VictorJuiz/thesis huggingface dataset:
Enhancing the investigation of malware-related crimes using semantic technologies
Keywords: IOC
Threat intelligence
Intelligence
Investigation
Semantic
Malware
Cybercrime

The expansion of technology connectivity and the pervasiveness of data in our society pose both challenges and opportunities for the government and the private sector. Big companies like Google and Facebook are in the forefront of successfully tackling the challenge of extracting meaning from this data deluge: building rich profiles of people and networks enable them to monetise and make profits by selling such profiles for targeted marketing purposes. For most organisations, though, the challenge of generating actionable intelligence from the available data sources is still daunting.
In the government sector, one of the sectors that could benefit significantly from data-driven intelligence is that of Law Enforcement. However, the deficit of specialized personnel and tools which extract meaningful information from data (as Chapter~\ ef{sec:intro} shows) is directly linked to weak investigation capabilities, ultimately hampering catching serious organised organisations.
As the literature review shows, the available forensic tools are just starting to change the focus from improving processing performance to facilitating investigation and exploration. One example is the increasing adoption of domain taxonomies to describe data.
This thesis addresses the capability gaps by demonstrating that analysts working in law enforcement would benefit from an data exploration tool leveraging specific semantic features. In addition to semantic search and integration of data (features already provided by many semantic data exploration tools), allowing the investigators to materialise classes, object properties and datatype properties could help them shaping their knowledge during the course of an investigation. Moreover, the ability of expressing knowledge in terms of semantic queries and rules could enhance information exchange between analysts.
A prototype was developed to assess the feasibility of the idea and validate it with actual investigators. Their feedback after testing the prototype indicated that such computer-provided features could indeed support the reasoning of the human analyst, making cybercrime investigation more efficient.
Improving the specification of the target difference in the sample size calculation of a randomised trial of treatments for osteoarthritis
Keywords: target difference
simulation
systematic review
discrete choice experiment
minimum clinical important difference
MCID

The sample size of a clinical trial is the number of participants the trial aims to recruit. Sample size is a critical aspect of clinical trial design and has ethical and financial implications. The sample size depends on the target difference, the difference in outcome that the trial is powered to detect. This thesis aims to improve methods for specifying the target difference in randomised trials of osteoarthritis.
I conducted a systematic review of sample size calculations in hip and knee osteoarthritis trials published in 2016. It found that most sample size calculations were poorly reported and could not be reproduced. The target difference in the sample size calculation was commonly justified by a published minimum clinically important difference (MCID).
Several versions of the WOMAC (Western Ontario and McMaster Universities Osteoarthritis Index) were commonly used in hip and knee osteoarthritis trials. It was often unclear which version was used, hindering interpretation of trial results.
I conducted a discrete choice experiment examining patient preferences when choosing between osteoarthritis medications. Duration of treatment effect was shown to be important to participants, viewed with similar importance to the amount of symptom relief provided and risks of the treatment.
I analysed a cohort of people with osteoarthritis and showed that MCID estimates for the WOMAC varied across different follow-up time points. However, there was no visual trend in the change in MCID estimates over time. Longitudinal methods were feasible to calculate MCID estimates, but did not improve precision.
A simulation study that I conducted found that the pattern of the treatment effect (its duration and consistency) affected the optimal statistical method of analysis for a randomised trial using the WOMAC as the primary outcome.
Future research is needed to examine whether the findings are generalisable to different datasets, outcome measures and health conditions.
Structural studies of the type three secretion system export apparatus
Keywords: T3SS
flagella
protein secretion
cryo-EM

One of the most widespread bacterial secretion systems is the type three secretion system (T3SS), which is critical for the virulence of many pathogens and responsible for assembly of the bacterial flagellum. The virulence-associated T3SS is a molecular syringe that uses a highly conserved export apparatus (EA) to secrete effector proteins through a needle directly into the host cell cytoplasm. The flagellar T3SS secretes flagellar subunits through the EA which then self-assemble into a filament. Despite recent progress in the structural biology of T3SS, the highly conserved membrane domains of the five inner membrane proteins of the EA have evaded structural characterisation.
Here, multiple cryo-EM structures of complexes of the three core EA proteins from both flagella (FliPQR) and injectisomes (SctRST) are presented, revealing a pseudohexameric, helical complex. Remarkably, the complex is made up of a series of long, highly kinked helical hairpins rather than the predicted canonical transmembrane helices. Many of the hydrophobic residues predicted to lie in transmembrane helices are instead buried at the interfaces between subunits, leaving only a small membrane domain. In the assembled T3SS this complex is encased in the basal body, above the plane of the inner membrane, and connects to the helical filament, whose helical parameters it matches. The membrane domain of the fourth export apparatus protein, FlhB/SctU, is shown to form a complex with FliPQR, and the complex structure suggests a mechanism of how interactions between FlhB and FliPQR could lead to opening of the complex. Finally, stable rings of full-length FlhA/SctV, the last EA protein, were prepared and cryo-EM confirmed the structure of the nonameric cytoplasmic domain. While little high-resolution information of the membrane domain was obtained, these studies provide a framework for future studies.
Together these results reveal the structure of part of the secretion pathway and suggest that the core of the export apparatus templates the assembly of the helical filament.
Visions of citizenship and state: debating Jews and Judaism in eighteenth-century Prussia
Keywords: Kant
Dohm
Enlightenment
Jews
Prussia
Jewish emancipation

