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How to improve the sustainability of logistics on the Coherent Campus at Newcastle University?
Get PDFPh. D. ThesisThe aim of this thesis was to improve the sustainability of logistics on the Coherent
Campus at Newcastle University.
The wider problems of unsustainable nature of urban freight logistics, at an
international, national and local level, were emergent in the academic peer reviewed
literature, with 77% of all articles reviewed published after 2011. The literature revealed
challenges to all three pillars of sustainability: economic, social and environmental. As
part of the scoping, a semi-systematic literature review was combined with a sociotechnical
theoretical framing and four research questions were identified:
RQ1: How to improve the sustainability of logistics on the Coherent Campus at
Newcastle University?
RQ2: To what extent can sustainable HEI logistics only be achieved through sustainable
procurement practices?
RQ3: How effective were participatory research approaches in facilitating this
improvement?
RQ4: What novel approaches for policy and practice locally, nationally and at an EU
level could be developed from this work?
A research philosophy grounded in the social sciences, pragmatism, abduction,
constructionism and pluralist ontology was chosen; methodologically, a systems
approach of Action Research was selected. Within that, the Design and Monitoring
Framework, the Business Model CANVAS, archival procurement data, and empirical
traffic surveys were all deployed. A pilot demonstration of a receiver-led inbound
consolidation centre service was trialled.
RQ1 confirmed the utility of the approach adopted, and the intervention demonstrated,
potentially yielding a circa 16% reduction in freight vehicles coming to campus. RQ2
was answered in the negative, but assessed the successful action taken. The
effectiveness of the participatory research approaches taken was confirmed in answer to
RQ3. Policy recommendations were developed and detailed in answer to RQ4. A novel
contribution to theoretical knowledge was made, in the development and presentation of
practical knowing, in the form of a socio-technical framing.Newcastle University, European Commission’s Seventh
Framework Programme (FP7/2007-2013), European Green Car
Initiativ
The development of a quantitative and qualitative protocol for assessing the welfare of laboratory mice
Get PDFPhD ThesisMice are the most commonly used species for biomedical research. Maintaining high levels of welfare for these animals is critical for the individual animal and for ensuring the scientific data collected from them is of high quality. An efficient protocol for assessing laboratory mouse welfare should include physiological, psychological and environmental indicators, and should be able to recognise both welfare strengths and shortcomings. The protocols that are currently used often lack indicators which assess the animal’s psychological state, which is necessary for a holistic assessment and critical for animal welfare. This study aimed to develop a holistic protocol for the assessment of laboratory mouse welfare when the assessment is made in an audit or every day. The development of the protocol involved three stages: [1] validity, practicability and reliability assessment of existing indicators, through a Delphi consultation technique, [2] the validation of a novel indicator (Qualitative Behavioural Assessment –QBA) for the assessment of emotional expressions, [3] the reliability and practicability assessment of the developed laboratory mouse welfare protocol. The Delphi consultation identified hunched posture, coat condition, the exhibition of normal and abnormal behaviour and usage of nesting material as the most valid, reliable and practical indicators for welfare assessment in a laboratory environment. The most common handling method for laboratory mice is tail handling, which produces anxiety thus new techniques have been developed for handling laboratory mice such as tube handling. QBA showed a high intra and inter-observer agreement in the assessment of emotional states for laboratory mice that had undergone handling by two different techniques. This study demonstrated that mice handled by their tail were described as "anxious/fearful" whereas mice handled by a tunnel were described as "confident/ playful." The final protocols for an audit and everyday welfare assessment of laboratory mice demonstrated to be practical and reliable between assessors with experience in laboratory mice. These protocols can be used in laboratory facilities for assessing laboratory mice welfare, incorporating psychological state using QBA. The 3-phase method used to construct the final protocol showed to be a comprehensive process which explored well-know and novel indicators and comprises all aspects of mouse laboratory welfare including QBA as a novel method of assessing psychological state. The process of developing a protocol for assessing laboratory mouse welfare is critical and considering experts, previous and novel indicators can improve the assessment quality by including all the components of the definition of welfare.Colciencia
Bacterial DNA replication initiation : structural and functional analysisof the master initiator DnaA
