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Audience 2.0 : new dynamics of audience reception in the age of social media
Full text linkPhD ThesisRecent years have seen a rise in interest in 'interactive' audiences, with the ongoing spread of digital
media enabling media viewers to develop new participative and collaborative activities. As a hub of
communication, the Internet has become a crucial enabling platform for these new forms of audience
engagement. Audiences migrate to social media to share impressions, interpretations and issues with
the content they view, an action which, it is argued, 'makes visible' the often-unseen processes that
constitute audience reception. Using the microblogging site Tumblr as case study, this thesis makes a
case for developing an integrative approach to media reception, by consolidating knowledge from
film studies, fan studies, and participatory cultures, that these subjects might better address the
mutable nature of the modern audience. This thesis commits to a radical contextualist approach which
challenges the application of ‘linear’ frameworks to postmodern audiencehood, drawing specifically
on the research of danah boyd, Henry Jenkins and Carolyn Michelle. This study contributes original
knowledge on young adult's processes of ‘meaning-making’ when online, by examining (1) contexts
of social media engagement in the audience's daily life (2) the forms of interpretative work produced
online in relation to film texts (3) the social and cultural implications of this online audience activity.
The research questions for this study are as follows:
• How do social networking sites such as Tumblr figure in young adult’s daily media use? How
do Tumblr users engage with film content when interacting online?
• How are Tumblr users utilising the site in their reception of film texts? What are the forms of
receptive work taking place online?
• How does the audience interpret and reflect on their online activity? What do these practices
reveal about the nature of online audiencehood?
The study employs online ethnographic methods, including participant observation and Skype
interview, to detail the processes of online audience reception. An intensive period of fieldwork was
undertaken, consisting of 12 months participant observation of 150 users within the Tumblr
community, followed by a series of 24 online interviews, carried out synchronously (via Skype) and
asynchronously (via email). The ethnographic data collected for this study was analysed thematically
in order to produce an initial conceptual guide to online audience engagement. This study identifies
several key themes which typify audience work on this site, including ‘performance’, ‘anonymity’,
and ‘bricolage’. The study finds that the 'exhibitive' quality of online interpretative work, being
intrinsically informed by the contextual collapse between public and private in online spaces,
promotes self-conscious responses whereby audiences can actively assert their sense of self and their
place within a wider social and cultural sphere. This appears to have specific generational resonances,
as critical discourses on the ideological basis of the film industry are increasingly propagated amongst
Tumblr’s young adult userbase. The thesis concludes with an interrogation of the thresholds of
participation in interactive audience engagement and the implications this has for the future of
audience research. It is argued that the role of social media in audience enquiry should not be
understood merely as a new source of data about audiences, but rather as a crucial enabling platform
for audience participation and contribution
Mechanistic modelling of microscale chromatography
Full text linkPh. D. Thesis.Microscale chromatography as an experimental tool has shown much utility in process development due to
reduced material consumption and ease of parallelisation which are of major benefit when compared to
conventional lab-scale studies. Microscale columns are commonly used in early process development where the
most impactful decisions, such as choice of unit operation, purification strategy, resin, and the choice of
candidate are made with limited resources and knowledge. Understanding the behaviour of microscale
chromatography and better applying the knowledge gained from microscale studies to large scale
chromatography may allow faster, more efficient and more robust early process development, and therefore
more effective processes once a bioprocess is fully developed and products commercialised. It is the overall aim
of the project to develop a model to determine large scale mass transfer parameters describing a lab-scale
chromatographic process from microscale data, and allow one to simulate and optimise large scale separations
whilst enjoying the benefits of reduced resource consumption of the microscale domain.
From the outset, characterisation ofthe differences between lab-scale columns operated on a conventional Fast
Protein Liquid Chromatography (FPLC) system and microscale columns on a robotic Liquid Handling System (LHS)
was performed. Determining the common metrics of column performance, HETP, asymmetry and experimentto-experiment or column-to-column variation between columns and experiments provides an understanding of
some of the key differences between lab-scale and microscale column formats with regards to system, scale and
data quality, as well as providing an opportunity to optimise the experimental design of microscale experiments.
