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Ideology and Radicalisation: Applying Hannah Arendt’s Criteria of Ideology to Conceptualise Elements of the Mindset of the Islamic Radical
Get PDFPh. D. ThesisA violent and complex phenomenon referred to by many observers as Islamic
radicalisation has affected certain individuals linked to Muslim societies. Research
studying Islamic radicalisation has been trying, through different frameworks, to
construct a standard profile of a typical Islamic radical, but without success. This thesis
argues that the violent Islamic radical is an abstract, political person comprising of the
Arendtian ideological mindset and, hence, may be identified as an Islamic ideologue.
The study develops and applies a novel theoretical framework to conceptualise the
mindset of the central character of Islamic radicalisation. In Part One, I glean five
essential elements of an ideological mindset from Hannah Arendt as my theoretical
framework, namely: the superhuman source as origin of thought; the claim to global
domination; violence and the call for action; the objective enemy; and rejection of
factual reality. I follow Hans Joerg Sigwart who developed the method
“characterology” from Arendt to conceptualise a character from the discursive
practices of six online magazines (4 English and 2 Urdu) published by Al-Qaida (AQ),
Islamic State (IS) and Tahreek-e-Taliban (TT). In Part Two, I apply the Arendtian
framework to this unique set of empirical material. I conduct a thematic analysis
technique to detect, quote and analyse exemplary texts from the magazines that
resonate with the Arendtian theoretical articulations of the five elements of an
ideological mindset. The research affirms that all five Arendtian elements are part of
the character’s mindset that has been discursively constructed by these three Islamist
organisations. The study also summarises the ideas/themes detected through the
Arendtian framework and used by the organisations to create a conceptual tool entitled
‘The Map of Ideas Linked to Islamic Radicals’ (MILIR). MILIR can act as the standard
profile of the abstract person known as Islamic radical. It can also inform deradicalisation policy
Designing interactive technology for cross-cultural appreciation of intangible cultural heritage: Chinese traditional painting and puppetry
Get PDFPh. D. ThesisDigital heritage is becoming a significant component of cultural heritage, and cultural
organisations are increasingly using interactive technologies to showcase and safeguard
heritage assets. However, few studies focus on using interactive technology to enhance the
appreciation of Intangible Cultural Heritage (ICH) amongst cross-cultural audiences.
This dissertation explores the design of interactive technologies to support the cultural
appreciation, learning, and experience of Chinese ICH. In addition, the research seeks to
explore the value of Human-Computer Interaction (HCI) design strategies in supporting the
appreciation of ICH. The research uses HCI design strategies to specifically explore how
interactive technology might be effectively utilised in two case-study contexts, supporting
traditional Chinese painting and traditional Chinese puppetry.
To this end, in stage one of the research, a qualitative study involving interviews, workshops,
and fieldwork for design was undertaken with potential cross-cultural audiences and both
Chinese and international painting and puppetry practitioners. Based on the results of these
studies, several suggestions were developed for safeguarding ICH across cultural boundaries.
In the next stage of the research, two interactive applications were designed and deployed that
supported cross-cultural audiences’ appreciation of traditional of ICH. One application
explored Chinese painting, the other Chinese puppetry. Using both qualitative and
quantitative methods, studies were conducted that examined the efficacy of both applications
and offered suggestions for a holistic approach to cross-cultural appreciation through the use
of interactive applications. The analysis focuses on the use of element-based archiving to
increase aesthetic appreciation, gestural/tangible interfaces for cultural engagement, and the
use of interactive access to inspire self-expression and collaborative appreciation.
Finally, this research relies on practical methods to deconstruct cultural elements from the
HCI perspective and enhance the cross-cultural appreciation of Chinese ICH. It thus provides
a framework for assisting non-Chinese people to better understand the cultural significance of
Chinese ICH. The findings have design implications for both HCI researchers and digital
heritage researchers
Signal processing and machine learning techniques for automatic image-based facial expression recognition
Get PDFPhD ThesisIn this thesis novel signal processing and machine learning techniques are
proposed and evaluated for automatic image-based facial expression recognition,
which are aimed to progress towards real world operation.