This dissertation explores debates about Jews and Judaism in eighteenth-century Prussia. Methodologically, it adopts the contextual approach associated with the Cambridge School of intellectual history, exploring the complex connection between attitudes towards Jews, and the intellectual influences of the eighteenth-century German Enlightenment. It builds upon recent scholarship which stresses the importance of seeing eighteenth- and nineteenth-century German Jewry in its own terms and not through the lens of the Holocaust. The primary aim of this dissertation is to show that the eighteenth century witnessed a remarkable transformation in perceptions of Jews and Judaism — a transformation which helped lay the groundwork for the Jewish entry into modernity. By treating the entire chronological span of the eighteenth century, this study not only sheds new light on familiar terrain, such as Christian Wilhelm von Dohm’s famous plea for emancipation; it also addresses themes which have largely been neglected. Chapter 1 investigates the origins of the eighteenth-century Jewish question, exploring early modern German responses to the experience of Jewish social mobility. Chapter 2 examines and conceptualises mid-eighteenth-century utilitarian arguments for toleration vis-à-vis Jews. Chapter 3 offers a reassessment of Dohm’s humanitarian arguments for emancipation. Chapter 4 treats the debate about Jewish military service. Chapter 5 studies Immanuel Kant’s influence on late eighteenth-century controversies about Jewish religious reform.
Synthesizing the quality of study methodology and evidence to support guidelines for optimal treatment of falciparum malaria in pregnancy
Keywords: Plasmodium falciparum
pregnancy
artemisinin
quinine
malaria
treatment
infectious diseases
epidemiology
tropical medicine

Pregnant women are particularly susceptible to malaria, which is the leading cause of mortality and morbidity of the mother and fetus in the tropics. The current World Health Organization (WHO) recommended study design for assessing antimalarial efficacy excludes pregnant women, which has resulted in fewer studies on treatment efficacy and greater variability of study designs in pregnant women. Based on limited evidence, WHO has recommended quinine (with clindamycin, if available) for first-trimester and artemisinin-based combination therapy (ACT) for second- and third-trimester women since 2015. The data on the safety of artemisinin-derivatives in the first trimester have been collected, mostly from inadvertent treatments, over two decades, and form reassuring evidence of safety, strikingly different to animal-based reproductive health studies. This thesis aims to summarize the evidence on the efficacy of antimalarials for uncomplicated falciparum malaria in pregnancy and to improve future research in tropical infectious diseases in pregnancy.
Secondary data from prospective studies that assessed antimalarial efficacy by polymerase chain reaction were sought. Individual patient data of 4968 pregnant women (92% of all published work) from 19 studies in ten countries were pooled in a standardized format and analysed. These confirmed that quinine is less effective and less tolerable than ACTs. Quinine is also less suitable for elimination because of a higher risk of gametocyte development. Among ACTs, artemether-lumefantrine (AL) showed a slightly lower efficacy. In the second and third trimesters, the risks of congenital abnormality, miscarriage, stillbirth, preterm birth and small-for-gestational-age were similar among the four major ACTs (namely, AL, artesunate-amodiaquine, artesunate-mefloquine and dihydroartemisinin-piperaquine).
Study designs need to be tailored for pregnant women. It is probably necessary to follow up pregnant women for longer to assess efficacy accurately, but proof can only be obtained by including them alongside non-pregnant reproductive-age women. To assess pregnancy outcomes, precise and reliable estimates of gestational age and longitudinal recording of repetitive malaria episodes through to delivery are essential.
Quinine monotherapy should be replaced with ACTs for treating uncomplicated Plasmodium falciparum malaria in pregnant women. For AL, the most commonly used compound, dose optimization studies are needed. Investigations to find safe and effective drugs for pregnant women should be continued as every effort to prevent and reduce recurrence contributes to health of the mother and fetus.
Testing gravity with black holes
Keywords: Ringdown
Black Holes
Gravity

