VictorJuiz/thesis huggingface dataset:
Machine learning applications and observation of Higgs boson decays into a pair of bottom quarks with the ATLAS detector

The discovery in 2012 of the Higgs boson at the Large Hadron Collider (LHC) represents a milestone for the Standard Model (SM) of particle physics. Most of the SM Higgs production and decay rates have been measured at the LHC with increased precision.
This thesis presents the analysis that led to the observation of the SM Higgs boson decay into pairs of bottom quarks. The analysis exploits the production of a Higgs boson associated with a vector boson whose signatures enable efficient triggering and powerful background reduction. The main strategy to maximise the signal sensitivity is based on a multivariate approach. The analysis is performed on a dataset corresponding to a luminosity of 79.8 fb-1; collected by the ATLAS experiment during Run-2 at a centre-of-mass energy of 13 TeV. An excess of events over the expected background is found with an observed (expected) significance of 4.9 (4.3) standard deviation. A combination with results from other H → bb searches provides an observed (expected) significance of 5.4 (5.5). The corresponding ratio between the signal yield and the SM expectation is 1.01 ± 0.12 (stat.) + 0.16 - 0.15 (syst.).
The measurement of cross sections in exclusive regions of phase space of the VH production times the H → bb branching ratio is reported as well. These measurements are used to search for possible deviations from the SM with an effective field theory approach, based on anomalous couplings of the Higgs boson.
This thesis also describes a novel technique for the fast simulation of the forward calorimeter response, based on similarity search methods. The new simulation approach outperforms the default technique used by ATLAS.

Keywords: bottom quarks
Fast Simulation
Standard Model
ATLAS
Similarity Search
Higgs boson
LHC
Effective Field Theory
Machine Learning
Advisor: Bortoletto, D
The regulation of international commercial arbitrators

International commercial arbitration has established itself as the main dispute resolution mechanism for international commercial disputes. This increased visibility has drawn attention to arbitrators’ public role, leading to a well-established general perception that arbitrators are bound to special obligations, such as the duty to be independent and impartial or the obligation to assure that arbitral proceedings are not abused to achieve nefarious goals. Despite this general acknowledgement, little attention has been paid to the mechanisms that ensure that arbitrators adhere to these obligations. In particular, there has been limited analysis of the underlying mechanisms that incentivise the production and enforcement of professional norms in this field.
This thesis argues that the particulars of the arbitration market largely explains why the evolution of the regulation of international arbitrators has not matched those of other professions. At the same time, it will argue that those same particularities create incentives for several actors, most notably the arbitral community itself, to step in and occupy this regulatory vacuum. In particular, it explores the notion that the market strategies employed by arbitrators, arbitral institutions and other members of the arbitral community have the production of professional norms as a by-product. It further explores how the arbitral market tends to create an environment where compliance with professional norms is rewarded, leading, at the same time, the arbitral community to work as a network that promotes adherence to professional norms through mostly informal sanctions.

Keywords: dispute resolution
international commercial arbitrators
regulation
arbitration
arbitration market
Advisor: Bettina, L
Ab initio theory of polarons

The polaron is a quasiparticle formed by collectively dressing an electron with a phonon cloud. It emerges in a crystal lattice when an extra electron is trapped at the lattice distortion induced by itself. Due to its unique role and technological implications, this subject has consistently received attention for many years. To date, first-principle studies of polarons in materials are still based on direct calculations with large simulation cells. In this thesis we develop a theoretical and computational framework that allows for the modelling of lattice polarons in different materials of interest, but using unit-cell calculations of electronic, vibrational properties and electron-phonon couplings. We explain the architecture of the implementation in detail, and propose a self-interaction corrected DFT scheme for the validation of our methodology and implementation. We present extensive tests and benchmark for the code. We apply this new approach to investigate polaron properties in LiF and Li2O2 as prototypical bulk materials that host large and small polarons. We demonstrate that our method can describe both large and small polarons on the same footing, and capture both Fr ̈ohlich-type polar electron-phonon coupling and non-Fr ̈ohlich couplings to acoustic and optical phonons. Furthermore, we report cal- culations of formation energy, excitation energy, and wavefunction of polarons. To establish a quantitative understanding of which KS states and phonon modes con- tribute to the formation of polarons, we analysis the polaron spectral decomposition in a spirit similar to the Eliashberg spectral function. The last part of the thesis is devoted to explore the dimensionality effect on the polaron properties in h-BN. In this case, we compare the polaron energies for a localised hole between the h-BN in bulk and in monolayer, and show that the two-dimensional hole polaron trapped in the h-BN monolayer exhibits a layer formation energy in comparison to the bulk one. This work will open the door to predictive calculations of polarons in more complicated systems, such as van der Waals heterostructure and interfacial systems, and constitutes as a first step toward complete ab initio many-body calculations of polarons in real materials.

Keywords: Electronic structure
Electron-phonon coupling
First-principles calculations
Polarons
Advisor: Giustino, F
Labour market effects of social programmes: evidence from Ethiopia’s productive safety net

This thesis assesses how a large safety-net programme in rural Ethiopia affects local labour markets. Combining repeated cross-sections of the National Labour Force Survey with information on the geographical targeting of the programme, a differencein- differences approach is used to estimate whether employment outcomes have changed differently over time in targeted districts relative to those that did not receive the programme.
The results suggest that a combination of public works employment and unconditional transfers to food-insecure households does not affect the local labour supply in this rural economy. I explore whether differential trends and population composition could explain these results, which are more likely due to programme design. Albeit scantily observed, the wages of private sector labourers also seem unaffected, in contrast to findings from similar studies focusing on labour markets from other developing countries outside Africa.

