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Discretising quantum field theory using wavelets
No full textTheoretical thesis.Bibliography: pages 43-44Chapter 1: Introduction -- Chapter 2: The Ising Model -- Chapter 3: Wavelets -- Chapter 4: Wavelet-Ising Model -- Chapter 5: ConclusionIn this thesis, I develop a new discretisation scheme offered by wavelet analysis. Daubechies wavelets of orderK ≥3 are used to encode the quantum field theory of the 1D transverse Ising model in a discrete approximation. I then analytically determine the energy spectrum, which is used to construct the correlation matrix. This allows for the calculation of bipartite von Neumann entropy,which acts a measure of entanglement entropy for block spin chains. These results are qualitativelyand quantitatively compared to the discrete and continuous Ising models as a gauge of the method'ssuccess as an alternative discretisation scheme.1 online resource (44 pages
Investigating the success of Acinetobacter baumannii in the clinical setting
No full textEmpirical thesis.Includes bibliographical references.Chapter 1. Introduction -- Chapter 2. Homologs of theAcinetobacter baumannii aceI transporter represent a newfamily of bacterial multidrug efflux systems -- Chapter 3. Regulation of the aceI multidrug efflux pump gene in Acinetobacter baumannii -- Chapter 4. Fluorescence-‐based flow sorting in parallel with transposon insertion site sequencing identifies multidrug efflux systems in Acinetobacter baumannii -- Chapter 5. Interactions between co-‐cultures of clinical isolates of Acinetobacter baumannii and Klebsiella pneumoniae -- Chapter 6. Conclusions and future perspectives -- Appendices.Acinetobacter baumannii is an increasingly problematic hospital-associated opportunistic human pathogen that causes a range of infections such as respiratory, urinary tract and blood infections. The ability of nosocomial A. baumannii isolates to resist a diverse range of antimicrobial compounds and persist in clinical settings makes it a growing public health problem.Multidrug efflux pumps are significant contributors to antimicrobial resistance determinant in this microorganism. Five multidrug efflux pump superfamilies have been well described in bacteria, and characterized representatives of each of these five families are found in A. baumannii. In addition to drug efflux pumps and other resistance determinants, the capability of this pathogen to flourish in mixed species biofilm communities contributes to its success in the clinical setting.Recently, AceI from A. baumannii has been shown to be a novel chlorhexidine efflux pump. In this study, 23 homologs of aceI from different bacteria were cloned and expressed, and many of the homologs were found to confer resistance to additional biocides, including benzalkonium, dequalinium, proflavine, and acriflavine. Fluorimetric transport assays indicated that an AceI homolog from Vibrio parahaemolyticus mediated resistance to proflavine and acriflavine via an active efflux mechanism. Thus, this group of AceI homologs represent a new multidrug efflux protein family, the proteobacterial antimicrobial compound efflux (PACE) family. This is the first new multidrug efflux family to be found in the past 15 years.The function of AceR, a putative LysR family transcriptional regulator located adjacent to aceI in the A. baumannii genome, was investigated. AceR was demonstrated to be an activator of aceI gene expression, and induction is responsive to the AceI substrate chlorhexidine. AceR was demonstrated to bind in a chlorhexidine-inducible manner with a region of DNA upstream of the putative aceI promoter. AceR represents the first regulator of a PACE family pump to be functionally characterized.A novel high-throughput screening approach was developed to identify genes encoding multidrug efflux pumps and regulators in A. baumannii. This innovative screening method combines fluorescence-activated cell sorting (FACS) in parallel with transposon directed insertion sequencing (TraDIS). The feasibility of this method was demonstrated using a population of more than 100,000 random mutants shocked with ethidium bromide, a common substrate of multidrug efflux pumps. Ethidium bromide is differentially fluorescent inside and outside the bacterial cytoplasm due to its ability to bind nucleic acids. Cells containing the highest and the lowest concentrations of ethidium were collected, as the fluorescence intensity of the mutant cells can be distinguished by FACS. TraDIS was then applied to determine the genomic locations of transposon insertion within the collected mutants. AdeABC, AdeIJK, and AmvA efflux proteins were identified as the major ethidium efflux systems in A. baumannii, and a new transcriptional regulator that controls amvA expression was identified.Another aspect of this work focused on clinical strains of A. baumannii and Klebsiella pneumoniae isolated from a respiratory tract infection from a single patient. Co-culture