In this thesis, I study the ways in which modified theories of gravity might be tested for using black holes. In particular, I focus on ways in which the gravitational waves emitted during the ‘ringdown’ of a perturbed black hole may be affected.
I will develop and demonstrate the use of a framework for analysing the evolution of perturbations in arbitrary modified gravity theories in both cosmological and black hole backgrounds. I will use this to show that the characteristic Quasi-normal mode (QNM) spectrum of frequencies for the gravitational waves emitted from a perturbed black hole may be altered even in the case that the background black hole is identical to a general relativistic black hole. This is purely due to the presence, and coupling to, additional gravitational degrees of freedom.
I will also explore the landscape of hairy black hole solutions in the wake of the multi- messenger observation of GW/GRB170817, and show that it is increasingly difficult to endow a black hole with scalar hair in modified gravity given the constraint that gravita- tional waves must propagate at the speed of light.
In addition, black hole perturbations in General Relativity are analysed, with analytic expressions for QNM frequencies calculated for scalar, vector, and gravitational perturba- tions to a slowly rotating Kerr-(Anti-)de Sitter black hole.
Finally, I will examine the specific case of black hole perturbations in Horndeski the- ory, demonstrating the qualitative difference in gravitational wave emission from a per- turbed black hole in General Relativity and in Horndeski gravity. I will also forecast the detectability of such a modified gravitational wave signal, and estimate what constraints one might be able to place on fundamental parameters of Horndeski gravity through gravi- tational wave observations.
Exploring the use of routine data for recruitment and follow-up in large randomised trials
Keywords: Clinical trial methodology
Population Health
Electronic health records

Timely recruitment and comprehensive follow-up of patients are vital to the success of randomised controlled trials (RCTs) but both present issues. This thesis aims to investigate how routine data can be used for recruitment to clinical trials, whether there are any biases introduced by using routine data, and to determine whether routine data can be used as a follow-up method in clinical trials.
The literature on the use of routine data for recruitment and follow-up are explored in two systematic literature searches. Both reviews highlight that routine data can be used for recruitment and follow-up in RCTs. One finding is that these methodological aspects of RCTs, particularly when not pertaining to the results, are often not reported.
Using data from two large cardiovascular disease trials, the Heart Protection Study (HPS) and the Randomized EValuation of the Effects of Anacetrapib through Lipid-modification trial (REVEAL), that used electronic health records to recruit patients, the demographics of those entering the trial and declining to participate are investigated. A significant sex difference is observed, with females being less likely than males to progress through the recruitment pathway of both clinical trials. Attendance at follow-up visits and adherence to treatment were also significantly worse in females than in males. This disparity may leave studies underpowered for sex specific effects. These factors potentially limit the ability to establish the safety and efficacy of interventions in females and have the potential to have serious adverse public health consequences.
The use of routine data for follow-up is investigated by comparing the outcomes from HPS (non-fatal myocardial infarction, non-fatal stroke, revascularisation, and major vascular event) and the outcomes reported in Hospital Episode Statistics (HES) during the same time period. All of the trial outcomes were well recorded in the HES dataset, with no significant differences between males and females in their reporting of events. The use of routine data for follow-up in RCTs could reduce the frequency of study visits, which may aid recruitment.
Routine health records contain a wealth of information about patients that can be used to optimise both recruitment to trials and the follow-up of patients. The use of electronic health records (EHR) has the potential to provide more cost-effective and efficient methods for research.
Rape adjudication and prosecution in India: a reflection of female autonomy or masculine cultures?
Keywords: India
Criminal law
Rape law

