VictorJuiz/thesis huggingface dataset:
Evolutionary drivers of the rise and fall of a dominant hybrid MRSA, ST239
Keywords: Bioinformatics
Antimicrobial resistance
MRSA
Fitness
Epidemiology
Chromosomal replacement
SCCmec
Evolution

Staphylococcus aureus infections pose a serious challenge in healthcare due to the emergence of resistance to multiple antibiotics. ST239 is a multidrug-resistant MRSA strain that has been responsible for epidemics in healthcare settings across the globe since the late 1970s. However, in recent years there have been reports of strains that have successfully replaced ST239 as the dominant strain in clinical environments.
In 2004, Robinson and Enright hypothesised that ST239 is a natural hybrid that formed through a single large chromosomal replacement event between two distantly-related S. aureus strains, where 20% of the ancestral ST8-like genome was replaced with the homologous region from an ST30-like ancestor. In this thesis, I use a diverse range of ST239, ST8 and ST30 sequences from publicly-available sequencing repositories to make genomic comparisons between ST239 and its hypothesised ancestors. I confirm that the evolution of ST239 is consistent with the Robinson-Enright model, and investigate how the acquired and backbone regions of ST239 have adapted to evolutionary pressures in the same genome. There is evidence of weaker selective constraints on the acquired region of ST239 compared to the genomic backbone, as well as evidence of parallel evolution in antimicrobial resistance and virulence related genes, which suggests that antibiotics and the host immune response are important evolutionary pressures faced by ST239. This is consistent with the close relationship between ST239 and the SCCmec-III element, which encodes multiple antimicrobial resistance genes. In over 40,000 S. aureus sequences, SCCmec-III is strongly linked to ST239, with only a few rare exceptions. In contrast with previous estimates, the most recent common ancestor of the ST239 sequences is dated several years prior to the clinical introduction of methicillin, which suggests that use of earlier antimicrobials is more likely to have driven the global emergence of ST239.
Finally, I develop a method to calculate the relative competitive ability of a collection of 15 S. aureus isolates in co-culture, including ST239, ST8 and ST30 isolates, through whole-genome sequencing. Competitive ability and growth rate are not correlated, suggesting that these two fitness measures are independent. The ST239 isolates have greater antimicrobial resistance and overall lower fitness, however, fitness and antimicrobial resistance are not correlated. This may indicate that, although ST239 has been a globally successful multidrug-resistant epidemic MRSA strain, the extreme genetic transfer events in its early evolution have had an overall negative impact on fitness, contributing to its eventual decline.
Precision fits for the LHC and beyond
Keywords: QCD
LHC physics
SMEFT

In this thesis we consider the phenomenology of Quantum Chromodynamics (QCD) and the Standard Model Effective Field Theory (SMEFT), with reference to the ongoing experiments at the Large Hadron Collider (LHC). Our emphasis is on constraining free parameters of the theories, such that the precision of theoretical calculations for the LHC are able to match the high level of experimental precision now available.
To this end, we discuss two fitting frameworks which aim to be robust and reliable ways to extract these free parameters of QCD and the SMEFT. In QCD we wish to extract the strong coupling constant at the mass of the Z boson, αs(MZ), and in the SMEFT we want to constrain the free parameters of the theory which allow for deviations from the Standard Model.
We will first introduce QCD and the SMEFT and theoretically motivate our studies. We then move on to introduce the fitting framework used to extract the strong coupling constant. We will use parton distribution functions (PDFs) to determine the strong coupling; PDFs themselves must also be extracted from data, and their determination introduces many sources of methodological uncertainties which can propagate into our determination of αs(MZ). We will discuss the tools developed in order to quantify these uncertainties and obtain a reliable estimate of αs(MZ).
In the second part of this thesis, we will discuss a novel framework developed to determine the free parameters of the SMEFT. Initially we will motivate and outline the new methodology, which we denote SMEFiT, and then apply the framework to a detailed analysis of the top sector at the LHC.
Constitutional change and the rule of recognition
Keywords: HLA Hart
constitutional theory
unconstitutional change
rule of recognition
jurisprudence
constitutional change
philosophy of law