This was performed through evaluating methods of improving resolution, including fashioning rigs to use
microscale columns on a conventional system, evaluating various tracer substances and evaluating a novel
strategy of pre-filling collection plates.
Investigations into ascertaining the dynamic binding capacity (DBC) of IgG to Protein A resin using microscale
data has been performed with 3 microscale column volumes at several residence times using the high
throughput system, and repeated at lab scale, with further work into understanding the effect of intermittent
flow on resin: target interaction by mimicking the microscale operation on a larger system.
This effort has led towards data used to calibrate a mechanistic model of chromatography at both lab scale and
microscale with the intention of predicting lab scale behaviour. By correcting for scale, operational and flow
effects, one may predict large scale performance through calibrating a model with microscale data, enabling
better process understanding with reduced material consumption.EPSR
Voicing Contrast in Najdi Arabic Stops: Implications for Laryngeal Realism
Full text linkPh.D. (Integrated) ThesisThe present study investigates the phonetic and phonological aspects of the voicing contrast in stops in Najdi Arabic, a dialect that has been found to contrast prevoiced and aspirated stops. This study discusses the implications of the acoustic correlates of Voiceless and Voiced stops for the phonological representation of the voicing contrast in this variety and examines the connection between the acoustic signal and the distinctive features that specify the opposition by employing the types of evidence proposed in the realm of laryngeal realism. These types of evidence include the manifestation of acoustic correlates of stops in various positions, speech rate effect on aspiration and prevoicing, and the Voiceless and Voiced stops’ behaviour in stop-stop clusters across word boundary in terms of regressive voicing assimilation.
The manifestation of the acoustic correlates of Voiceless and Voiced stops shows that Voiceless stops are aspirated in the examined positions whereas Voiced stops show robust prevoicing in utterance-initial and utterance-medial contexts. The acoustic correlates also show that Voiceless stops are robustly accompanied by longer closure, longer burst, higher F0 and F1 onset, and lower burst intensity. Voiced stops, on the other hand, are robustly accompanied by shorter closure (utterance-medially), shorter burst, lower F0 and F1, and higher burst intensity. Speech rate affects both aspiration and prevoicing in Voiceless and Voiced stops, respectively. Prevoicing and aspiration are lengthened in normal speech rate in comparison to fast speech rate. Stop-stop cluster results show that both Voiceless and Voiced stops trigger some (de)voicing in the preceding member of the cluster. The acoustic analysis reveals that Voiceless stops show voicing assimilation in F0/F1 and burst intensity but not in voicing in the closure. For Voiced stops, the results show a degree of devoicing in their closure but not in F0/F1 and burst intensity.
The results suggest that Voiceless and Voiced stops in Najdi Arabic have features from both aspirating and voicing languages. This claim is supported by the three types of evidence implemented in this study. The assumption that both Voiceless and Voiced stops are specified implicates that the voicing contrast in Najdi Arabic is overspecified in the phonology with two features, [spread glottis] and [voice]. Applying the numeric values of phonetic distinctive features proposed by Beckman et al. (2013), on the scale of 1 to 9, the present study claims that Voiced stops in Najdi Arabic are specified with [9 voice] while Voiceless stops are specified with [8 spread glottis], mainly because of the existence of moderate aspiration in utterance-initial Voiceless stops and the robust prevoicing found in utterance-initial and utterance-medial Voiced stops (1 means inactive, 9 means highly active). The phonological repercussions for the proposed overspecification in the voicing contrast in
Najdi Arabic are discussed with a specific focus on the inclusion of such a patterning in theoretical models of voicing
New insights on SepL, the gatekeeper component in Type 3 secretion system of enteropathogenic E. coli, though functional interchangeability studies
Full text linkPhD ThesisThe pathogenesis of many gram-negative bacteria depends on Type Three secretion
systems (T3SSs) that deliver subversive effector proteins into the infected host cell. These
injectosomes evolved from flagellar export apparatus with significant homology
remaining between components that form the T3SS/flagella export channel (which spans
the bacterial envelope) and the sorting platform that controls the timing and hierarchy of
substrate export. There are distinct T3SS families where high protein homology is a
feature within, but not between families. One family is represented by the
enteropathogenic E. coli (EPEC) T3SS encoded-alongside genes for T3SS substrates
(several T3SS components; translocators (link T3SS to host cell); effectors, chaperones (aid
stability/export of T3SS substrates), regulators, and intimin surface protein-on a 41-gene
region called LEE (Locus of Enterocyte Effacement). Unexpectedly, LEE was found in an
Edwardsiella tarda (E. tarda) strain with genetic rearrangement linked to gene loss and
disruption. However, recent studies support functionality with the discovery of
unprecedented divergence indicative of a district T3SS family. Preliminary functional
interchangeability studies identified E. tarda T3SS proteins that could and, more
interestingly, could not functionally substitute their EPEC counterparts. The divergence
level did not predict functionality. Studies with support complementation defects for five
E. tarda T3SS proteins are described here, which revealed unexpectedly novel functions
for SepL (the gatekeeper controlling switching from translocator to effector substrates).
