VictorJuiz/thesis huggingface dataset:
Theoretical studies of tunnel-coupled double quantum dots
Keywords: strongly-correlated electrons
Kondo physics
many-body physics

We study the low-temperature physics arising in models of a strongly correlated, tunnel-coupled double quantum dot (DQD), particularly the two-impurity Anderson model (2AIM) and the two-impurity Kondo model (2IKM), employing a combination of physical arguments and the Numerical Renormalisation Group.
These models exhibit a rich range of Kondo physics. In the regime with essentially one electron on each dot, there is a competition between the Kondo effect and the interdot exchange interaction. This competition gives rise to a quantum phase transition (QPT) between local singlet and Kondo singlet phases in the 2IKM, which becomes a continuous crossover in the 2AIM as a result of the interlead charge transfer present. The 2IKM is known to exhibit two-channel Kondo (2CK) physics at the QPT, and we investigate whether this is also the case for the 2AIM at the crossover. We find that while in principle 2CK physics can be observed in the 2AIM, extremely low temperatures are required, such that it is unlikely that 2CK physics will be observed in an experimental DQD system in the near future.
We have studied the effect of a magnetic field on the 2AIM and the 2IKM, finding that both the zero-field QPT in the 2IKM and the zero-field crossover in the 2AIM, persist to finite field. This presents the possibility of observing 2CK physics in an experimental DQD at finite field, but we find that the temperatures required to do so are extremely low. We show that longer even-numbered chains of spins also exhibit QPTs at finite field, and argue that a 2N-spin chain should undergo N QPTs as field is increased (starting deep in the local singlet phase at zero field).
We have also carried out a joint theoretical-experimental study of a carbon nanotube based DQD, in collaboration with Dr. Mark Buitelaar et al. The agreement between experimental and theoretical results is good, and the experiments are able to access the crossover present in the 2AIM at finite field. Furthermore, the experiments show the wide range of physics exhibited by DQD systems, and illustrate the utility of such systems in probing correlated electron physics.
Structure-function relationship studies in the disulfide-bond reductase DsbD and a c-type apocytochrome
Keywords: apocytochrome c-b562
DsbD
disulfide bond reduction
c-type cytochrome formation

The efficient covalent attachment of heme to c-type apocytochromes in the periplasm of Gram-negative bacteria requires the provision of reductant. Heme attachment is facilitated by a system of eight proteins, the Cytochrome c maturation (Ccm) system. The disulfide bond oxidoreductase DsbD, a member of the Disulfide bond formation system (Dsb), transfers reductant to the Ccm system via interaction with one of its proteins, CcmG. This study is focused on two key proteins of these systems, the periplasmic disulfide bond oxidoreductase DsbD and a c-type apocytochrome, apocytochrome c-b562. A new method was established to assess the function of DsbD by linking it to the levels of c-type cytochrome maturation. This method was used to evaluate the activity of a range of DsbD variants. In addition, analysis of the biophysical properties of apocytochrome c-b562 was carried out using NMR spectroscopy. For this analysis, backbone assignments were completed for both oxidation states of the protein. Finally, studies aimed to determine the biophysical properties of the residues of the CXXCH heme binding motif were performed.
Investigation into the mechanisms of cytoophidia assembly in drosophila melanogaster
Keywords: CTP synthase
Drosophila

Subcellular sequestration of proteins within membrane bound compartments is widely acknowledged to be an important mode of enzymatic regulation. Recently a novel paradigm for metabolic enzyme compartmentalisation has become apparent with the identification of several proteins which are able to form filamentous structures in vivo. Multiple studies independently identified the essential de novo pyrimidine biosynthesis enzyme CTP synthetase as a major constituent of a novel filamentous structure which has been termed “the cytoophidium”. Cytoophidia have been observed to form in multiple organisms including bacteria (C. crescentus), yeast (S. cerevisiae) and fruit fly (D. melanogaster) as well as in human cultured cells.
In this thesis I describe the development and results of a high throughput genomescale screen to identify factors involved in cytoophidia biogenesis. Observations of tissue specific CTPS distribution lead to the identification of the well-conserved growth regulator dm/dMyc as an essential factor for CTPS regulation in vivo. These results provide new insights into the coordination of cellular growth and metabolic regulation during normal development and indicate the potential of CTPS/cytoophidia as a future therapeutic target.
How regulation and competition influence discrimination in broadband traffic management: a comparative study of net neutrality in the United States and the United Kingdom
Keywords: traffic management
Internet
broadband
regulation
net neutrality