Get PDFPhD ThesisThe essential process of DNA replication begins with initiator proteins binding to origins of replication and triggering DNA synthesis. The highly conserved bacterial master initiator protein, DnaA, performs several key activities at the bacterial origin (oriC) to initiate replication. DnaA binds specifically to oriC and assembles into a filament that engages and stretches a single DNA strand to induce duplex unwinding. Subsequently, DnaA recruits a loading complex that deposits the replicative helicases around single DNA strands. In this thesis I have investigated the molecular mechanisms underpinning some of the essential activities of DnaA in the model organism Bacillus subtilis. Using a chimeric DnaA system I was able to identify several activities required for origin unwinding by DnaA bound to a specific DnaA-box located upstream of the site of unwinding. This result suggested that the protein binding here is directly involved in unwinding the DNA duplex, and the likely role of the upstream region is to increase the local DnaA concentration at the site of unwinding.To unwind oriC, DnaA engages and stretches a specific DNA strand with a recently identified repeating tri-nucleotide motif, termed the DnaA-tri os, providing the specific sequence. Utilising an inducible heterologous replication initiation system I determined which DnaA residues from a region implicated in ssDNA binding were essential in vivo. Using recombinant DnaA protein variants, two isoleucine residues were determined to be required for forming filaments on ssDNA and unwinding the DNA duplex in vitro. Further work is required to determine if these residues are required for the specific interaction with DnaA-trios or more generally for DNA binding/unwinding. A range of essential residues required for the interaction between DnaA and thefirmicute specific initiation accessory protein DnaD, the first step in helicase recruitment, were identified. The DnaA residues overlap with a binding site for the developmental regulator, SirA, a developmentally expressed inhibitor of DNA replication initiation. This suggested that SirA functions by blocking the interaction between DnaA and DnaD, preventing helicase loading. I found that SirA inhibits the interaction of DnaA with DnaD, providing a molecular mechanism for this SirA activity and revealing, for the first time, an endogenous system for regulating helicase recruitment in bacteri
Investigation of biofilms associated with chronic otitis media with effusion and adenoids hypertrophy
Get PDFPh. D. ThesisChronic otitis media with effusion (COME) is the most common cause of acquired hearing loss in young children. Bacterial biofilm is an important contributor to the aetiopathogenesis of COME, although conventional culture generally recovers few microorganisms from the middle ear. Extracellular DNA (eDNA) is a key structural component within the matrix of many microbial biofilms including those associated with COME. The aims of this study were to characterise microbial populations associated with COME, and to explore the efficacy of the DNase, NucB, to control in vitro biofilms associated with COME.
Methods were established to culture biofilms in vitro and to challenge with NucB. NucB efficiently disrupted biofilms of clinically isolated Staphylococcus aureus strains either alone or in combination with the antibiotic Co-amoxiclav. Concentrations of NucB 100-fold higher than those required for biofilm inhibition had no toxic effects on human epithelial cells.
Twenty-seven bacterial species were isolated from middle ear effusion fluids (MEEFs) of 34 patients with COME. Culture-positive MEEFs were increased two-fold following optimisation of the culture methods. Microbiome analysis of MEEFs by 16S rDNA sequencing identified the majority of the cultured species and several additional species. Similar species were also detected by 16S rRNA gene sequencing of microbial DNA from adenoids.
The ability of 23 bacterial isolates from MEEF to form biofilm was assessed. Twenty strains formed biofilms, and 16 of these were sensitive to NucB. Imaging analysis showed significant structural alterations in biofilms of the selected COME isolates after NucB treatment.
In conclusion, this study has provided further insights into the microbiology of middle ear infections and has shown that many bacteria from this environment are capable of forming biofilms. NucB alone or in combination with antibiotics may potentially be a potent and safe agent to control biofilm-associated conditions including COME.Iraqi Ministry of Higher Education and Scientific Research, Kirkuk Universit
Preclinical testing of a targeted TRAIL therapeutic for bone sarcoma
Get PDFPhD ThesisBackground: TNF-related apoptosis-inducing ligand (TRAIL) can induce cell death in
cancer cells after binding to its TRAIL receptors [TRAILR, Death Receptor 4 (DR4) and
Death Receptor 5 (DR5)] while sparing non-malignant cells. The application of TRAIL
provides an approach that can potentially overcome drug resistance and toxicity
associated with high doses of conventional therapies. It could be administered alone or
in combination with conventional therapies and, therefore, may offer a promising new
approach to bone sarcoma treatment. Enhancing the cytotoxic effect of TRAIL involves
targeting a tumour associated antigen (TAA). Here, the aim was to characterise bone
sarcoma cells for TRAILR expression and to assess the effectiveness, both in vitro and
in vivo of a novel TRAIL construct, neural/glial antigen 2 (NG2) targeted TRAIL
(ScFvNG2-Fc-scTRAIL).