Further investigation revealed that i) SepL, 3 (CesT, CesAB, CesD2), an effector (EspF), and
two T3SS components (EscC, EscD) each control the cellular O127-antigen level; ii) SepL
protects Tir from cleavage; and iii) SepL, CesT, CesAB, and CesD2 protect EspF from
cleavage. Cleavage event requires EscU; the latter has auto-proteolytic activity linked to
regulating substrate export hierarchy. Importantly, these activities were not shared by the
E. tarda homologs with domain swap experiments linking different SepL functionalities to
one or more of its three X-bundling domains.Taibah University and the Saudi Arabian Cultural Bureau
(SACB
Quantification of the demands of elite rugby union players and understanding the subsequent physiological and epigenetic responses : b an applied approach towards prescription and individualisation
Full text linkPhd ThesisThe development of effective training load monitoring tools has enabled key insights into elite rugby union players' training and game demands and significantly improved the physical management of players. Whilst the use of training load quantification methods is common practice in elite sport, in the scientific literature, little information is known about the training and periodisation strategies of professional rugby union clubs, and how this may change throughout a competitive season. Throughout a season, coaches and practitioners face frequent decisions on daily training sessions, team selection, and competition scheduling. Understanding the load imposed on players from training and competition informs and aids this decision making. These decisions are integral to the optimisation of repeated player performance throughout a season. Diagnostic tools provide another piece of the puzzle to support player management decisions.
The integration of both diagnostic measures and workload quantification aids the understanding of the dose-response relationship between fatigue and physiological adaptation. Building an effective individualised training load monitoring system is key within an elite rugby union club. Currently, practitioners are exposed to vast amounts of information that can be collected on individual athletes, slowing and limiting the ability to make effective choices on players’ health and performance. There is a need to synthesise this process and optimise athlete monitoring without creating additional staff and player burden.
This thesis aimed to explore the multitude of factors that may influence the optimisation of elite rugby union players and explored the reasons for variation between individual players. The first part of this thesis quantified the external training load demands throughout a competitive season and evaluated the stress-induced effects of acute and chronic rugby training and match-play. Data from Chapter 4 demonstrated a strategical variation in training load prescription throughout a competitive season and showed key differences in external load metrics between position and the match status of players. Chapter 5 assessed changes in performance measures, biomarkers and subjective wellness throughout a full professional season. Certain periods of the season reported significant deviations from baseline measures and associations were observed between GPS variables and measures of performance and biomarkers.
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The second part of the thesis explored novel circulating miRNA (ci-miRNA) biomarkers and their role in the observed variation between players in response to training. Chapter 6 revealed associations between specific ci-miRNAs and anthropometric and performance variables that are consistent with the current understanding of plausible biological mechanisms. Lastly, Chapter 7 revealed the variability in training-induced responses to preseason training and, reported associations between certain baseline ci-miRNA levels with the observed anthropometric and strength changes.