Telecommunications policy debates concerning the contentious issue of net neutrality have revolved around a number of broadband network operator behaviors, including discriminatory traffic management – differential treatment of network traffic associated with different Internet applications for the purpose of managing performance. Some stakeholders have advocated for regulatory intervention to prevent network operators from discriminating to the detriment of independent application innovation. Others would prefer to rely on competition between network operators to discipline operator behavior.
Fixed-line broadband markets in the United Kingdom and the United States have differed substantially with respect to discrimination, competition, and regulation. The UK has experienced intense competition and pervasive discriminatory traffic management without triggering regulatory activity. The US has seen much less discrimination, limited competition, and regulatory threat followed by regulatory intervention. This thesis uses elite interviews, participant observation, and documentary analysis in a comparative study of these two cases between the mid-2000s and 2011 to determine why network operators take up discriminatory traffic management (or not) and how competition and the regulatory environment affect traffic management outcomes.
This thesis demonstrates that network operators take up discriminatory traffic management primarily to control cost, performance, or both. Competition promotes rather than deters discrimination because it drives broadband prices down, encouraging operators to manage high-volume applications whose traffic incurs high costs. Regulatory threat can be sufficient to counteract these desires, but in its absence and without concerns vocalized by interest groups, discriminatory approaches endure. Telecommunications regulators intervene to safeguard nondiscrimination when they conceive of their remits as encompassing social and industrial policymaking, are ambivalent about litigation risk, and are driven by their leaders’ reputational agendas, as in the case of the Federal Communications Commission. With a narrower perception of its remit and more concern for its organizational reputation, Ofcom exemplifies the characteristics that inhibit traffic management regulation.
Aspects of dark matter phenomenology
Keywords: supersymmetry
dark matter

Identifying the relic particles that constitute the cold dark matter in our Universe is an outstanding problem in astro-particle physics. Direct detection experiments are among the most promising methods of detecting particle dark matter through non-gravitational interactions. In this thesis, the usual assumptions made when calculating the event rate at direct detection experiments are examined. Varying astrophysical parameters and the dark matter velocity distribution leads to significant changes in acceptance regions and exclusion curves for scenarios in which the tail of the velocity distribution is sampled; this includes 'light dark matter' (mass less than 10 GeV) and 'inelastic dark matter'. The DAMA and CoGeNT collaborations both report an annual modulation in their event rate that they attribute to dark matter. Two analyses of these experiments are performed. In the first, it is shown that these experiments can be compatible with each other and with the constraints from other direct detection experiments. This requires some isospin violation in the couplings of dark matter to protons and neutrons and a small inelastic splitting to boost the modulation fraction. The second analysis provides a comparison of the modulation signals free from all astrophysical parameters, under the assumption that dark matter scatters elastically. Again it is found that some isospin violation and a boosted modulation fraction is required in order that DAMA and CoGeNT are consistent with all experiments. A boosted modulation fraction may arise from a velocity distribution different from the Maxwell-Boltzmann distribution, which is usually assumed. Finally, a supersymmetric theory in which the dark matter candidate is a mixture of left- and right-handed sneutrino is considered. This theory has many novel signatures at colliders, indirect detection and direct detection experiments.
Cassius Dio, human nature and the late Roman Republic
Keywords: Roman History
Cassius Dio
Roman Republic