Methods: Bone sarcoma cell lines were characterised for TRAILR and NG2 expression
on RNA and protein level. Together with non-malignant cell lines, they were exposed
to the novel TRAIL therapeutic (ScFvNG2-Fc-scTRAIL) in vitro and then tested in vivo in
a newly developed xenograft model of dedifferentiated chondrosarcoma.
Results: Surface DR5 was expressed in all cell lines examined (very high: HT1080,
MG63; moderate: SW153, U2OS, TC71). NG2 was also expressed (very high: SW1353,
MG63; moderate: U2OS, HT1080). ScFvNG2-Fc-scTRAIL demonstrated enhanced
cytotoxicity in DR5- and NG2-expressing cell lines (MG63>HT1080>U2OS), which
increased with doxorubicin and was also found in vivo when engrafting a luciferase
expressing HT1080 cell line in a dedifferentiated chondrosarcoma mouse model.
Conclusion: I demonstrate that a novel targeted TRAIL therapeutic, ScFvNG2-FcscTRAIL, has a selective and significant cytotoxic effect on cell lines expressing both cell
surface DR5 and NG2, and these cytotoxic effects can be enhanced further with
doxorubicin. Such combinations could minimise the risk of treatment failure due to
drug resistance, a common problem of single agent approaches. Furthermore, these
findings provide a framework for the clinical development of ScFvNG2-Fc-scTRAIL and
could potentially be used in the neoadjuvant setting, which would be a shift from the
usual convention of prioritising excision of the sarcoma
Understanding the Role of Citizen Generated Data in the Context of Public Health – A Case Study on Breastfeeding and FeedFinder
Get PDFPh. D. Thesis.Exclusive breastfeeding is recommended by the World Health Organisation until an
infant is 6 months old. Yet, despite this, the UK has the lowest rates of breastfeeding
seen across the world with only 1% of mothers exclusively breastfeeding at 6 months.
While promoting breastfeeding is considered a public health priority in the UK, budget
cuts and subsequent reduction in local authority services have made it difficult to
provide consistent support for women choosing to breastfeed. As such, ‘Breastfeeding
Welcome’ campaigns that aim to provide localised support for women and organisations
have either disappeared or are poorly resourced. Against this background, FeedFinder
has been developed to provide a platform for women to find, rate and review places in
real-time based on how breastfeeding friendly they are. The application has been used
by over 14000 women, mapping over 5000 venues with reviews from across the UK,
with some reviews now seen for venues in Asia, America and Australia. FeedFinder is a
civic technology, that is, where citizens have the potential to contribute to the shaping
of communities, environments and potential local service delivery mediated through
technology.
The main aim of this research was to understand how FeedFinder and the data it
provides might be used to leverage community support for women choosing to
breastfeed in public. Three strands of research contribute to the process of achieving
the overall aim; (1) understanding FeedFinder, its users and the data it provides, (2)
investigating if FeedFinder is a useful tool to professionals and voluntary groups who
promote and support breastfeeding and (3) design and evaluation of a new geoanalytics website for support of breastfeeding which includes a community
breastfeeding policy to offer practical guidance to public-facing organisations seeking to
improve provision and support for breastfeeding women.
The research followed a mixed methods and action research approach, being driven by
the needs and values of the multiple stakeholders involved; parents, public health
improvement practitioners, infant feeding coordinators, breastfeeding peer support
workers and local public-facing organisations. Following the completion of strand 2 of
the research, it was clear that FeedFinder was useful for parents but the process to
access the data for breastfeeding support or local public-facing organisations to use was
not efficient. This led to the iterative design and development of the FeedFinder
website, community breastfeeding policy, poster and video followed by an evaluation
with stakeholders (strand 3).
The newly developed FeedFinder website and community breastfeeding policy have
shown promising potential to provide a tool for local communities to do more to
support breastfeeding. The expert evaluation revealed that breastfeeding support
services welcome the website in practice, though some concerns persisted on trust and
legitimacy of data therein. This thesis describes the way in which citizen-generated data
can be utilised in public health provision while outlining the key limitations and
concluding with recommendations for sectors with potential to impact on improving the
breastfeeding rates across the UK and so meeting recommendations for optimum infant
feeding.EPSR
Development of novel computational methods suitable for modelling intrinsically disordered proteins
Get PDFPhD ThesisProteins without a stable tertiary structure are known as intrinsically disordered or metamorphic.