In summary, this thesis emphasises that even within a team sport, managing individual players is crucial to optimising performance; a one size fits all approach is not appropriate. A consistent and effective monitoring system needs to observe both external load and measures of fatigue, in order to inform and support the decision making of practitioners. Additionally, there is a great potential for the use of epigenetic information to inform practitioners of player management processes. However, this research in an elite sport setting is very much in its infancy and caution should be taken trying to implement this strategy
Investigation of human C12orf65 and mtRF1, members of the mitochondria translation release factor family
Full text linkPhD ThesisMitochondria contain their own DNA (mtDNA) and protein synthesis machinery. Human mtDNA encodes for two rRNAs, 22 tRNAs and 13 polypeptides. Those polypeptides are subunits of complexes involved in oxidative phosphorylation and their translation is driven by the mitoribosome. Translation consists of four phases - initiation, elongation, termination and mitoribosome recycling- with translation factors required at each step.
My work focused on termination, which requires the action of release factors. In human mitochondria, there are four proteins in the release factor family: mRF1a, ICT1, mtRF1 and C12orf65. Termination occurs once a release factor recognises a stop codon (UAA or UAG) in the A site of the mitoribosome. This changes the mitoribosome conformation, inducing the polypeptide’s release. Only mtRF1a recognizes stop codons and terminates translation for all the 13 mtDNA-encoded polypeptides. However, all four members contain the GGQ motif involved in peptide release. ICT1 is a component of the mitoribosome large subunit. My research focused on the functions of mtRF1 and C12orf65 which are yet unknown, although it was observed that patients with C12orf65 pathogenic variants show impaired mitochondria translation.
My research hypothesis was that C12orf65 and mtRF1 initiate termination in mitoribosomes that stall during translation. Stalling has multiple causes including mRNA pseudoknot structures, defective tRNA or insufficient amino acids. Release factors would recognise mRNA targets to the same effect as stop codons.
To test this, I aimed to identify mRNA targets specific to mtRF1. I also aimed to detect proteins C12orf65 interacted with to confirm whether it was involved in termination. I used cross-linking and immunoprecipitation of the mitoribosome, BioID2 and CRISPR-Cas9 techniques. Thus, I obtained and characterized two BioID2 cell lines that helped locate C12orf65 interactors involved in translation. Moreover, I established a C12orf65 knockout cell line that presents a growth defect, further demonstrating C12orf65’s involvement in cell viability.European Union’s Horizon 2020 research and innovation programm
Characterisation of a pair of copper storage proteins from pathogenic bacteria
Full text linkPh. D. ThesisNeisseria gonorrhoeae is a pathogenic Gram-negative bacterium that causes human
gonorrhoeal disease. Its genome encodes a putative periplasmic homologue of a new family of
copper storage proteins (Csp) recently described in methanotrophic bacteria. Although
members of this protein family are abundant in pathogenic bacteria, the presence of this
periplasmic Csp in N. gonorrhoeae is almost unique. Most Csp genes in pathogenic bacterial
genomes lack a signal peptide and are therefore presumed to be cytosolic. For example, the
Csp protein encoded in genomes of Salmonella sp. lacks a signal sequence. However, the N.
gonorrhoeae Csp possesses a putative Tat signal for targeting it to the periplasm. Salmonella
enterica is an important global pathogen, consisting of more than 2500 various serovars that
can be host-specific or can have a broad range of hosts, whereas N. gonorrhoeae is highly
specialised for infecting humans. Antibiotic resistance in both of these bacteria, N.
gonorrhoeae and S. enterica, further enhances their risk to human health.
Copper is a redox active metal that is essential for several biological functions as a
cofactor used by a number of copper-dependent enzymes. However, excess copper is toxic;
thus, its homeostasis is carefully regulated through a system of protein transporters, sensors,
trafficking proteins, and storage proteins. The Waldron lab is studying the form and function
of these Csp proteins in pathogenic bacteria, as copper is known to play an important role in
the innate immune system’s ability to fight infection. It is anticipated that a putative role for N.
gonorrhoeae Csp1 and Salmonella Csp3 in defending these pathogens from attack by the
immune system would make these proteins potential therapeutic targets for future antibiotics.
