Advisor: Korsunsky, A
Regulation of the expression and positioning of chemotaxis and motor proteins in Rhodobacter sphaeroides

Bacteria achieve directed motion through their environments by integrating propulsion with chemical detection in the process of chemotaxis. Central to this process are the macromolecular protein structures of the flagellar motor and the chemoreceptor arrays, which are responsible for motility and chemical sensing, respectively. These protein complexes localise to different discrete subcellular positions in different bacterial species, and their correct subcellular localisation is often essential to their function.
In the monotrichous α‐proteobacterium Rhodobacter sphaeroides, the flagellum is subpolar and two distinct sets of chemotaxis proteins localise to discrete polar and cytoplasmic positions within the cell.
In this study, the development of software for the analysis of fluorescent microscopy images allowed cellular morphologies and the localisation and distribution of the chemoreceptor arrays of R.sphaeroides to be characterised in detail, showing that protein partitioning at cell division results in an asymmetric separation of both cytoplasmic and membrane‐bound protein components between daughter cells.
The design of a fluorescence‐based assay for the analysis of gene expression assisted in demonstrating that expression of both the chemotaxis and motor genes of R.sphaeroides is regulated by the sigma factor, FliA, and its inhibitor, FlgM. FliA was then used to achieve varying expression of the chemotaxis genes, and the concentration dependence of array clustering was explored in microscopy images, revealing important differences between cluster formation in R.sphaeroides and other species.,/p>
Additionally, FliA was identified as a regulator of flagellar number in R.sphaeroides, controlling a negative feedback‐loop in the hierarchy of flagellar assembly that represses flagellar formation upon secretion of FlgM. The complex regulatory pathway controlling R.sphaeroides flagellar assembly is the first identified system where completion of a single flagellum directly inhibits the production of a second, a mechanism that may be important to many monotrichous bacterial species.

Keywords: Rhodobacter sphaeroides
FliA
gene expression
FlgM
microscopy
Advisor: Armitage, J