This thesis builds on recent scholarship on Dio’s φύσις model to argue that Dio’s view of the fall of the Republic can be explained in terms of his interest in the relationship between human nature and political constitution. Chapter One examines Dio’s thinking on Classical debates surrounding the issue of φύσις and is dedicated to a detailed discussion of the terms that are important to Dio’s understanding of Republican political life. The second chapter examines the relationship between φύσις and Roman theories of moral decline in the late Republic. Chapter Three examines the influence of Thucydides on Dio. Chapter Four examines Dio’s reliance on Classical theories of democracy and monarchy. These four chapters, grouped into two sections, show how he explains the downfall of the Republic in the face of human ambition. Section Three will be the first of two case studies, exploring the life of Cicero, one of the main protagonists in Dio’s history of the late Republic. In Chapter Five, I examine Dio’s account of Cicero’s career up to the civil war between Pompey and Caesar. Chapter Six explores Cicero’s role in politics in the immediate aftermath of Caesar’s death, first examining the amnesty speech and then the debate between Cicero and Calenus. Chapter Seven examines the dialogue between Cicero and Philiscus, found in Book 38. In Section Four is my other case study, Caesar. Chapter Eight discusses Caesar as a Republican politician. In Chapter Nine, I examine Dio’s version of the mutiny at Vesontio and Caesar’s speech. Chapter Ten examines Dio’s portrayal of Caesar after he becomes dictator and the speech he delivers to the senate. The Epilogue ties together the main conclusions of the thesis and examines how the ideas explored by Dio in his explanation of the fall of the Republic are resolved in his portrait of the reign of Augustus.
Reformed epistemology and naturalistic explanations of religious belief: an inquiry into the epistemological implications of the cognitive science of religion
Keywords: Etiology of Belief
Knowledge
Reformed Epistemology
Cognitive Science of Religion
Rationality

Reformed Epistemology is an influential view in contemporary philosophy of religion, according to which theistic beliefs that are the product of our native, non-inferential cognitive faculties often constitute knowledge if God exists. My aim in this thesis is to ascertain whether Reformed Epistemology is viable in light of contemporary scientific explanations of the mechanisms of religious belief- formation, especially the Cognitive Science of Religion (CSR). I argue for a qualified “yes.” To begin with, I attempt to carefully reconstruct and scrutinise some currently popular “debunking arguments” from CSR’s findings, which aim to show that non-inferential religious beliefs are not knowledge, even if true, given the causal origins that CSR ascribes to them. I try to show that in various ways these arguments fail. Subsequently, I attempt to find a better such argument. The strongest debunking argument, I contend, is one that focuses upon the diverse and mutually inconsistent outputs of the religious belief-producing mechanisms described by CSR. However, I go on to argue that even supposing that this argument succeeds in showing that religious beliefs that are partly the product of contingent cultural influences are not knowledge even if true, there remains a body of what I term “core propositions”—propositions concerning the existence of some kind of personal, supernatural creator and moral lawgiver, in which humans are naturally disposed to believe regardless of their particular cultural setting— that can be known if God exists. Finally, I try to show that merely having this core supernaturalistic knowledge would provide someone with the cognitive contact with God that is sufficient for having a personal relationship with God (if God exists), even if only de re relationship. I argue, moreover, that God would have positively good reasons for creating a world in which human beliefs about life’s most important matters, including religious matters, are significantly dependent upon testimony and hence subject to the ebbs and flows of cultural tides.
Sulfonamide supported catalysts for the ring opening polymerisation of cyclic esters
Keywords: organometalics
caprolactone
titanium
biodegradeable
group 4
polymerisation
plastic
catalysis
sulfonamide
zirconium
aluminium
ring opening polymerisation
hafnium
lactide
cyclic esters
inorganic chemistry

