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Machine Learning and Probabilistic Methods for Network Security Assessment
Full text linkPh. D. ThesisComputer networks comprised of many hosts are vulnerable to cyber attacks. One attack
can take the form of the exploitation of multiple vulnerabilities in the network along with
lateral movement between hosts. In order to analyse the security of a network, it is common
practice to run a vulnerability scan to report the presence of vulnerabilities in the network
and prioritise them with an importance score. The scoring mechanism used primarily in the
literature and in industry ignores how multiple vulnerabilities could be used in conjunction
with one another to achieve a goal that previously was not possible. Attack graphs are a
common solution to this problem, where a scan along with the topology of the network is
turned into a graph that models how hosts and vulnerabilities can be connected. For a large
network these attack graphs can be thousands of nodes in size, so in order to gain insight
from them in an automated way, they can be turned into Bayesian attack graphs (BAGs) to
model the security of the network probabilistically. The aim of this thesis is to work towards
the automation of gathering insight from vulnerability scans of a network, primarily through
the generation of BAGs.
The main contributions of this thesis are as follows:
1. Creation of a unified formalism for the structure of BAGs and how other graphs can be
translated into this formalism.
2. Classification of vulnerabilities using neural networks.
3. Design and evaluation of a novel technique for approximation in the computation of
access probabilities in BAGs (referred to in the literature as the static analysis of BAGs)
with no requirement for the base graph to be acyclic. 4. Implementation and comparison of three stochastic simulation techniques for inference
on BAGs with evidence (referred to in the literature as the dynamic analysis of BAGs),
enabling security measure evaluation and sensitivity analysis.
5. Demonstration of a sensitivity analysis for BAG priors and a novel method for quick
computation of sensitivities that is more readily analysed than the traditional technique.
6. Development and demonstration of a fully containerised pipeline to automatically
process vulnerability scans and generate the corresponding attack graph.
With a single formalism for attack graphs, alongside an open-source attack graph generation
pipeline, our work serves to enable future progress and collaboration in the field of
processing vulnerability scans using attack graphs by simplifying the process of generating
the graphs and having a mathematical basis for their evaluation. We design, implement, and
evaluate various techniques for calculations on BAGs. For the process of computation of
access probabilities we provide an algorithm that requires no processing or trimming of the
initial graph, and for inference on BAGs we recommend likelihood weighting as the best
performing sampling technique of the three we implement. We also show how inference
techniques can be applied to sensitivity analysis on BAGs, and provide a new method that
allows for more efficient and interpretable sensitivity analysis, enabling more productive
research into the area in future. This research was originally undertaken in collaboration with
XQ Cyber.EPSR
The influences of microstructural processes on concrete exposed to high temperatures
Full text linkPh. D. ThesisConcrete is the most widely used construction material across the world. It is a heterogeneous material consisting of cement paste, fine and coarse aggregates, and it is a multi-phase porous media with dry air, liquid water, vapour and other kinds of fluids filling the pores. The hygro-thermo-chemo-mechanical behaviours of concrete under elevated temperature have been investigated for decades at the macroscale level using experimental methods and numerical simulations, including material strength, material properties, variables (e.g. pore pressure) and even microstructural properties. However, the findings are generally empirically in nature, and the mechanisms underneath all these macroscopic behaviours are still not clear. The objective of this thesis is to contribute to the understanding of the influences of microstructural processes on the macro-level behaviour of concrete at elevated temperatures through a combined numerical and experimental study. The work uses finite element analysis with a fully coupled hygro-thermo-chemo-mechanical model in combination with water vapour sorption isotherms measurements using the ‘Dynamic Vapour Sorption’ method. Numerical parametric studies have been conducted for nine properties rooted in the micro-scale. These have confirmed that: permeability is key to the development of gas pressures; the description of the heat and mass boundary conditions can have a considerable effect on the predicted results; the amount of water introduced into the system as a result of dehydration of the cement paste, the influence of micro-scale gas flow behaviour and the evolution of capillary pressures are all found to have a considerable effect on the development of macro-scale behaviours. Furthermore, the transient behaviour of moisture under elevated temperatures are found to be significantly affected by the formulation of the sorption isotherm, especially where that relates to microstructural behaviour. To further investigate this and potential contradictions between theoretical or observed microstructural behaviour and macro-scale model formulations, a series of experiments were conducted to measure water vapour sorption isotherms using the ‘Dynamic Vapour Sorption (DVS)’ method. Investigations were carried out to determine the potential microstructural changes of hardened cement pastes (CEMI with water to cement ratio of 0.4) subjected to different relative humidity ranges. The results indicate that the microstructure of cement paste is not affected by elevated temperatures until 80°C, after removing confounding effects from irreversible changes upon first drying and harsh drying. The only microstructural changes consistent with the presented results, during desorption and adsorption, appear to be reversible. The temperature dependency of sorption isotherms was investigated as well. The results confirm and extend the interpretation that the adsorption isotherm is near-equilibrium, and the