A thorough evaluation of the performance of certain image-based expression
recognition techniques is performed using a posed database and for the rst time
three progressively more challenging spontaneous databases. These methods
exploit the principles of sparse representation theory with identity-independent
expression recognition using di erence images.
The second contribution exploits a low complexity method to extract geometric
features from facial expression images. The misalignment problem of the training
images is solved and the performance of both geometric and appearance features
is assessed on the same three spontaneous databases. A deep network framework
that contains auto-encoders is used to form an improved classi er.
The nal work focuses upon enhancing the expression recognition performance by
the selection and fusion of di erent types of features comprising geometric
features and two sorts of appearance features. This provides a rich feature vector
by which the best representation of the spontaneous facial features is obtained.
Subsequently, the computational complexity is reduced by maintaining important
location information by concentrating on the crucial roles of the facial regions as
the basic processing instead of the entire face, where the local binary patterns and
local phase quantization features are extracted automatically by means of
detecting two important regions of the face. Next, an automatic method for
splitting the training e ort of the initial network into several networks and
multi-classi ers namely a surface network and bottom network are used to solve
the problem and to enhance the performance.
All methods are evaluated in a MATLAB framework and confusion matrices and
average facial expression recognition accuracy are used as the performance
metrics.Ministry of Higher Education
and Scienti c Research in Iraq (MOHESR
Impact of mitochondrial alterations on prostate cancer progression
Get PDFPh. D. Thesis.Cancer metabolism is characterised by a ‘Warburg shift’ to aerobic glycolysis with decreased
mitochondrial oxidative phosphorylation (OXPHOS), feasibly mediated by alterations in
mitochondrial DNA (mtDNA). However, despite recent advances in our understanding of
nuclear genomic alterations in prostate cancer, there remains a paucity of data evaluating the
impact of mitochondrial alterations in prostate cancer progression.
Therefore, using publicly available genomic datasets, the mitochondrial molecular landscape
of aggressive prostate cancer was characterized. This revealed a spectrum of mtDNA
mutations under clonal selection pressures, reduced mtDNA copy number, and a
transcriptomic profile composed of reduced mitochondrial and increased nuclear OXPHOS
gene expression.
In order to assess the downstream impact of these alterations and aid clinical translation, I
developed an automated assay to evaluate proteomic OXPHOS defects in archived prostate
cancer tissue microarrays at the single cell level. Upon unpicking widespread multi-faceted
heterogeneity in OXPHOS protein expression, patients with low complex I abundance and
increased mitochondrial mass appeared to be at increased risk of all-cause mortality at 20-
year follow-up.
The prognostic value of both mitochondrial molecular alterations and proteomic OXPHOS
defects was enriched in patients with PTEN-loss and TMPRSS2:ERG fusion. Given that
mitochondrial alterations and prostate cancer risk features are also associated with advancing
age, transgenic models were generated to elucidate the impact of age-related systemic
mitochondrial dysfunction on PTEN-deficient prostate cancer progression. Despite early
mortality due to accelerated age-related phenotypes, attenuated tumour progression was
observed, suggesting a tumour suppressive effect of systemic mitochondrial dysfunction.
In conclusion, mitochondrial alterations exert diverse systemic and local effects on prostate
cancer progression. Leveraging mitochondrial tissue biomarkers and mitochondrial-targeted
systemic therapies may provide a novel approach for identifying aggressive prostate cancer
and suppressing progression to lethal disease
Identification and characterisation of novel mechanisms affecting prostate cancer cell growth
Get PDFPh. D. Thesis.Prostate cancer development and progression to lethal metastatic castration-resistant
prostate cancer (CRPCa) is driven by the androgen receptor. Androgen deprivation
therapy (ADT) is the first line of treatment used to control cancer growth. Although ADT
is usually effective, the recurrence of castration-resistant prostate cancer is common and
ultimately lethal. Progression to CRPCa is thought to involve persistence of AR signalling
and reprogramming of the AR transcriptional landscape, allowing tumour cells to
continue to grow despite low levels of circulating androgens.