Keywords: Provision and Effects of Welfare Programs
Productive Safety Net Programme
Labour Markets
Ethiopia
Advisor: Fenske, J
Synthetic post- translational protein modification as a switch for activity

The ‘post-translational mutagenesis’ chemistry, utilising a bio-orthogonal radical reaction with Dha on proteins, has opened up a vast range of novel possibilities in generating post- translational modification (PTM) mimics. Two case studies are described in this thesis, around the theme of PTMs as switches for protein-protein interactions. The first case study recapitulates the natural PTMs H3K36me2 and -me3. Functional evidence from in vivo observations suggests that the chromodomain reader protein MRG15 should preferentially bind H3K36me3 over its dimethyl counterpart. However, in vitro studies using peptides or isolated H3 as a substrate have failed to recapitulate this observation. Here, using synthetic, ‘post-translational mutagenesis’, fully-intact model nucleosomes containing both H3K36me2 and H3K36me3 were generated. Binding of MRG15 to these intact nucleosomes revealed a marked preference for H3K36me3 containing nucleosomes over those containing H3K36me2, recapitulating physiologically relevant observations. A model was suggested in which the H3K36 side chain is normally sequestered in intact nucleosomes in a hydrogen bonding interaction with the phosphate of the DNA backbone, and the interaction entirely abrogated only when the third methyl group is added to form H3K36me3, providing a ‘methyl- switch’ mechanism for context-dependent reader selectivity. The second case study was centred around installing a natural PTM in an unnatural location to produce a novel sensor. Dha chemistry was once again employed to install O- and N-linked GlcNAc mimics in the complement determining region (CDR) of a nanobody cAbLys3, with the aim of reversibly blocking its antigen binding capacity. Enzymatic extension of cAbLys3- O-GlcNAc to produce an Fc decasaccharide was also investigated as an alternative means of tuning a nanobody’s effects for potential therapeutic applications. Overall, the aim of this thesis was to demonstrate the use of the post-translational mutagenesis method to install mimics of labile PTMs; both to study their function in a natural setting, and to create novel biosensors.

Keywords: Histone
H3K36me3
H3K36me2
Dehydroalanine
cAbLys3
Chromodomain
MRG15
Post-translational modification
Advisor: Davis, BG
Esashi, F
Evolutionary drivers of the rise and fall of a dominant hybrid MRSA, ST239

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.

Keywords: Bioinformatics
Antimicrobial resistance
MRSA
Fitness
Epidemiology
Chromosomal replacement
SCCmec
Evolution
Advisor: MacLean, C
Wilson, D
Structure-aware machine learning over multi-relational databases

We consider the problem of computing machine learning models over multi-relational databases. The mainstream approach involves a costly repeated loop that data scientists have to deal with on a daily basis: select features from data residing in relational databases using feature extraction queries involving joins, projections, and aggregations; export the training dataset defined by such queries; convert this dataset into the format of an external learning tool; and train the desired model using this tool.
In this thesis, we advocate for an alternative approach that avoids this loops and instead tightly integrates the query and learning tasks into one unified solution. The primary observation is that the data-intensive computation for a variety of learning tasks can be expressed as group-by aggregates over the join of the database relations.
This observation allows us to employ a combination of known and novel state-of-the-art query evaluation techniques, which exploit structure in the query and data to optimize the computation of the aggregates. As a result, we show that, for a class of machine learning models, our integrated, structure-aware approach for the end-to-end learning of models over databases can be asymptotically faster than the mainstream solution that first constructs the feature extraction query. This class of models includes supervised machine learning problems for regression and classification, as well as unsupervised learning problems.
This theoretical development informed the design and implementation of LMFAO (Layered Multiple Functional Aggregate Optimization), an in-memory optimization and execution engine for batches of aggregates over the input database. LMFAO consists of several layers of logical and code optimizations that systematically exploit factorization, sharing of computation, parallelism, and code specialization.
We conducted two types of performance benchmarks. First, we benchmark LMFAO against PostgreSQL, MonetDB, and a commercial database management system for the computation of aggregate batches. Then, we compare the performance of LMFAO against several machine learning packages commonly used in data science for the end-to-end learning pipeline of a variety of models over databases. In all benchmarks, LMFAO is able to outperform the competitors with a speedup of up to three orders of magnitude. In many cases, LMFAO can compute the end-to-end learning pipeline even faster than it takes the machine learning competitors to construct the input training dataset.

Advisor: Olteanu, D
Precision fits for the LHC and beyond

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.

Keywords: QCD
LHC physics
SMEFT
Advisor: Salam, G
Rojo, J
Constitutional change and the rule of recognition

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.

Keywords: HLA Hart
constitutional theory
unconstitutional change
rule of recognition
jurisprudence
constitutional change
philosophy of law
Advisor: Lamond, G
Investigating speech motor control using vocal tract imaging, fMRI, and brain stimulation

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.

Keywords: Speech
Vocal Tract
Brain Stimulation
Stuttering
Movement Inhibition
fMRI
Advisor: Watkins, K
Connectivity-specified targeting and manipulation of the motor thalamus

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.

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
Advisor: Sharott, A
Magill, P
Brown, P