This thesis has two objectives. The first is to reflect on the social foundations of legal change, and of change in constitutional law in particular, by developing HLA Hart’s account of ultimate rules of recognition. It argues that any change in accordance with pre-existing ultimate rules of recognition should be viewed as meaningfully coming from within a legal system. This is so even if the change in question is not a result of an exercise of a legal power to make law. Thus, rules of recognition provide an independent ground of lawfulness of legal change. However, as customary social rules, they also open the law to change that does not obey any pre-existing legal conditions of change. Such change cannot happen through an exercise of a legal power to make law, but it is here argued that an alternative notion of a ‘legal ability’ to influence change should be used. The thesis also argues that such change of ultimate rules ought to be seen as revolutionary in some, but not all, instances.
Second, the thesis applies the jurisprudential framework of rules of recognition to the debates about constitutionality of constitutional change (but only in respect to change in constitutional law). It argues that some kinds change in constitutional law, perceived as normal by participants of legal practices, cannot be understood as ‘constitutional’ on a prominent view which identifies constitutionality of change with it being a result of an exercise of a legal power to effect the change. This ‘powers view’ is deficient because it does not appreciate the role of ultimate rules of recognition in grounding lawfulness of legal change. The thesis analyses the complex nexus of amendment powers, pretended powers (‘pious fictions’), and rules of recognition, thus giving a jurisprudentially sophisticated picture of constitutional change.
Investigating speech motor control using vocal tract imaging, fMRI, and brain stimulation
Keywords: Speech
Vocal Tract
Brain Stimulation
Stuttering
Movement Inhibition
fMRI

The aim of this thesis was to understand speech motor control in both people who are typically fluent (PWTF) and people who stutter (PWS). To do this, I used a multi-modal approach including vocal tract MRI, functional MRI during task and brain stimulation. These methods allowed me to explore speech motor control from the brain’s control of speech to the movement of the articulators.
First, I conducted a systematic review of previous studies of articulation in PWS that used a variety of different methods. Technological advances over the last 15 years have offered new insight into the speech motor control of PWS by measuring precise movements of the articulators involved in speech.
I then used vocal tract MRI (vtMRI) to look at the speech movements in PWS. As this is a novel technique, experiments have been designed to first replicate and then extend key results identified via the systematic review that used alternative methods. We found that PWS, on average, produced more variable movements than typically fluent speakers even during fluent productions of simple nonwords. This indicates general, trait-level differences in the control of the articulators between PWS and people who are typically fluent.
I used functional MRI of the brain to investigate differences in the neural control of speech in PWS and PWTF. I used a task known as the Stop-Signal task that was previously used to investigate inhibitory motor control in both speech and manual movements (Xue, Aron & Poldrack, 2008). The results support the role of an over-active inhibitory response in PWS compared with controls.
Finally, I designed a study to investigate whether transcranial direct current stimulation (tDCS) can modulate speech articulation in a typically fluent population. I used both behavioural and electrophysiological outcomes to assess the role of tDCS in modulating performance on a complex articulation task. TDCS did not modulate performance on a complex articulation task in healthy young adults. TDCS applied concurrently with task learning also failed to modulate cortical excitability in expected ways.
Connectivity-specified targeting and manipulation of the motor thalamus
Keywords: Motor skill learning
Cerebellum
Basal ganglia
Frontal cortex
Motor sequences
Optogenetic silencing
Procedural learning
In vivo electrophysiology
Motor thalamus
ArchT
Operant behaviour
Kir2.1
Thalamocortical