studies of these two pathogens showed complex, multifaceted interactions that were dependent on their growth state and media. Metabolic profiling showed that the two pathogens had very different carbon utilization capabilities, and cross-feeding studies indicated that A. baumannii was able to utilize a secreted metabolite from K. pneumoniae as a sole carbon source. Transcriptomic analysis of the two strains co-grown in a biofilm identified significant changes in the expression levels of genes encoding surface structure biogenesis, amino acid catabolism and transport, as well as biofilm formation.Overall, this thesis provides new insight into the function and regulation of a novel class of multidrug efflux pumps, enabled the development of a new approach for identifying drug efflux pumps and their regulators, and provides a first look at the molecular and physiological interactions of two co-isolated pathogens.Mode of access: World wide web1 online resource (xxii, 153 pages) colour illustration
Teaching English to high school students in rural and urban areas in Vietnam: students' listening competence and teachers' perceptions
No full textTheoretical thesis.Bibliography: pages 84-90.Chapter 1. Introduction -- Chapter 2. Literature review -- Chapter 3. Research methodology -- Chapter 4. Findings -- Chapter 5. Discussion and implications -- Chapter 6. Conclusion -- References -- Appendices.This study explores the differences in English listening competence of urban and rural high school students in Northern Vietnam. English listening competence is critical to young people's employabibity in contexts where English is used. It is affected by a number of factors in the teaching and learning process, such as learners' background, and social and pedagogical factors (Field, 2010; Goh, 1999). This mixed-methods case study was conducted in English classes in two high schools, in urban and rural regions of Vietnam. Both student and teacher data were collected through administering a listening test and questionnaire for students, plus a questionnaire and follow-up interviews to explore teachers' perceptions. The collected data then was analyzed by thematic coding and constant comparative method. The results reveal a remarkable divergence in listening competence between students in the two contexts. Three groups of factors interfere with students' achievement in their English listening skills. These are teacher factors (teacher beliefs and frustration), school factors ( exposure time), and social factors ( career orientation, perception of the value of English, and learning conditions). The study draws some conclusions for pedagogy and teacher development.Mode of access: World wide web1 online resource (ix, 153 pages) illustration
Metaphors they lived by in Ancient Egypt: analysing the prophecy of Neferty & the admonitions of Ipuwer
No full textTheoretical thesis.Bibliography: pages 74-861: Introduction -- 2: History of studying the texts: A critical theory -- 3: Theoretical approach: conceptual metaphor theory -- 4: Methodology -- 5: Analysis -- 6: Discussion -- 7: Concluding remarks -- Bibliography -- AppendicesFor the ancient Egyptians, metaphors were predominant throughout the written expression of their civilisation, a feature that has captured significant academic attention. Yet, in spite of metaphor having long been a focus of Egyptological studies, it has frequently been treated as merely a means of linguistic ornamentation, without a deeper meaning or function in its respective text. The aim of this thesis is to identify, quantify, and qualify the metaphors employed within the Middle Kingdom texts The Prophecy of Neferty and The Admonitions of Ipuwer, in order to assess the rhetorical and ideological function of the metaphors within these literary texts. This was achieved through modern methods of metaphor analysis, namely, Conceptual Metaphor Theory. In the rhetoric of Neferty and Ipuwer, metaphors were predominantly assigned negative evaluations. The accumulation of these negative metaphors was not accidental on the part of the Egyptians, but rather, when holistically analysed, they are shown to cluster and point to the underlying mega metaphors ISFET IS BAD and MA'AT IS GOOD. While one might argue that these thematic ideological concepts of ISFET and MA'AT are already recognisable to readers in a cursory reading, an analysis of the metaphors in these texts demonstrates that metaphor is not used for mere ornamentation or as a method for padding out gaps in a text.Instead, metaphor is an integral part of rhetorically shaping and driving the compositional essence of these two narratives.1 online resource (xii, 110 pages
Uncovering the functions of genes in the pathogen acinetobacter baumannii