The overall aim of this study was to identify and characterise mechanisms affecting
prostate cancer cell growth. To do this I used RNA-sequencing in the androgenresponsive
LNCaP cell line, coupled with previously published RNA-sequencing of
advanced prostate cancer treated with ADT and clinical prostate cancer expression data
to identify androgen-regulated genes, alternative isoforms and pathways. A set of 660
genes showed reciprocal changes in expression in response to acute androgen
stimulation in culture, and androgen deprivation in patients with prostate cancer. A
multiple dataset meta-analysis strategy coupled with gene ontology analysis has
identified glycosylation as a novel androgen regulated pathway. Although patterns of
glycosylation are known to change in prostate cancer the mechanisms underlying these
changes are not well understood. The data in this study suggest androgens may increase
the aggressiveness and metastatic potential of PCa cells through mediating changes in
glycosylation patterns.
Further investigation into the sialyltransferase enzyme ST6Gal1 has shown that high
levels alter the expression of key epithelial to mesenchymal transition (EMT) makers and
increase the invasion potential of prostate cancer cells, whilst reduction significantly
decreased cell proliferation, cell to matrix adhesion, migration and invasion capability.
Together with the androgen regulated transcriptional changes, the RNA sequencing data
also identified a number of androgen regulated alternative mRNA isoforms, including
promoter switches for the RLN1 and RLN2 genes. In summary correlation of gene expression changes in prostate cancer cells in response
to acute androgen stimulation with those repressed in patients by ADT has revealed a
new panel of clinically relevant androgen regulated genes. Analysis of this panel has
demonstrated important androgen control over glycosylation modifications has important
implications for prostate cancer biology, and also suggests further targets for future
analysis.Prostate Cancer UK (PCUK
Synthetic DNA and RNA origami scaffolds, towards in vitro and in vivo applications
Get PDFPh. D. Thesis.Nucleic acid self-assembly is a branch of nanotechnology that consists in the use of DNA
and RNA, not only as genetic material, but also as structural medium. In the last 30 years
this technique developed from the simplest structures into more refined constructions that
could require thousands of interacting sequences.
DNA origami were presented by Rothemund as the evolution of DNA assemblies. Origami
are nanostructures formed by a long single strand, the scaffold, held together by many
shorter oligonucleotides, the staples. Later research showed how to functionalize the
origami staples increasing the applicability.
Bacteriophage genomes were used as convenient source of single stranded DNA scaffold.
Today the potential biotechnological applications require to be bio-orthogonal and easily
transferable from academic research to industrial ones. To solve these problems we can
rely on the powerful tools of synthetic biology.
I focused on the synthesis, analysis and application of synthetic scaffolds based on the
combinatorial De Bruijn (DB) sequence. DB scaffolds are designed to be bio-orthogonal,
uniquely addressable and thermodynamically optimized.
I demonstrated their folding efficiency in DNA origami and RNA/DNA hybrid origami.
DB scaffolds were analyzed in vivo in E: coli to asses their bio-orthogonality.
Finally I designed a research tool to improve our knowledge on origami folding dynamics.
The system includes functionalized origami encapsulated in giant unilamellar vesicles.
The system allows the analysis of the origami using high throughput technologies, and
can simulate a simple cell-like environment facilitating the intermediate steps towards the
in vivo origami folding.