The December 16, 2012 Delhi gang-rape case sparked a sorely-needed debate in India on the issues of consent in rape law, leading to the Justice Verma Committee report and the 2013 criminal amendment to rape law. This thesis undertakes a comprehensive analysis of Indian judicial decisions adjudicating rape, to ascertain (whether and) how underlying preconceptions and prejudices (continue to) percolate through sexual assault cases in a variety of settings (despite the 2013 amendment) and ultimately shape their outcome.
This thesis notes that the 2013 Amendments brought about some key reforms in the rape law, such as: an expansion in the definition of rape (beyond penile-vaginal intercourse); a new positive definition of ‘consent’ in section 375; and the addition of circumstances falling within category of ‘aggravated rape’ in section 376(2). This thesis argues that despite the sweeping changes introduced by the Parliament’s decisions, the statutory law still falls short of goals set by the Verma Committee report. There also appears to be legal gaps that exist in statutory law pertaining to previous sexual experience of the complainant and application of mens rea in rape law. Using direct evidence from the sample of cases, this thesis then presents the argument that the judicial discourse pertaining to rape reveals that statutory legal changes were not sufficiently powerful to dislodge deep-seated stereotypes amongst either the male or female judges. The complete silence on concepts such as bodily integrity and sexual autonomy, the lack of engagement with the new definition of consent, the absence of reference to the reversal of the burden of proof under section 114A in aggravated rape cases, the emphasis on factors like absence of resistance, and the dominance of stereotypes in the post-2013 law judgments indicate that there is a huge disconnect between the Parliament’s intention and the Judiciary’s implementation.
Z-nucleic acids in virus-host interactions
Keywords: ZIKV
ZBP1
DAI
VZV
Nucleic acid sensing
Necroptosis
Pattern recognition receptors
MCMV

One of the biggest threats faced by cells is infection. When a virus infects a cell, its nucleic acids can be recognised by cellular sensors, which activate potent antiviral innate immune responses, such as interferons and cell death. These initial responses are vital in preventing the spread of infection to surrounding cells. Critically, nucleic acid sensors must have mechanisms of recognising foreign, aberrant or mislocalised nucleic acids and distinguishing them from unperturbed cellular nucleic acids. Alternative conformations of nucleic acids may represent a molecular sign of virus infection that can be sensed. Double-stranded DNA and RNA can adopt different helical conformations, including the unusual Zconformation. The existence of proteins containing Z-binding domains (ZBDs) suggests Z-nucleic acids have important but so far poorly characterised biological functions. One such protein is Z-DNA binding protein-1 (ZBP1/DAI/DLM1). Using mouse cytomegalovirus as a model, we demonstrated that ZBP1 mediates virusinduced necroptotic cell death in a manner dependent on its two ZBDs. This suggests that the trigger for ZBP1 may be a Z-conformation nucleic acid. Knock-in mice, in which the ZBDs of ZBP1 are mutated, were more susceptible to virus infection. In addition to these mouse studies, we have demonstrated that ZBP1 also activates ZBD-dependent necroptosis in human cells and established and validated an assay for screening of small molecule or viral protein antagonists of ZBP1- mediated necroptosis in a human cell line.
The values of freedom and the moral foundations of freedom-centred justice
Keywords: Freedom
Value Theory
Conceptual Analysis
Liberalism

What role should freedom play in a theory of justice? In this thesis I defend the view that freedom has non-specific value (i.e. that there is value in having freedom as such and not only in having certain specific valuable freedoms), and I examine the moral foundations of freedomcentred justice (i.e. of a theory of justice that is concerned with distributing freedom as such). The main contribution of this thesis consists in offering an in-depth examination of two distinct classes of reasons that justify attributing non-specific value to freedom: axiological reasons that appeal to the good, and deontic reasons that appeal to the right.
Good-based accounts include the views that interpret the value of freedom in person-affecting terms – especially, the Benefit View, which attributes personal value to freedom – as well as views that claim that it is impersonally good that persons have freedom. I focus then on examining the different senses in which people benefit from having freedom (Benefit View), since freedom is objectively valuable for the achievement of wellbeing, agency, autonomy, and human excellence. I also put forward a critique of the perfectionist foundations of freedomcentred justice, and I examine whether the moral foundations of freedom-centred justice can appeal exclusively to the Benefit View, or whether freedom-centred justice must (also) appeal to deontic reasons.
I put forward a critique of moralised accounts of the value of freedom, and I defend a nonmoralised interpretation of the Status View – i.e. the view that interprets the value of freedom in deontic terms and that appeals to the value of refraining from interfering with people’s freedom in recognition of people’s moral status as agents. In particular, I argue that interference with people’s freedom is pro tanto disvaluable, including when it is directed at preventing people from performing severely wrong actions, if in ideal theory we take people’s lack of disposition to act immorally as parametric (i.e. if we assume full compliance). Finally, I argue that distinguishing between the Benefit View and the Status View has implications for the conceptual analysis of freedom, shedding light on debates concerning the relations between freedom and ability: freedom is an interpretative concept and different ways of valuing freedom inform, and can actually determine, what freedom is (i.e. the definition of freedom).