No full textTheoretical thesis.Bibliography: pages 56-69.1. Introduction -- 2. Methods -- 3. Results and discussion -- 4. Conclusions and Future DirectionsCurrently, only approximately 2% of the genome of the multi-drug resistant organism Acinetobacter baumannii has been experimentally characterised. Unfortunately, this is not uncommon. The experimental verification of gene functions is now lagging behind the rapidly increasing amount of sequence data generated via high - throughput next generation sequencing technology. However, using cellular fluorescence as a proxy for phenotypic data, TraDISort (Transposon - Directed Insertion Site Sequencing and Fluorescence Activated Cell Sorting) is a novel high - throughput protocol able to provide phenotypic data for a multitude of mutants in one experiment. In this thesis, data from a TraDISort experiment performed on an A. baumannii transposon mutant library treated with a sub - inhibitory concentration of the DNA/RNA intercalating fluorescent biocide ethidium bromide was bioinformatically analysed. TraDI Sort uncovered significant ethidium bromide efflux systems in A. baumannii , exposed a novel gene potentially involved with ethidium bromide resistance , and consistently selected genes related to DNA, transcription, and translation. FACS gating procedures also predisposed TraDISort to select for mutants with altered morphologies, including genes involved with shape - regulation and cell - division, confirmed via phase - contrast microscopy. Combined with alternative compounds possessing different cellular targets and/or sites of accumulation, TraDISort possesses great potential in probing the functions of numerous genes with diverse functions.1 online resource (80 pages
Evaluating hypothesis-inconsistent evidence: The effects of background knowledge, order, and strength of arguments
No full textEmpirical thesis.Bibliography: pages 73-82Introduction -- General Method -- Pilot Study -- Experiment 1 -- Experiment 2 -- General DiscussionCoherence-based models of reasoning suggest that the ways in which individuals incorporate information into a decision representation varies dependent upon whether it is hypothesis-consistent or hypothesis-inconsistent. This is particularly relevant in a legal context as in order to produce a judgment or decision, legal decision makers must decide which pieces of information are relevant to their preferred explanation of the case and what information will be filtered out. Background knowledge, order of information presentation, and strength of arguments have been highlighted as important to decision making. However, these elements have not yet been explored together to determine whether there are any interaction effects upon decisions made in the face of hypothesis-inconsistent information. Through the use of fictional murder and robbery scenarios, two experiments were conducted in order to determine the effects of incriminating and non-incriminating evidence on decision making in conditions of varying suspect-related background information and order of evidence presentation. Additionally, each experiment looked at different strengths of hypothesis-inconsistent arguments. In both experiments, the relationship between decision making and order of non-incriminating evidence presentation was different dependent upon background information, however, this relationship also varied between the murder and robbery scenarios. These experiments have added to the literature which suggest that the preconceptions of investigators can bias their evaluation and perception of subsequent information, and that order of evidence presentation impacts subsequent judgments of guilt. Additional research is required to determine whether these findings may generalise to more complex investigative representations.1 online resource (xiii, 104 pages
Studies of braided non-Abelian anyons using anyonic tensor networks
No full textEmpirical thesis.Bibliography: pages 119-128.1. Introduction -- 2. Tensor network states and algorithms -- 3. Theory of anyons -- 4. Anyonic matrix product states with U(1) symmetry -- 5. Implementation of time evolving block decimation algorithm for anyonic systems -- 6. Phase transitions in braided non-Abelian anyonic system -- 7. Single particle dynamics using quantum walks -- 8. Summary and outlook -- Appendices -- References.The content of this thesis can be broadly summarised into two categories: first, I constructed modified numerical algorithms based on tensor networks to simulate systems of anyons in low dimensions, and second, I used those methods to study the topological phases the anyons form when they braid around one another.Anyons are point-like particles which are neither bosons nor fermions. All point-like particles in our three dimensional world are either bosons or fermions and have an exchange factor of +1 and -1 respectively, when a pair of those particles exchange positions. Anyons on the other hand represent new possibilities that are capable of existing only in two dimensions, and have non-trivial exchange factors, which can either be a complex number or even a matrix acting on a space of degenerate states. These unusual particles have some