This study explored the copper binding properties of Csp1 from N. gonorrhoeae and of
Csp3 from S. enterica, in order to understand how they may be able to aid virulence, either
through sequestration of excess copper, thereby reducing copper toxicity, or by storing copper
during times of abundance and subsequent release of copper during copper deficiency. Copper
binding by the Csp proteins was assessed, and the crystal structure of Salmonella Csp3 was
determined. We concluded that Csps bind a large number of copper ions, likely as a storage
mechanism, within a four-helix bundle structure that could be targeted in future drug discovery
programmes
Terrestrial carbon storage and sequestration potential of institutionally managed estates
Full text linkPh. D. ThesisMany institutions have declared a climate emergency and are committed to ambitious net-zero carbon aims. However, few institutional carbon management plans consider the terrestrial carbon store of the estate in a quantitative or qualitative way. Using Newcastle University as a case study, this research demonstrated ways to quantify and potentially augment the soil and tree carbon stocks of institutional estates by changes in land management. The terrestrial carbon store of Newcastle University’s estate was quantified with field work, and scenarios of the off-setting of institutional carbon emissions were derived by considering alternative land management. Additionally, the application of wheat straw biomass and its biochar to urban soil was investigated for carbon sequestration. To quantify the current carbon storage baseline of the institutional estate, soil and tree carbon was surveyed for two research farms, campus green spaces, and a sports field. The total terrestrial carbon stock of Newcastle University’s estate was found to be 17 times greater than the annual institutional CO2 equivalents-C emissions in 2019-20. Newcastle University could off-set half of its institutional CO2 equivalents-C emissions over a period of 40 years by converting its farms into woodland. Reverting farm management to practices shown on old maps from 1900 with more permanent grasslands could off-set 64 percent of institutional CO2 equivalents-C emissions over a period of 5 years. Other measure such as doubling the number of free-standing trees on the farms, converting all lawns on the central campus into urban woodland, or amending the Newcastle Helix brownfield reclamation site soil with 2% biochar would off-set less than 3 percent of institutional emissions over 40 years. Interviews with estate, farm and carbon managers revealed reluctance to accept the dramatic land management changes which would be needed for tangible off-setting of institutional emissions, but it will be difficult to achieve net-zero carbon emission aims without serious consideration of off-setting opportunities in Newcastle University’s estate.UKCRI
Performance modelling and analysis of systems under attack and misbehaviour
Full text linkPhD ThesisComputing systems are growing increasingly complex, incorporating multiple interactive
components. Performance is a critical attribute in evaluating computing systems. Most
computing systems are now connected to networks, either private or public, raising concerns
about vulnerability and exposure to threats and attacks. A secure system requires effective
security protocols and techniques that do not negatively compromise performance. Analysing
a system’s behaviour under attack and misbehaviour can assist in determining where a
problem is located so as to direct additional resources appropriately. The overall aim of this
thesis is to model the performance of secure systems where behaviour changes in response to
attacks and misbehaviour. Performance Evaluation Process Algebra (PEPA) modelling is
employed to convert formal security protocols and methods into formal performance models.
This thesis addresses the impact and cost of cyber-attacks on the performance of webbased sales systems. PEPA models are proposed for two scenarios, with and without the
attacks, to understand how the system behaves in different scenarios to provide a sustainable
level of performance. It also explores the performance cost of a security protocol, an
anonymous and failure resilient fair-exchange e-commerce protocol. The proposed PEPA
models were formulated with and without anonymity in order to explore its overhead.
Additionally, we modelled a basic protocol with no misbehviour, not requiring the active
involvement of a Trusted Third Party (TTP), and an extended protocol, for which the TTP’s
participation is essential to resolve disputes. These models provide an insight into the
protocol’s behaviour and the associated performance cost.