desorption isotherm is not. These results are qualitatively confirmed by classical Density Functional Theory (DFT) theory. It is also confirmed that the adsorption isotherm is weakly temperature-dependent and desorption is much less temperature-dependent than from desiccator tests, where a marked increase of cavitation pressure is observed in the desorption branch with increased temperature. Additionally, the mechanism of interlayer water was investigated in this project by drying the samples to nominal RH=0%, instead of drying at 5% RH. The results suggested that the interlayer water play a significant role in the desorption range below 5% RH and the hysteresis in isotherms suggested that until the interlayer water was evaporated sufficiently, the interlayer spaces were never filled even when re-wetting to full saturation. All these results and their implications indicate the need for a revision of the models linking water content with humidity at high temperature, with possibly important implications for the understanding and prediction of temperature-induced damage in concrete.
All these results indicated that microstructural processes have significant influences on the behaviours of concrete at the macroscale level when exposed to high temperature. However, these microstructural processes are still vague, which are strongly affected by the pore size distribution that needs to be explored and clarified further
Graphene resonators for mass sensing applications
Full text linkPhD ThesisGraphene’s exceptional physical and mechanical properties make it an excellent
nanomaterial for MEMS/NEMS devices with wide reaching applications. This
thesis explores graphene as a nanomaterial, its use in mass sensing applications
and the suitability of existing theoretical models to describe its behaviour as a
rectangular resonator. Several local and nonlocal continuum models have been
proposed in literature for the vibration analysis of graphene resonators. But with
very little experimental data to validate these theoretical models, most of the
solutions employed to solve these models compare their results with results from
other theoretical models, leading to doubts about their validity and accuracy. In
addition to providing a guide for determining the suitable theoretical model for
different sized rectangular graphene resonators, this work establishes that a
small-scale parameter 0 of any value between 0 and 2 needs to be
incorporated in any local continuum modelled applied to micro-sized graphene
sheets to avoid overestimation of the frequency of the sheets. A fabrication route
for NEMS and MEMS devices with rectangular graphene resonators up to 32
by 7 is also developed with the provision for magnetomotive actuation via
Lorentz force with possible capacitive readout capabilities. This is important as
the use of graphene in MEMS/NEMS is being hurriedly transitioned from the
Research space to the marketplace
Design, synthesis and SAR Evaluation of novel benzoxa-[2,1,3]-diazole amino acid hydrazides against my cobacterium tuberculosis
Full text linkPhD ThesisThe major challenges of tuberculosis (TB) treatment are the emergence of
the drug-resistant strains and the higher risk of hepatotoxicity with prolonged
treatment. Therefore, efforts to effectively control TB require the discovery and
development of new therapeutic options possessing new mechanisms of action.
This project focused on the design and synthesis of novel agents targeting
Mycobacterium tuberculosis (Mtb). We have successfully synthesised 170
hydrazides with 40 of those intermediates being converted to benzoxa-[2,1,3]-
diazole substituted amino acid hydrazides 65. The resulting compounds were
screened against susceptible and resistant Mtb strains utilising a Resazurin
Microtiter Assay (REMA). A subsequent structure activity relationship (SAR)
strategy investigated the structural modification of the benzo-[2,1,3]-diazole
peptidomimetics architecture 65 as the main focus of the research presented in
this thesis. The findings from this SAR study indicate that an increased size
of the amino acid side chain, incorporation of heavy halogens at the meta
position of the aryl hydrazine, the L-configuration of the amino acid and the
benzoxa-[2,1,3]-diazole moiety each play a key role in improving the
antitubercular activitySaudi Ministry of Education and Taibah Universit
Jordanian Cinema and Gender Regimes: Representations and Audience Reception
Full text linkPh. D. Thesis.This thesis investigates the reception of gender regime representations in selected
contemporary Jordanian films among a Jordanian audience. The study adopts an audience
reception theoretical framework that is mainly influenced by Janet Staiger’s theorization of
audiences and their film reception, which is based on the audience, text, context nexus.