surprising properties. For example, states with anyonic excitations are known be resilient against local perturbations, which simply means that, you may perturb their local environments, and they would still retain their quantum properties - a property exclusive only to anyons. This property has motivated scientists to sometimes call them topological charges. Anyons have motivated many recent developments in science and technology. I mention two of them. Firstly, just as bosons give rise to unique phases of matter such as Bose-Einstein condensates, and fermions allow for degenerate Fermi gases, interacting anyons can form new phases of matter, and it is still a subject of intense research, as we have as yet little understanding of these new forms of matter. Secondly, the topological nature of anyons, i.e. their fault tolerance, make them to be among the leading prospective candidate particles to realise a quantum computer. This inspired a different field of research called topological quantum computation. As important as anyons tend to be, in reality, collective systems of anyons are very challenging to study analytically and numerically, due to the exponential growth of the state space of such systems with the number of particles. It is in fact this exponential growth that makes anyons to be usable for quantum computation.In the past, common numerical techniques used to study quantum many body systems included exact diagonalisation (ED) and Monte Carlo (MC) methods. Tensor network techniques are a more modern approach which have lots of advantages. I will list only two of them: 1) they are able to simulate very large system sizes and even infinite-sized systems which are not possible with ED, and 2) they can treat systems of fermions and anyons which are problematic for MC methods.In the first phase of this thesis, I extended the anyonic tensor network algorithms, by incorporating U(1) symmetry to give a modified ansatz AnyonxU(1) tensor networks, which are capable of simulating anyonic systems at any rational filling fraction. By testing the ansatz with the time evolving block decimation algorithm, I benchmarked these methods by using it to confirm previously known results for simple models, including a one-dimensional chain of itinerant and localised anyons, and a two-leg ladder where anyons hop between sites and use available vacancies to exchange positions with other anyons. I performed test simulations with four different particle types, namely, Fibonacci and Ising anyons, which are non-Abelian anyons, and spinless fermions and hardcore bosons, which can be treated as "simple types" of anyons. I compared the results with known exact results obtained using other methods,and got very good performances with relative error of around e < 10-4 in the ground state energy.After being satisfied with the performance of the numerical algorithms, I then proceeded to the second phase where I used the numerical methods to study some models of non-Abelian anyons that naturally allows for exchange of anyons. I proposed a lattice model of anyons, which I dubbed anyonic Hubbard model, which is a pair of coupled chains of anyons (or simply called anyonic ladder). Each site of the ladder can either host a single anyonic charge, or it can be empty. The anyons are able to move around, interact with one another, and exchange positions with other anyons, where vacancies exist. Exchange of anyons is a non-trivial process which may influence the formation of different kinds of new phases of matter. I studied this model using the two prominent species of anyons: Fibonacci and Ising anyons, and made a number of interesting discoveries about their phase diagrams. I identified new phases of matter arising from the interaction of these anyons and their exchange "braid" statistics.Mode of access: World wide web1 online resource (xxii, 128 pages) diagrams, graph
Molecular mechanisms of neuronal death in glaucoma: development of a gene therapy approach for neuroprotection
No full textEmpirical thesis.Bibliography: pages 207-238.Chapter 1. Introduction -- Chapter 2. Material and methods -- Chapter 3. Protective role of brain derived neurotrophic factor in neuronal cells -- Chapter 4. mechanistic insights into the pharmacological targeting of TrkB receptor -- Chapter 5. Effect of TrkB modulation by PTPN11 gene targeting in SH-SY5Y cells -- Chapter 6. SHP2 upregulation impair inner retinal environment and negatively regulates TrkB receptor activity -- Chapter 7. SHP2 gene therapy is effective in RGC neuroprotection in experimental glaucoma -- Chapter 8. Conclusion and future directions -- References.In glaucoma, loss of retinal ganglion cells (RGCs) and axons leads to blindness; preservation of RGC neurons is therefore a major therapeutic goal. Increasing pressure (intraocular pressure, IOP) is a major risk factor in primary open angle glaucoma (POAG). Therapeutic lowering of IOP has been shown to be protective against glaucoma. However, despite