An attack graph is a popular method to support a defender in understanding an attacker’s
behaviour. It also supports the defender in detecting possible threats, thereby improving a
system’s security status. Developing a PEPA model version of an attack graph can advance
understanding and identification of key risks, and assist the defender with implementing
appropriate countermeasures. This thesis developed two methods to automate the generation
of the PEPA model based on a pre-existing attack graph specification. The first method is
simple, generating a single sequential component to represent both a system and an attacker.
The second method has more potential, by generating a PEPA model with two sequential
components representing a system and an attacker, as well as the system equation to define
how they interact. The attacker component enables us to explicitly incorporate attacker
skills into the model. We use case studies to demonstrate how the PEPA models generated
are used to perform path analysis and sensitivity analysis, as well as estimate the time
required for each path. The defender can use this to determine the amount of safe time
remaining before the system is compromised, and rank the risk from all attack paths. In
addition, we developed PEPA models for an attack graph considering two criteria: attacker
expertise and the availability of exploit code to estimate time needed to breach the system.
We proposed three attacker skill levels: beginner, intermediate, and expert. The adaptability
of our proposed PEPA models were improved by incorporating learning behaviours for both
attacker and defender, to demonstrate how this affects the time required to compromise the
system.
The models in this thesis demonstrate an approach to integrating security and performance
concerns to advance understanding of system and attacker behaviour. The performance analysis undertaken indicates where problems may arise and additional resources needed. This
analysis could be extended in the future to consider alternative design options and dynamic
reconfiguration. Understanding the impact of attackers on system behaviour increases our
ability to design systems that can adapt and tolerate attacks. This thesis represents an initial
step toward greater understanding of the impact of attacks on system performance
A biochemical and biophysical study on cell division proteins from Staphylococcus aureus and biofilm proteins from Bacillus subtilis.
Full text linkPhD ThesisPart I
Cell division in bacteria is tightly regulated by a multiprotein complex called the divisome.
Proteins in the divisome couple cell division and growth, ensuring that a single copy of the
chromosome is present in each resulting daughter cell, and preventing more than one instance
of division from occurring at any one time. This thesis concerns a combination of biophysical
and biochemical techniques used to study the cell division proteins DivIVA, Stk1 and GpsB
from Staphylococcus aureus. A model of the solution molecular envelope of DivIVA is derived
by small-angle X-ray scattering and compared to a previously proposed model of the protein
from Bacillus subtilis. The molecular mechanisms of DivIVA oligomerization are probed
through use of size-exclusion chromatography coupled multi-angle light scattering on various
truncations of the protein. The structure of the N-terminal domain of S. aureus GpsB is solved
and used to rationalise the interaction between GpsB and PBP4. Attempts are made to
determine an interaction network between the cell division proteins and members of the
peptidoglycan and wall-teichoic acid synthesis machinery by several biochemical and
biophysical assays.
Part II
Biofilms are communities of sessile bacteria that form on a wide variety of natural and manmade surfaces, sometimes at a detriment to human health. Bacteria in biofilms are held together
by a viscous extracellular matrix consisting of polysaccharides, lipids, proteins, and
extracellular DNA (eDNA). Species of Bacillus are known to secrete two structurally similar
endonucleases, Nuclease A and B (NucA & NucB), into their environment as a means of taking
up eDNA either to enhance their genetic diversity, or for metabolic purposes, respectively. As
a mechanism of protection from self-induced genome degradation, NucA is co-expressed with
a proposed inhibitor, Nin. A combination of biophysical/chemical techniques are used to probe
the interaction between NucA/B and Nin from Bacillus subtilis. In vitro studies show that
NucA and NucB bind to Nin and that Nin inhibits their endonuclease activity. The affinity of
the interactions between NucA or NucB and Nin are probed and found to be sub-nanomolar.
The structures of NucA/NucB in complex with Nin are solved by X-ray crystallography,
revealing the mechanism of inhibition by Nin, and allowing for the calculated dismantling of
the complexes by site-directed mutagenesis