Understanding the nature and consequences of information flow between the basal ganglia, cerebellum, thalamus and motor cortex on the acquisition and execution of motor skills may lead to better circuit therapies for brain disorders. Although basal ganglia and cerebellar output is thought to influence motor cortex activity via projections arising from distinct zones of ventral ‘motor’ thalamic nuclei (ventral medial [VM], ventral anterior [VA] and ventral lateral [VL] nuclei), the consequences of their activity on motor skills in rodents remains uncertain. Here, we first utilise an anterograde transsynaptic viral strategy to confirm that anatomically and functionally distinct basal ganglia-recipient and cerebellar-recipient neuron populations exist in the mouse motor thalamus. To address the behavioural significance of these two neuron populations for motor skill learning, Vglut2-Cre mice with either targeted chronic motor thalamus silencing (using overexpression of the inward-rectifier potassium channel Kir2.1) or acute optogenetic silencing of VM or VL (using the light-sensitive proton pump ArchT) thalamus were trained in a novel operant task monitoring the self-paced acquisition of a covert, temporally-constrained lever press sequence (fixed ratio of 3 lever presses within 2 seconds [FR3/2s]) over multiple sessions. Surprisingly, rather than causing gross motor impairment or impaired acquisition of the FR3/2s action pattern, mice receiving acute VM-ArchT silencing or chronic motor thalamus silencing showed faster early learning of the sequence compared to controls or VL-ArchT silencing. Simultaneous adaptation of peak within-press acceleration with learning was deficient in mice receiving VL-ArchT silencing. Our results suggest that manipulating the motor thalamus in mice can alter the pattern of within-day and between-day performance gains during task acquisition, potentially via downstream network effects which promote learning occurring via competing circuits.
Is noise driving job creation?
Keywords: Information Frictions
Business Cycles
Labour Markets
News shocks
Search and Matching

This paper studies the effect of noise on the expected value of a firm-worker match in the labour market. In the data, such noise shocks would look like spontaneous increases in labour demand, which cannot rationally be justified by the current and future productivity of the employed worker. A significant amount of noise in the labour market would prevent the correct identification of the response of labour market variables with respect to news shocks. The paper applies the empirical approaches in Blanchard et. al. (2013) and Forni et. al. (2017) to the labour market to estimate the extent to which aggregate job creation is driven by noise rather than news. Based on the estimation of the DSGE model and the structural VAR model using US data, the paper finds that it is unlikely that noise shocks play a significant role in hiring and job creation, as on the aggregate level firms generally anticipate the future output produced by newly hired workers correctly.
Search for the decay of the Standard Model Higgs boson to muon pairs with the atlas detector at the LHC
Keywords: mumu
Higgs
ATLAS
LHC
muon pairs

The Standard Model predicts the Higgs boson to interact with all massive particles. At present, experimental evidence exists for the inter- actions with bosons and third generation fermions. This thesis focuses on the search for the decay of the Higgs boson to muon pairs, the most sensitive way of probing the interactions with second generation fermions. The search uses proton-proton collision data collected at the centre-of-mass energy √s = 13 TeV collected by the ATLAS experi- ment between 2015 and 2018 and corresponds to an integrated luminosity of 140 fb−1. The analysis selects events with oppositely charged muon pairs and splits them in categories using a gradient boosting classifier to maximise the sensitivity. A simultaneous maximum-likelihood fit is performed in all analysis categories to extract the signal strength and evaluate the compatibility of the data with the background-only hypothesis. The signal strength is measured to be 0.5 ± 0.7, where the uncertainty is dominated by the statistical uncertainty on the data. The observed (expected) significance is found to be 0.8 (1.5) σ. The sensitivity projection for the 3000 fb−1 dataset collected at 14 TeV estimates that the signal strength will be measured to 13% and still limited by the statistical uncertainty on the data.
The petrology and transformation history of continental crust in the Tso Morari complex, Ladakh, Himalaya
Keywords: coesite
continental subduction
geochronology
petrology
metamorphism
Tso Morari
ultrahigh pressure
eclogite