These proteins denoted as IDPs – or protein domains denoted as IDRs – exert crucial roles in
cellular signalling, growth and molecular recognition events. Due to their high
plasticity, IDPs and IDRs are very challenging for experimental and computational
structural studies. To enable these, all-atom molecular dynamics (MD) simulations are used, as
they provide insight into structure and dynamics at the atomistic level of detail. However, the
current generalist physical models (protein force fields and solvent models) used in MD simulations
are unable to generate satisfactory ensembles for IDPs/IDRs when compared to existing experimental
data.
This work aimed to improve on the state-of-the-art accuracy for simulations of IDPs/IDRs without
sacrificing accuracy for folded domains. Herein, the accuracy of several different force fields
frequently used for simulations of proteins was compared, in simulations of both ordered and
disordered systems. The results showed that each force field has strengths and limitations.
Given the fact that interactions with the solvent are pivotal for accurate simulations
of intrinsically disordered proteins, a novel solvation model was developed, denoted as
Charge-Augmented 3 Point water model for Intrinsically disordered Proteins (CAIPi3P). CAIPi3P
model was generated through systematic scanning of the dipole moment values
calculated for the popular TIP3P three-point water model. By increasing the dipole
magnitude, the agreement between experimental and calculated small-angle X-ray scattering
(SAXS) curves was massively improved for a series of model IDRs.
To further improve the simulations of proteins containing IDRs, a novel method to assemble force
field parameters has been developed. Denoted as Hybrid_FF, it merges parameters from different
established force-fields, performing well for structured and disordered regions
(AMBER99SB-ILDN and AMBER03ws, respectively), parametrising each secondary structure
differently. Testing these joint parameters for a series of IDR-containing proteins showed
that such an approach improved the accuracy of the sampled configurations for
long disordered regions.
Finally, a software to estimate and analyse the transition dynamics of intrinsically disordered
regions has been developed in this work. Named structural quantifier of entropy (SQuE), it uses a
first-order approximation to the probability distribution to assess the structural entropy for
protein transitions barriers. It is expected that tools developed in this study will generate more
accurate IDP/IDR ensembles, broadening the range of biologically relevant systems amenable
to atomistic molecular dynamics simulations
The Rational Design of a Bio-electrochemical System A quantitative investigation into the design of a commercially viable microbial electrolysis cell for domestic wastewater treatment and hydrogen production
Get PDFPh. D. Thesis.Reducing energy use is a key challenge for the wastewater industry. Microbial electrolysis cells
(MEC) may provide a solution. No commercially viable bio-electrochemical has yet been developed,
despite over 40,000 publications. This thesis seeks to serve as a guide to a commercially
viable MEC design. Cost-performance targets are presented for MEC to be financially competitive
with activated sludge treatment (AS). By reducing the cost of the anode and current collector by
90%, a viable organic loading rate (OLR) is shown to be between 800 and 1,400g-COD/m3/d, if
MEC serve a 20 year lifetime. An order of magnitude greater than previously achieved in pilot
reactors - although acetate concentrations, a known direct food source for electrogenic species, are
typically low (c.10mg-COD/l). A high performance MEC will be dependent upon sufficient concentrations
of readily-digestible substrate close to a colonisable anode surface. To quantify a viable
MEC design, a macro-model was developed using the Navier-Stokes equations and Monod kinetics.
The model predicts MEC performance over a range of acetate concentrations and anode interstices
distances, the space between anodes. To calibrate the model and differentiate biofilm kinetics from
total microbial kinetics, the concept of current degradation rate is introduced. Models were calibrated
against empirical observations of MEC performing under controlled conditions, analogous
to those found in domestic wastewater, with a mean accuracy of 85.6%. Acetate concentrations (10-
50mg-COD/l), conductivity (770 15 S/cm), temperature (10 0.5 C) and pH (7.50 0.05) were
carefully controlled. Maximum acetate degradation rates of 10mg-COD/l were observed. Coulombic
efficiencies and current densities were both observed to increase with concentration. To achieve
the current produced in the laboratory, biofilms must have had higher local ORR than found in the
bulk microbial community. As such, decreasing anode interstices distances significantly improved
ORR for all modelled concentrations. In combination with pre-treatment technologies, MEC may
surpass target ORR. However, material costs to break-even are low due to the requirements for
additional anode materials.EPSRC and Northumbrian Wate
Designing and exploring student-led online learning environments
Get PDFPh. D. ThesisThe recent surge in the popularity of massive open online courses (MOOCs) has demonstrated
both the demand for, and potential of, self-directed online learning. Despite this success,
prominent online learning platforms, such as Coursera, offer limited opportunities for learners to
form lasting social networks. On the other hand, connectivist courses have enabled free flowing,
learner centric interactions through a mix of mainstream social networking and communications
tools, but have been criticised for creating a chaotic learner experience. Additionally, MOOCs
have only recently started engaging with their potential for advancement in social skills (such
as collaboration, bond-creation, negotiation) or offering the opportunity to study civic-minded
content.