IOP lowering many patients continue to demonstrate progressive glaucomatous neuropathy thus warranting additional intervention strategies. Brain-derived neurotrophic factor (BDNF) and its high affinity receptor tropomyosin receptor kinase B (TrkB) are reported to play important role in preservation of RGCs. In this thesis, I have investigated BDNF-TrkB signaling in neuronal cells and have explored the binding pattern of agonist and antagonist to the neurotrophin receptors. I have also investigated TrkB activity by modulating Shp2 phosphatase (PTPN11) in SH-SY5Y cells, in both healthy rodents and an experimental glaucoma animal model, using viral vector gene therapy. The results show that BDNF regulates the GSK3β activity in RGC-5, PC-12 and animal RGCs. Shp2 modulation regulates TrkB phosphorylation and endoplasmic stress response in SH-SY5Y and in the RGCs of both healthy and experimental glaucoma animal models. Shp2 overexpression in SH-SY5Y cells and animal retina, was associated with TrkB antagonism, reduced neuritogenesis, loss of retinal structural & functional integrity and enhanced ER stress response leading to apoptotic changes. Conversely, Shp2 knock down in an animal model of elevated IOP resulted in protection of the retinal structural and functional integrity. These observations correlated with enhanced TrkB phosphorylation in RGCs in response to genetic knockdown of Shp2 expression in experimental animal glaucoma model. The current findings reinforce the role played by Shp2 in regulating signaling in neuronal cells and highlight that Shp2 dysregulation is detrimental for the inner retina. Based on these observations we propose that selective targeting of Shp2 in RGCs may be a promising therapeutic strategy in glaucoma.Mode of access: World wide web1 online resource (xxi, 238 pages) colour illustration
Investigating first year science students' academic writing development
No full textTheoretical thesis.Bibliography: pages 82-107Chapter 1: Introduction -- Chapter 2: Literature Review -- Chapter 3: Methodology -- Chapter 4: Findings -- Chapter 5: ConclusionThis study investigates academic writing tutors' perceptions of their students' performance and compares it with an analysis of first-year science students' academic writing. Specifically, it examines the challenges tutors perceive students to face when writing in academic contexts and then explores the linguistics resources students choose when writing in a scientific academic context. To achieve this aim, two sets of data were collected: tutor interviews and students' texts. The data from the tutor interviews was analysed to reveal academic writing tutors' perceptions of their students' academic writing abilities and challenges. The students' texts were then analysed to examine how effectively students make meanings valued in scientific contexts. To examine students' texts, Systemic Functional Linguistic analysis is employed; specifically, the study examines the ideational meanings (i.e., experiential and textual meanings) and textual meanings within the texts. The findings reveal that the students of science face some linguistics challenges across both the LexicoGrammar (e.g., under-using more valued specialised and technical entities; overusing less valued logical relations) and the Discourse Semantics (e.g., thematic progression). The data also show that there is some alignment between tutors' perceptions of students' writing development and their actual writing performance (e.g., lack of lexical variation and cohesion across the text). The study concludes with a discussion proposing the most critical areas for instructional intervention to focus to assist students in overcoming these linguistic challenges.1 online resource (vii, 117 pages) illustrations, some colou
Integrating research using animal-borne telemetry with the needs of conservation management
No full text1. Animal-borne telemetry has revolutionized our ability to study animal movement, species physiology, demography and social structures, changing environments and the threats that animals are experiencing. While there will always be a need for basic ecological research and discovery, the current conservation crisis demands we look more pragmatically at the data required to make informed management decisions. 2. Here, we define a framework that distinguishes how research using animal telemetry devices can influence conservation. We then discuss two critical questions which aim to directly connect telemetry-derived data to applied conservation decision-making: (i) Would my choice of action change if I had more data? (ii) Is the expected gain worth the money and time required to collect more data? 3. Policy implications. To answer questions about integrating telemetry-derived data with applied conservation, we suggest the use of value of information analysis to quantitatively assess the return-on-investment of animal telemetry-derived data for conservation decision-making.7 page(s