Moreover, the gender theoretical framework of this research is inspired by multiple intersecting
concepts, mainly Judith Butler’s conception of gender as a social construct and performative
act, R.W. Connell’s theorization of gender regimes and gender roles as social practices, and the
notions of femininity and masculinity which are crucial to underpin the understanding of
gendered social expectations important in gender regimes. The study is also influenced by
research exploring film, gender, society, and media in Jordan and the Arab world.
Utilizing a qualitative methodology focusing on the empirical study of film audience
reception, my fieldwork in Jordan in 2019 involved organising three screenings for each of the
three selected Jordanian films followed by focus groups with a group of Jordanian women and
men in higher education. Follow-up interviews and a Facebook poll on reception of Jordanian
films were also included in the qualitative analysis. A thematic analysis of the fieldwork data,
managed and coded on NVivo qualitative data analysis software, was conducted to arrive at the
findings of this study.
Major findings indicate that the audience participating in the current study tend to have
different perspectives regarding Jordanian films; while at times they seem to be reinforcing the
gender regime that endorses a patriarchal social structure at other instances it can be read that
some audience members attempt to subvert gender norms that create this regime. Through
tensions, transformations, critiques, and contrasting understandings in the focus group
discussions and follow-up interviews, a context of change appears to be evoked by the audience
responses to the conservative representations of Jordan society in the films, specifically with
regards to gender regimes in the Jordanian context
Subjective Bayesian Methods in the Design and Analysis of Clinical Trials
Full text linkPh. D. ThesisAssurance provides a Bayesian alternative to commonly used frequentist sample size calculation methods. As part of sample size calculations, an estimate of a treatment’s effect
size or a test’s accuracy is typically required. When using Bayesian methods, these unknown quantities can be represented with a prior distribution, rather than using a single
point estimate, allowing for more nuanced information about the unknown quantity to be
incorporated into the sample size calculation.
In this thesis, we first review common sample size calculation methods and elicitation
techniques. We consider the problem of aggregating expert prior beliefs to form a single
prior distribution, to be used in sample size calculations. Common methods of prior
distribution aggregation include mathematical methods, which use a mathematical rule
to combine priors, and behavioural methods, which provide experts with a framework to
assist them in creating an aggregate prior during a group discussion.
Though not a recent development, assurance is not commonly used in practice. We
provide a case study of a diagnostic study, investigating a novel diagnostic test for Motor
Neurone Disease, for which prior distributions are elicited and aggregated across experts,
and sample size calculations are conducted using both frequentist and assurance methods.
As a result of the requirements involved in using each method of aggregation, few
comparisons between behavioural and mathematical aggregation methods exist. In order
to make comparisons, we structured a series of elicitations as part of the case study. We
demonstrate how any method of aggregation outperforms individual experts, and that the
Sheffield Elicitation Framework and Classical Method perform best out of the aggregation
methods compared. We also demonstrate that all of the considered aggregation methods
perform better than a randomly selected individual expert.
In order to explore the behaviour of assurance, we provide a number of simulation
studies comparing assurance and power calculations. We investigate the sensitivity of
power and assurance to changes in input parameters, the effect of misrepresenting an effect
size, and the effect of using different prior distributions in the design and analysis stages
of assurance calculations. We consider these behaviours for both Normal and binomial
observations.
We use the resulting aggregated prior distributions for assurance and power calculations, to determine appropriate sample sizes within the case study and more generally. We
compare assurance calculations with different priors, analysis methods and target values
to further demonstrate differences between assurance and power, and their properties. We
demonstrate how the choice of model and prior distribution can have a large impact on
the final results of a sample size calculation
Engineered barriers for geological disposal of radioactive waste : b microbial interactions and their limits with thermo-hydro-mechanical-chemical processes at the waste canister/bentonite interface
Full text linkPhD ThesisNuclear waste is a global problem, with many countries in the process of creating deep
geological repositories to store this waste. In proposed repository designs MX80 bentonite
clay has been selected as the buffer and backfill. Extensive studies have been carried out on
the geomechanical properties of the clay; however, the role of microbes has not been fully
investigated. Specifically, in the UK, iron-reducing bacteria are a concern as carbon steel
waste canisters will contribute iron oxides and rust products to the immediate environment.