Ultrahigh-pressure (UHP) metamorphism has long been associated with deep subduction. UHP minerals, such as coesite and microdiamond, are often found in discrete mafic units, hosted in larger scale continental terranes, such as in the mafic eclogites of the Tso Morari complex, Ladakh, Himalaya. Terranes such as these have commonly been overprinted by amphibolite facies, Barrovian metamorphism, so their early history is difficult to decipher. Samples of mafic eclogite dykes hosted in low-strain metagranite were collected from the centre of the Tso Morari complex in Ladakh, Himalaya, where the granite has been observed to transition into granite gneiss towards the highstrain mafic–felsic lithological boundary. All three of these lithologies are shown to preserve high pressure metamorphism indicating that the entire unit must also have been subducted to high pressure conditions. Low-strain metagranites provide a window into the early history of the rocks, where feldspar, white mica and pseudomorphs after cordierite preserve evidence of hydrothermal alteration prior to high pressure metamorphism. Kyanite inclusions within garnet also indicate that the high-Al bulk composition of the granite gneiss must have been achieved prior to garnet growth, also indicating that hydrothermal alteration prior to garnet growth may have been significant. Palisade quartz microtextures after coesite in the matrix of a granite indicate that part of the dome transformed at ultrahigh-pressure conditions and preserves the first reported evidence of twinning in coesite recorded in quartz. Elemental zonation within garnets from mafic eclogite and granite gneiss protoliths show a similar zoning pattern in rocks of different bulk compositions, indicating that both rock types share a similar prograde high-pressure metamorphic evolution, where highest pressure conditions are preserved in the garnet rims. Previous modelling of mafic eclogites has shown that there are two possible isopleth intersections for garnet core growth at ca. 20-23 kbar, 520-550°C and 10-13 kbar, 575-625°C. However, alteration of inclusion assemblages has made it difficult to determine the actual conditions of core growth. Combined modelling of mafic and felsic protoliths, shows that the lower pressure intercept of 10-14 kbar, 410-460°C is common in both bulk compositions in water undersaturated conditions. A new and precise U-Pb age of zircon crystallisation at 46.9 ± 0.04 Ma is interpreted as the age of eclogite-facies metamorphism. U-Pb ages of xenotime, titanite and rutile are interpreted as ages representing crustal conditions, indicating that the Tso Morari complex was exhumed from ultrahigh-pressure to crustal conditions in <1 Myr before stalling in the lower crust.
First impression biases and the value of blind auditioning
Keywords: taste-based discrimination
blind audition
cognitive bias
first impression

Motivated by the performing arts, I investigate the repercussions of an evaluator's bias against a specific group of applicants, such as women, in a setting where the evaluator decides upfront between holding an informed or a blind audition. In the latter case, the evaluator learns neither the applicant's ability nor the gender. I show that a blind audition comes with a fundamental trade-off: it avoids misleading first impressions but prohibits the screening of applicants by ability. Above a threshold bias, the evaluator prefers a blind audition to provide high effort incentives exclusively for highly able applicants while low-ability applicants do not participate. For a low bias, requiring supplementary information about the applicant's type acts as an efficient screening device and, thereby, provides such targeted effort incentives. From a policy perspective, committing to no information can, therefore, be beneficial for the evaluator if he knows that he would otherwise not be impartial. Applicants' audition preferences differ by ability if the evaluator's bias against female applicants is low and differ by gender if the bias is large. Surprisingly, the preferences of a highly biased evaluator align with those of a highly able female. My model explains the empirical finding that blind auditions have increased the probability of women being hired via taste-based discrimination and challenges competing explanations grounded in statistical discrimination. Additionally, I show that uncertainty introduces the sizeable risk of market failure and may render informed auditions more profitable even if the evaluator is highly biased. From a policy perspective, ability-targeting interventions under uncertainty are, therefore, crucial to ensure equality of opportunity and to avoid zero-hour contracts.
Mohammed goes house-hunting: an experimental study of discrimination
Keywords: field experiment
discrimination

We conduct a field experiment in order to investigate discrimination against Muslims in the UK rental market. We find that Muslims are significantly less likely to receive a viewing, an extremely robust result that persists across genders, cities and landlord and property types. Further, there is evidence that even those landlords who do not formally discriminate are nonetheless less polite to Muslim applicants. Neither of the leading theories appear well suited to explain the discrimination observed in this study. On the one hand, discrimination completely disappears once we restrict attention to Muslim landlords, a fact that is difficult to reconcile with statistical models of discrimination. On the other hand, discrimination does not increase with interaction, in apparent contradiction of Becker’s ‘taste based’ model. We argue that a re-interpretation of the Becker model can explain our findings.
The Hellenistic terracottas from Demetrias
Keywords: Terracottas
Thessaly
cults
Demetrias
figurines