This Thesis describes the synthesis and characterisation of sulfonamide supported titanium, zirconium and aluminium complexes and their use as ring opening polymerisation catalysts for ε-caprolactone and rac-lactide.
Chapter 1 introduces polyester use, development and characterisation in general. Metal catalysed ring opening polymerisation of cyclic esters is considered in a literature review of the field. Titanium, zirconium and aluminium complexes supported by polydentate sulfonamide ligands are also discussed.
Chapter 2 describes the synthesis and characterisation of new sulfonamide supported titanium amide, isopropoxide and zirconium isopropoxide complexes. Their application as catalysts for the ring opening polymerisation of ε-caprolactone and rac-lactide is discussed and compared with known zirconium isopropoxide complexes supported by bis(phenolate) amine ligands.
Chapter 3 describes the synthesis and characterisation of Cs symmetric titanium amide and alkoxide complexes supported by dianionic, tri- and tetradentate sulfonamide ligands. Zirconium alkyl and amide complexes supported by C3- symmetric trianionic ‘tren’ type ligands bearing three different sulfonamide groups are also presented. The application of these complexes for the ring opening polymerisation of ε-caprolactone and rac-lactide is described and compared with the complexes presented in Chapter 2.
Chapter 4 provides an overview of the synthesis and characterisation of aluminium alkoxide and alkyl complexes supported by dianionic, tri- and tetradentate sulfonamide ligands. Solution state behaviour and solid state structures are presented and discussed. An assessment of these complexes for the ring opening polymerisation of rac-lactide is presented.
Chapter 5 presents full experimental procedures and characterisation data for the new complexes reported. CD Appendix contains .cif files for all new crystallographically characterised complexes described, and additional polymerisation graphs.
Cell stress response and hypoxia in breast cancer
Keywords: autophagy
hypoxia
ATF4
breast cancer

During severe hypoxia (<0.01% oxygen) the protein folding machinery becomes dysfunctional, resulting in the accumulation of unfolded proteins with consequent endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR) and autophagy, a process involved in the physiological turnover of cytoplasmic components. The link between the UPR and autophagy is not clearly defined. The aim of this thesis is to investigate the role of the induction of UPR under severe hypoxia in tumour survival and resistance to therapy. The results of this research suggest that the activating transcription factor 4 (ATF4), a component of the PKR-like ER kinase (PERK) pathway, fundamental in the UPR, is required for the ER-stress induced upregulation of autophagy. Mechanisms other than hypoxia for UPR induction were investigated, using the proteasome inhibitor bortezomib (BZ). BZ treatment increased ATF4 protein levels in MCF7 cells, even transfected with short-interference RNA (siRNA) against the classical UPR activator PERK, suggesting that the proteasomal stabilization is likely the main mechanism for ATF4 protein accumulation. The induction of autophagy by BZ is dependent upon the upregulation of the microtubule-associated protein 1 light chain 3B (LC3B), an autophagy marker, by ATF4 and acts as a survival mechanism. Hypoxia, UPR and autophagy markers (such as Pimonidazole, carbonic anhydrases IX (CAIX), C/EBP homologous protein (CHOP) and LC3B) were evaluated by immunohistochemical approach in spheroids, xenografts models and breast cancer samples. CHOP immunohistochemical staining was performed in breast cancer sections from a series of patients. CHOP was expressed in cells surrounding necrotic areas. No correlation were found with clinical outcome and further studies are needed.
The role of NLRs in induction and resolution of intestinal inflammation
Keywords: intestinal infections
immunology
inflammatory bowel diseases
colitis
Helicobacter
Citrobacter

Innate immune activation is thought to play a central role in IBD pathogenesis because genetic polymorphisms in NOD2 and NLRP3, cytosolic innate immune receptors belonging to the NLR family, have been associated with IBD susceptibility. However, the mechanisms through which NLR mutations predispose to IBD remain unclear. The aim of this project was to dissect the functional roles of different NLRs in intestinal inflammation. Using the well-established DSS-induced colitis model as well as experimental models of IBD based on infection with Helicobacter hepaticus, we found that Nod2 expression was significantly increased at the peak of intestinal inflammation, and remained elevated throughout the resolution process. This observation suggests a possible role for Nod2 in the resolution of inflammation. Conversely, upon infection with the acute intestinal pathogen Citrobacter rodentium, Nlrp3-/- mice suffered from increased bacterial colonization as early as 3 days post infection, resulting in exacerbated intestinal inflammation and severe weight loss. Analysis of irradiation bone marrow chimeras showed that the protection required Nlrp3 activation in the non-haematopoietic compartment. Furthermore, this protective mechanism was independent of the inflammasome-associated cytokines IL-1β or IL-18. Therefore, this study implicates Nlrp3 activation in intestinal tissue cells as having a crucial role in controlling pathogenic bacterial colonization, providing a potential mechanism by which NLRP3 polymorphisms could lead to increased susceptibility to IBD.
Mycoplasma pneumoniae and Bordetella pertussis in patients with persistent cough in primary care
Keywords: Cough
Mycoplasma pneumoniae
Whooping cough
Respiratory Tract Infection