Iron-reducing bacteria can reduce Fe(III) to Fe(II) and some species are adapted to high
temperatures and low water availability, in keeping with conditions within the repository.
Iron-interacting bacteria were found to be indigenous to MX80 bentonite and microbiallyinfluenced iron-reduction was observed up to groundwater salinities of 0.45 M NaCl. The
limits of this community at different temperatures and pressure were investigated through a
series of batch experiments and subsequent enrichments, where necessary. Fe(II), Fe(Total)
and pH were measured throughout the respective experiments and substrates were collected
and analysed by XRD, SEM and EDX. The indigenous iron-reducing community and various
iron substrates were used to investigate indirect interactions through a series of agar plate
experiments. The potential bacterial production of H2 and silica-solubilising ability was also
investigated. In some experiments steel was included to represent the waste canister, results
from these experiments suggest that bacteria play a role in passive protection of steel against
corrosion. Significant differences in plasticity and mineralogy of MX80 were seen in all biotic
experiments. Additionally, silica release coupled to metal / microbe interactions was
observed. Transformation of clay minerals through iron reduction or release of silica to
groundwater could significantly impact the geomechanical properties of MX80, and thus
negatively affect the function of the barrier.EPSR
Peptide gene expression profiles in response to fasting and re-feeding in hoarding and non-hoarding titmice species
Full text linkPh. D. Thesis.The avian appetite regulatory system has been continuously studied over the last decades but it is less well
understood than the mammalian system. It has also been studied much more in domestic birds than in wild
passerine species. This PhD aims to investigate the role of different neuropeptides as well as gut peptides in
controlling and regulating the ingestive behaviours of songbirds. My aim was to pinpoint candidate peptide
genes that may differentiate a hoarding from a non-hoarding bird species and I used non-hoarding great tits
(Parus major) and blue tits (Cyanistes caeruleus) to make comparisons with a closely-related hoarding
species, the coal tit (Periparus ater) In this context, I used molecular techniques combined with video
analysis to quantify selected peptide gene mRNAs suspected from the literature to play a major role in
controlling both food intake and hoarding behaviour. By identifying candidate peptide genes that respond to
an individual’s nutritional state, I was able to make some distinctions between hoarding and non-hoarding
species. I also established for the first time in passerines the tissue distribution of gene expression in the gut
for cholecystokinin (CCK), proglucagon (GCG), insulin and peptide YY. Overall, this study suggests that
proglucagon (GCG) both in the gut and the hindbrain, as well as hypothalamic agouti-related protein
(AGRP) and pro-opiomelanocortin (POMC) gene expression could be used as neural signals reporting the
nutritional state of titmice. Moreover, hypothalamic AGRP and POMC, and hindbrain GCG and POMC
seem to be involved in the regulation of food hoarding in coal tits. These observations support observations
from the hamster literature that peptides that are known to control and regulate food intake are also involved
in food hoarding
Targeting the clonal expansion of mitochondrial DNA mutations in ageing and disease
Full text linkPh. D. Thesis.The clonal expansion of mitochondrial DNA (mtDNA) mutations is believed to mediate the
presentation and severity of clinical symptoms of a wide range of inherited and age-related diseases.
The mechanisms of clonal expansion are not fully understood, however the ability of cells to
maintain their normal function in lower levels of mtDNA mutational heteroplasmy highlights the
importance of understanding clonal expansion in causing the progression of disease and might offer
an avenue for potential therapeutic intervention.
The origin and molecular nature of clonal expansion is explored in a range of mitochondrial
myopathies in this thesis, using immunofluorescence techniques and single cell molecular studies.
The data indicate that in skeletal muscle, clonal expansion originates in a perinuclear niche and
spreads transversely throughout a muscle fibre, regardless of how the mtDNA mutation originally
arose, and the size of deletion identified.