With my interdisciplinary approach I contributed to the advancement of nucleic acid
origami technology, taking advantage of tools and techniques from synthetic biology, origin
of life, bioinformatics along with more classical scientific disciplines.Faculty of Science, Agriculture and Engineering, Newcastle University
Vitamin D supplementation and vitamin D biomarkers in relation to sunlight exposure and musculoskeletal health in older adults using two different study designs
Get PDFPhD ThesisVitamin D plays a role in musculoskeletal (MSK) health through genomic and non-genomic pathways. In the UK, SACN used a 25(OH)D concentration of 25 nmol/L as the basis for setting the (Recommended Nutrient Intake) RNI of 10 μg/day based on MSK outcomes (rickets, osteomalacia, falls, muscle strength and function). In setting vitamin D recommendations for North Americans, the IOM used a 25(OH)D concentration of 50 nmol/L as the basis for setting the (Recommended Dietary Allowances) RDA of 15 μg/day, based onthe relationship between 25(OH)D and bone outcomes (rickets, osteomalacia, bone mineral density and calcium absorption). The differing thresholds used to define “vitamin D adequacy” may be due to (1) different MSK outcomes and approaches used to underpin the DRVs (2) geographical differences in vitamin D status and response to vitamin D supplementation and exposure to sunlight. Since vitamin D biomarkers and vitamin D supply required for optimum MSK function are not agreed universally, this thesis is set out to determine the effect of vitamin D supply on muscle function and to determine the association between commonly-used vitamin D biomarkers [25(OH)D and PTH] and muscle function [Grip Strength (GS), Timed-up and Go (TUG)] and bone health [quantitative ultrasound] in older adults using two different studies from the North East of England (55° North). In addition, because sunlight exposure is known to influence vitamin D biomarkers and response to vitamin D supplementation, this thesis also attempted to quantify the impact of sun exposure on vitamin D status in both studies. The first study was a Randomized Control Trial (RCT) of monthly vitamin D supplementation (12000 IU, 24000 IU and 48000 IU vitamin D3) for 1 year on MSK health [Vitamin Din Older People study-VDOP (n=379; age >70 years)]. The second study was a follow-up study of older adults at moderate risk of colon cancer [the Biomarkers of Risk of Colon Cancer Follow-Up study -BFU (n=47, age >49 years)]. Baseline findings from the VDOP study showed that plasma 25(OH)D concentration, 25 nmol/L throughout the year to maintain healthy musculoskeletal functioning.Commonwealth Scholarship Commissio
Microbial source tracking for the UK water industry
Get PDFEngD ThesisThis thesis evaluates the suitability of two emerging microbial source tracking (MST) techniques, host-associated E. coli biomarkers and community-based MST.
Previous human-associated E.coli markers (H8, H12, H14, H24) were evaluated for the first time in the UK; the sensitivity of H8 (10%) was lower than previously reported (50% (Gomi et al., 2014)) and if analysed through regulatory culture-based approaches alone, would have resulted in a high false negative rate (90%). In light of this, the Hu100 marker, with the highest abundance (2.64 x 106 gene copies/100 mL) across 14 wastewater treatment plants, was developed through interrogation of 263 E.coli genomes. The abundance of Hu100 was not significantly different to other markers, which, could be due to the large variability in the proportion of E.coli containing biomarkers. Due to this variation, it is recommend that the total marker abundance is used to compare different sites.
Community-based MST uses high-throughput sequencing to compare bacterial communities of environmental samples, such as sea water, faecal taxon libraries (FTLs) which contain bacterial communities from known sources. Simulated microbial communities were used to evaluate how the composition of FTLs affected the accuracy and sensitivity of community-based MST. The inclusion of local samples appears to be more important than the size of the FTL to the accuracy of community-based MST. Furthermore, the inclusion of a river water sample as a ‘background sample’, improved method sensitivity from a 5% mixture of the sewage bacterial community in river waste to a 2% contribution of sewage.
Two catchment studies highlighted the ubiquity of urban diffuse pollution, largely from septic tanks and misconnections, in rural and semi-rural catchments. Community-based MST showed a good correlation with human-associated markers and (rs >0.467, p <4.45x10-06), but only when human sources were dominant. Findings suggest that community-based MST is more useful than marker-based MST to survey catchments for a range of potential pollution sources.