Background Persistent cough following an acute respiratory tract infection is a challenging and frequently encountered problem in primary care. Mycoplasma pneumoniae (M. pneumoniae) and Bordetella pertussis (pertussis) particularly predispose patients to persistent cough. Whilst the incidence of M. pneumoniae is highest in children, pertussis may also occur in adults.
Method Four studies were conducted for this thesis. First, a systematic review to assess the diagnostic accuracy of symptoms and signs in the clinical recognition of M. pneumoniae. Second, a retrospective analysis of a cohort of children with persistent cough to assess the prognostic value of diagnosing M. pneumoniae. Third, a prospective cohort study to estimate the prevalence of M. pneumoniae and pertussis in children with persistent cough following recent changes in vaccination policy. Fourth, a double-blind randomised placebo-controlled trial to determine the effectiveness of montelukast in the treatment of persistent cough and pertussis-induced cough in adults.
Results M. pneumoniae and pertussis can each be found in one-sixth of children who present in primary care with persistent cough. Although coverage with the preschool pertussis booster vaccine is high, its efficacy wanes rapidly, with the likelihood of pertussis increasing by 30% per year after vaccination. Montelukast is not an effective treatment for persistent cough, but may be an effective treatment for pertussis-induced cough.
Median duration of cough in children with M. pneumoniae is only one-third of that in children with pertussis (39 days versus 118 days). However, the diagnostic accuracy of symptoms and signs in the clinical recognition of M. pneumoniae is limited. Since M. pneumoniae occurs in cyclical epidemics, clinicians should consider current prevalence of M. pneumoniae when making a clinical diagnosis.
Conclusions Diagnosing M. pneumoniae and pertussis can help clinicians give patients an explanation for their cough and inform them about its likely prognosis. At the moment, clinicians should adopt a conservative approach to managing postinfectious persistent cough. A further trial is needed to assess the efficacy of montelukast for the treatment of pertussis-induced cough.
The politics of sectarianism in the Gulf
Keywords: Kuwait
Saudi Arabia
Lebanon War (2006)
Iraq War
Arab Spring
Bahrain
sectarianism
Shiites

This thesis explores Shi’a-Sunni relations in Gulf politics during a period of regional upheaval, starting with the 2003 invasion of Iraq through the Arab revolts of early 2011. It seeks to understand the conditions under which sectarian distinctions become a prominent feature of the Gulf political landscape, focusing on the three Gulf countries that have been affected most by sectarian tensions: Bahrain, Saudi Arabia, and Kuwait.
The study analyzes the contagion effect of the civil war in Iraq, the 2006 war in Lebanon, and the Arab Spring on local sectarian dynamics in the three states. Specifically, it explores the role of domestic institutions—parliaments and other quasi-democratic structures, the media, and clerical establishments—in tempering or exacerbating sectarianism. It finds that the maturity and strength of participatory institutions in each state played a determinant role in the level of sectarianism resulting from dramatic shifts in the regional environment since the 2003 invasion of Iraq.
I conclude, therefore, that the real roots of the so-called “rise of the Shi’a” phenomena lie in the domestic political context of each state, rather than in the regional policies of Iran or the contagion effect of events in Iraq or Lebanon. Although the Gulf Shi’a took a degree of inspiration from the actions of their co-religionists in Iraq, Iran and Lebanon, they ultimately strove for greater rights in a non-sectarian, nationalist framework. The rise of sectarianism in the Gulf has been largely the product of excessive alarm by entrenched Sunni elites or the result of calculated attempts by regimes to discredit Shi’a political actors by portraying them as proxies for Iran, Iraq, or the Lebanese Hizballah. What is qualitatively different about the post-2003 period is not the level of mobilization by the Shi’a, but rather the intensity of threat perception by Gulf regimes and Sunni Islamists.