This thesis aims to explore learner-led online environments that offer a well-organised learner
experience as well as support the formation of diverse, impact-focused online learning communities. The research approach used is action research, in collaboration with an international
organisation of high schools (United World Colleges). The research is based on a series of international, extra-curricular and civic focused 5 week online courses for high school students. Three
different technological configurations are explored: mainstream social media, a custom built
learning platform and a hybrid of the two approaches. The course data (including participation
metrics, class forum discussions and post-course surveys) is analysed using a combination of
quantitative and qualitative methods. The research uses a theory-based approach to propose a
framework for the analysis of course discussion content, in order to build understanding of both
cognitive and social learning. This framework is first used to highlight different aspects of the
configurations of learning environments that can be used to support the building of learning communities. Then, a more refined version is applied in order to discuss pedagogical contributions
of both learners and facilitators within the courses.
Experiments with different sized courses in loosely-coupled social media environments found
that while it is possible to build a sufficiently-structured, impact-focused student-led course
using such an approach, learner experience becomes increasingly chaotic when the number of
participants exceeds 100. Social media channels, whilst helpful for driving engagement, lack
important features for community building and project development. These findings drove the
design of a learning management system, LearningCircle.io. The system was designed so that
course participants could be subdivided into smaller groups (classes of 100 and groups of 10), as
well as to provide a setting favourable to project discussions and feedback. In early experiments
where only LearningCircle.io was used for courses, learners faced challenges relating to communication. This led to designing a hybrid environment (using a mix of bespoke platform and
social media). When comparing interactions in loosely-coupled, platform and hybrid courses
I found that there are two kinds of trade-offs that designers have to consider when thinking
about structuring a learning environment. Firstly, there is a compromise between supporting
contribution to course co-creation (favouring loosely-coupled media) and higher learner satisfaction with course experience (favouring more structured, platform-based approaches). Secondly,
there exists a compromise between an increased risk of low learner interaction (significant
in platform-only environment) and an increased challenge associated with the layering and
scaffolding of interactions (significant in social media only environments). In addition to this
developed understanding of the trade-offs of the different online learning configurations, and to
the analytical framework developed alongside this understanding, this research also contributes a
set of design recommendations for learning platform and course designers
Effects of agricultural systems on egg nutritional quality
Get PDFPh. D. Thesis.Eggs are a rich source of nutrients beneficial to human health. Market analysis shows increasing
European egg production and consumption. Organic egg production differs from conventional
systems (free-range and indoor) in the exclusive use of organically grown feed. Organic and
conventional free-range systems share the free access to open-air runs but organic flocks have
greater management restrictions, which could potentially differentiate egg composition. In
order to investigate the effect of management on egg nutritional quality, three major egg
production systems were explored; caged, conventional free-range and organic. The hypothesis
developed is based on benefits of increasing pasture and free-range behaviour. To fully
investigate the effect, these systems were considered within a framework of a meta-analysis
(Chapter Two), a farm survey (Chapter Three) and a retail survey (Chapter Four). In all chapters
it was found that management does affect the overall egg nutritional quality, with organic
having higher omega-3 (n-3) fatty acids than free-range systems (P<0.05 (Chapter Two),
P<0.01 (Chapter Three) and P<0.001 (Chapter Four)) and higher carotenoids than all
conventional systems (P<0.001 in Chapter Four). At the same time Chapter Four detected
seasonal effect for vitamin D3 (P<0.001) and B2 (P<0.01) and interactions with management
(B9, D3). In Chapter Five, the effect of a sustainable and alternative protein source on egg fatty
acid profile was investigated to account for the impact of replacing soybean with insect meal
on egg fatty acid within an experimental trial framework. The partial replacement of soybean
with insect meal had both positive and negative effects on egg fatty acid composition, flagging
promising the replacement of soybean in terms of overall egg nutritional quality. Implications
of choosing organic over conventional eggs to human health are focused on higher intakes of
long chain n-3 fatty acids, carotenoids and potentially of vitamin A and E. Standardizing egg
concentration in vitamin D3, B2 and B9 between summer and winter is also suggested.the Sheepdrove trus