Investing ~£230k to perform MST in-house is the best option for Northumbrian Water, and other water companies, to incorporate qPCR and sequencing into their workflows. While >3000 samples need to be processed to achieve a return on investment, the business risk remains small, and other areas of the business will benefit from this investment.Northumbrian Water and EPSR
Understanding tutors use of "interactures" : a comparison study of three different content-based subject areas at the Universiti of Brunei Darrussalam
Get PDFPhD ThesisThis study adhered to the belief that interaction plays a significant role in the co-construction of new knowledge in the classroom. Though, to understand the highly complex and rapid flow of classroom interaction require a system of analysing classroom talk. Most studies conducted on classroom interaction took place in the language classroom context where the language was used not only as a means for acquiring new knowledge, it was also the aim of the subject (see Walsh, 2011). However, the context of the researchdoes not indicate that understanding the use of verbal interaction in other subject areas was insignificant. To understand the use of the Englishlanguage in a content-based classroom requires adopting a system for analysis such as the Self-Evaluating Teacher Talk framework (SETT) to assess the tutors’ Classroom Interaction Competence (CIC) (Walsh, 2006; 2011). By raising the tutors’ and students’ awareness of their CIC, this study hopes to encourage participation and thus create a collaborative environment. In this study, a comparison was made on the tutors' and students’ use of interactional features (interactures) (Walsh, 2006) using the mode from three different courses at the Universiti of Brunei Darussalam (UBD).In line with the works of Vygotsky on socio-culturaltheory and social-constructivist paradigm, this study sought to conduct a qualitative approach through the use of non-participant video observation and stimulated recall interviews. Purposive sampling was used whereby the classes were chosen according totheir use of the English language as the medium of instruction and the representation of different content-based subject areas in UBD. For each class, recurring video observation of the whole lesson (around 2 -4 hours) was conducted. The interviews conducted was within 1-3 days after the observation. Since the participants selected were voluntary, the number of students participating in the interviews varies from 2 to 12 participants per class. For each interview, a random section of the lesson was shown for 5-15 minutes, depending on the response from the participants, which pushed the interviews to last around 30-45 minutes. Theinterview questions were semi-structured, focusing partly around the interactures used in the lesson, and the participant’s response. Using the SETT Framework on the video transcriptions, the study compared the different ways content-based subject tutorsuse selected interactures as a tool in comparison to the SETT Framework. Using thematic analysis on the interview data confirmed the reoccurring themes that arose from the observation data and its reflection on the tutor's CIC. The conclusions revealed how specific interactures, such as the use of display questions and humour, could be used to encourage participation by expanding the students' answers. Furthermore, the different types of lessons,for example, the tutorial, could lead to changes in the waysthe tutors' and students’ use of interactures. This study also suggested that different courses and different tutors could influence the level of participation in the classroo
A surface topographical analysis of explanted knee prostheses
Get PDFPh. D. Thesis.In 2017 there were 106,334 primary and 6,502 revision knee replacement surgeries reported in England, Wales, Northern Ireland and the Isle of Man. Annual increases of both procedures are predicted. Analyses of explanted orthopaedic prostheses enables greater understanding of their true clinical performance and can lead to design improvements, increased longevity and enhanced patient safety and benefit. This thesis provides a thorough investigation into the surface topographical analysis of explanted knee prostheses and the relationship between in vivo surface topographical changes and patient and implant demographics. This is the largest surface topographical analysis of explanted knee prostheses to date within the United Kingdom. This work is the first to report the surface roughness of explanted Unicondylar Knee Replacement (UKR) prostheses. Within this thesis, 135 knee prostheses were retrieved from revision surgery, processed for analysis and catalogued with patient data. Non-contacting profilometry and semi-quantitative damage scoring were used to analyse the surface topography of explanted and reference Total Knee Replacements (TKRs) and UKRs with cobalt chromium alloy (CoCr) and oxidised zirconium (OxZr) femoral components. All explanted femoral components showed an increase in surface roughness between 33% and 263% after time in vivo. There were no correlations found between the surface roughness and the damage scores recorded on the explanted prostheses or between the surface topography measurements and the duration in vivo, side of implantation or patient age, BMI or gender. No differences were found between in vivo surface topographical changes recorded on retrieved TKR compared with retrieved UKR components. No differences were found between in vivo surface topographical changes recorded on retrieved CoCr components compared with retrieved OxZr components. This work provides valuable data concerning the true in vivo performance of knee replacement prostheses and contributes to furthering the understanding of the mechanisms of failure of these prostheses.School of Engineering at Newcastle Universit