The natural history of clonal expansion was explored in vivo using the heterozygous PolgA ‘mutator’
mouse model. A constant level of mtDNA mutations with increasing age was observed in these mice,
but a progressive increase in mitochondrial respiratory chain dysfunction. These findings indicate
that the mtDNA mutations were clonally expanding to higher heteroplasmy levels with ageing. The
process of clonal expansion was manipulated by treatment with nicotinamide riboside (NR), in an
attempt to increase mitochondrial biogenesis. NR supplementation resulted in increased
mitochondrial protein mass, although not a consistent increase in mtDNA copy number. NR was able
to attenuate age-associated respiratory chain complex IV dysfunction, however had no detectable
effect on complex I.
NR treatment had a complex effect on the mice, additionally showing an anti-inflammatory response
on transcriptional analysis, and protection from age-associated weight gain. These effects are similar
to those of a calorie restricted diet. NR supplementation it is unlikely to reverse the clonal expansion
of mtDNA mutations and prevent mitochondrial disease but has shown evidence of slowing the
process in colon. Mitochondrial disease is complex and heterogeneous, affecting a wide range of
tissues in a variety of ways. Whilst NR supplementation has shown benefit, it is likely that a complex
intervention would be required to better target the clonal expansion of mtDNA mutations.Wellcome Trus
Spatial and Long-term Variability in Demersal Fish Species of the Western North Sea
Full text linkPh. D. ThesisThis thesis explores historical and contemporary patterns of spatial and temporal change in
demersal fish species of the western North Sea. Comparing trawl data from over a century ago
with those from contemporary trawl surveys are challenged by biases associated with
differences in gear types and methods of operation. To compare contemporary data with rare
1892-1913 data from Northumberland Sea Fisheries Committee surveys on the
Northumberland coast (UK), an attempt was made to replicate the original trawl gear and
methods used by drawing on the literature, historical photographs and expertise of the trawl
industry. The replica gear, comprising a 6.7 m beam connecting two Brixham-style wroughtiron trawl heads with a triangular-shaped trawl net and rounded ground-rope, was trialled in
August 2018 and March 2019, and catches were compared with a modern otter trawl. In the
first trial period, the otter and replica beam trawl had similar efficiencies in catching flatfish,
whereas catches made by the replica gear in March were either very low or zero. As a result,
the otter trawl was employed in place of the replica gear in all subsequent resurveys and
catches were standardised for comparison with historical surveys. Catches revealed
substantial declines in the abundance of the overall inshore fish assemblage and among
individual species between 1899-1913 and 2018-2019. Elasmobranchs and historically
dominant species such as grey gurnard Eutrigla gurnardus were either completely absent or
rare in the 2018-2019 surveys. Abundance-size spectra also exhibited significant differences
between periods, declining more steeply in contemporary trawls. Analysis of demersal fish
stomach contents data revealed large shifts in diet composition over the period spanning
1896-2015. Bivalves dominated plaice Pleuronectes platessa, dab Limanda limanda and
haddock Melanogrammus aeglefinus diets in the early and mid-20th century but declined
ii
substantially in subsequent decades. Conversely, polychaetes increased in importance by
number and mass overtime and were the main prey resource for plaice in the 1970s and
2000s. These diet shifts point to likely changes in the benthic prey base of the North Sea, linked
to increased beam trawling in the 1960s-1970s, eutrophication, and climatic processes.
Finally, contemporary stomach contents and bulk stable isotope data were used as
complementary techniques to assess temporal and spatial variation in the diet within and
between two sympatric flatfishes, plaice and dab, in four coastal bays off the Northumberland
coast. Stomach data indicated similar diets and significant dietary overlap at short temporal
scales, yet dorsal muscle and liver tissue δ
13C, δ15N and δ
34S data revealed substantial interand intra-specific variation in resource use among sites and lower levels of niche overlap at
longer time scales. Sandeels Ammodytes tobianus were highly abundant in flatfish stomachs,
whereas Bayesian isotope mixing models indicated that squid were the important
contributors to both predators. Dorsal and liver isotope data also indicated that bivalves and
ophiuroids were major contributors to plaice and dab diet, respectively, across sites. These
findings provide evidence of profound change in demersal fish species and their trophic
ecology, further underpinning the value of using historical and contemporary data to elucidate
broad-scale temporal and spatial patterns of changeCefas Seedcorn, The Faculty of Science, Agriculture and Engineering (SAgE) at Newcastle Universit