This thesis provides a first contextual study of the terracottas from Hellenistic Demetrias. Focusing on the finds from the sanctuaries of the city (the Sanctuary of Pasikrata, of the Mother-of-the-Gods, the “Thesmophorion” and the Favissa on Hill 35), from the Anaktoron, from a Hellenistic house, and from the cemeteries, it covers the whole spectrum of life in the city, public and private, cultic and funerary. The material is presented by context, as it informs our understanding of the terracottas’ use and meaning. The main questions that this thesis addresses are the following: a) how typical was Demetrias as a Hellenistic city, through its terracottas? b) what can we learn about their use in the city? c) were specific types used in specific contexts? d) what can we learn about the cults and rituals in the city through the terracottas? e) what can we discern about workshops in the city? f) what can we learn about trade through the terracottas? g) did the coroplastic repertoire follow the general trends of the Hellenistic period? In order to address these questions, the thesis also focuses on re-contextualising the coroplastic material from the city that was considered lost (Sanctuary of Pasikrata, Sanctuary of the Mother-of-the-Gods, South Cemetery).
A case-study chapter focuses on the kausia-boy figurines from the city, which is a very important corpus of material, showing how the contextual approach informs us about the terracottas’ meaning.
Special focus is given to the city’s cults and rituals viewed through the terracottas. It is evident that at least two kourotrophic cults existed in the city, as well as possibly three cult spaces connected to the cult of the Mother-of-the-Gods. The terracottas used in the cemeteries are generally of higher quality than those in sanctuaries, indicating a conscious choice for more expensive specimens placed in graves.
Through the study of the diffusion of terracottas and the local production, it is clear that Demetrias, in terms of coroplastic production, was a cosmopolitan Hellenistic harbour with connections with much of the large coroplastic workshops of the Mediterranean, not just mainland Greece.
Musical monuments of Hungarian history: Ferenc Erkel’s pre-revolution operas
Keywords: National Opera
Hunyadi László
Ferenc Erkel
Bátori Mária
Hungarian Nationalism
Hungarian Opera

A rapidly shifting social and political climate characterised the period between the 1825 Hungarian Diet and the revolution of 1848. An inherited fear of nemzethalál, ‘nation death’, drove attempts to fight the spectre of obscurity through language cultivation, social-political reform, nation-building projects, and representing history artistically. Exemplified by the national theatre project, opera became embroiled in discourse surrounding the educative potential of Hungarian-language artforms. Anxieties stemming partially from imperialism shaped a cyclic understanding of a sinful past, punished present and uncertain future.
Erkel’s Bátori Mária which inaugurated the Nemzeti Színház, ‘National Theatre’, encapsulates an ambiguous representation of Hungary’s history. Abortive attempts to disrupt a series of calamities only reinforced the understanding of Árpád history as a cycle of trespasses with repercussions reverberating into the nineteenth century. As the 1840s progressed, the revolutionaries anticipated a rupture with the past. During the revolutionary year, the theatre staged a programme comprising musical-theatrical pieces embodying overt revolutionary messages. Numbers from Erkel’s second opera Hunyadi László, a work littered with anti-Habsburg textual and musical references, featured prominently in this repertoire. This study challenges traditional understandings of how Hunyadi László relates to revolutionary rhetoric, illuminating how the tropes of defeat, victimhood, sacrifice and resurrection are in tension in this medieval narrative.
Erkel’s operas composed in the pre-revolution decade illuminate how historical interpretation related to fears surrounding legacy. Operatic models familiar to the Pest-Buda audiences became vessels for presenting versions of history beholden to contemporary understandings of the past in relation to the future. The contrast between Bátori Mária and Hunyadi László not only reflects the rapid momentum radical ideologies gathered approaching 1848, but how historical interpretation shifted through political and artistic polemics. This study illuminates how anxieties relating to identity interpolate with presenting history on the stage in Erkel’s pre-revolution operas.