VictorJuiz/thesis huggingface dataset:
Genome structure in RNA viruses

RNA structures can have important and diverse functions. Influenza A viruses have eight negative sense RNA genome segments. When two influenza virus strains infect the same cell their progeny can package segments from both strains. This process, termed reassortment, can lead to rapid genetic shifts that have previously generated pandemic strains.
In this investigation the RNA-RNA interaction maps for several influenza viruses are generated using a high-throughput sequencing approach. This reveals extensive, redundant networks of RNA-RNA interactions between the genomic viral RNA segments. This analysis includes H1N1 and H3N2 reassortants, where these interactions can explain preferential cosegregation of segments during reassortment. It is also demonstrated, using chemical probing techniques, that there is extensive local RNA structure within the influenza genomic segments. Several structures conserved between the H1N1 and H3N2 viruses are identified, which may provide targets for future functional investigations. The structure of an influenza nucleoprotein, which binds to the influenza genomic RNA, is investigated. The first structure of a H3N2 virus NP is presented which shows high structural conservation with other influenza nucleoproteins.
In contrast to influenza viruses, the Severe Acute Respiratory Syndrome Coronavirus-2 genome is made up of a single positive sense strand of RNA. Sequencing approaches reveal that in virio the genome contains many structures formed mostly through short-range base paring (bases separated by <100 bp). A large number of structures are observed that are conserved amongst other coronaviruses and may provide targets for drug development. Overall, this work reveals the presence of diverse and abundant RNA structures in viruses from two families.

Keywords: RNA
Virology
SARS-CoV-2
Influenza
Advisor: Fodor, E
Bauer, D
Investigating the manufacturability of flexible thin-film device (TEG) using roll-to-roll

This thesis investigates how to large-scale manufacture flexible thin-film electronics using high-throughput/cost-effective roll-to-roll processing. In this case, a flexible/wearable thermoelectric generator is explored which can locally provide a continuous low-power source for a variety of wearable technologies, to be a competitive alternative to the portable (Li-ion) battery-based system (with typical issues of recharging, short lifetime, energy storage limit and replacement cost, etc.). One of the best conventional thermoelectric materials for wearable thermoelectric generators, bismuth telluride, is studied for scale-up in an industrial-scale roll-to-roll web coater. Magnetron sputtering is employed as a promising technique for scale-up because it is stable, controllable, continuous, already widely used in industrial manufacturing, scalable for fabricating high-quality films at moderate throughput speed, easily incorporated into the roll-to-roll process, compatible with fabrication lines (patternable).
Four key challenges are explored to achieve the goal of advanced roll-to-roll manufacture of flexible thermoelectric generators: (1) exploration of using very thin films to balance the fast roll-to-roll web speed and low vacuum-deposition rate; (2) post-deposition radiation treatments to improve thermoelectric performance and use of interlayers to improve mechanical resilience; (3) replacing a solid shadow mask by other approaches (compatible with roll-to-roll), to make in-line patterns; (4) exploring the preferred architecture of flexible thermoelectric generators suitable for both wearable applications and roll-to-roll.
Correspondingly, (1) a thinner bismuth telluride film is found to possess a greater thermoelectric performance which also satisfies a high deposition throughput; (2) two feasible post-deposition annealing means to be compatible with high-throughput roll-to-roll processes are studied, besides, two types of substrate-to-coating interlayers are proposed to improve the mechanical resilience of flexible thermoelectric films; (3) a selective metallisation technique is explored to pattern flexible thermoelectric generators; (4) the dimension of the thermoelectric strip and cheap/high-performance contact materials are studied, most interestingly a novel stacked design is invented for flexible thermoelectric generators.
These studies give a significant boost to the commercialisation of flexible thin-film electronics, to fulfil the increasing demand for flexible electronics in the upcoming era of the Internet of Things and Artificial Intelligence.

Advisor: Assender, H
Language is connection: The attitudes of education staff in Kununurra, Western Australia towards Indigenous languages and multilingualism

An exploratory, mixed-methods case study comprising of an online survey and semi-structured interviews was conducted with staff from schools and preschools in a remote town in Western Australia regarding attitudes towards multilingualism, traditional and modern Indigenous languages, the local Miriwoong language program, and the training which teachers receive in these areas. The small sample size was a limitation to generalisability of survey results, however it was clear that the attitude of education staff was generally positive. Qualitative interview responses gave rise to a framework of language as connection: to land and people, for both practical communication and the facilitation of respect, for Indigenous and non-Indigenous people, and resulting in a variety of desirable outcomes. These results can be linked to current issues in language policy and multilingual pedagogy.

Keywords: ALSLA
Teacher atitudes
Multilingualism
Reconciliation
Exploratory
Case study
Decolonising methodology
English as an additional language
Online survey
Kriol
Connection
Australia
Language revitalisation
Langauge revival
Yearning methodology
Miriwoong
Heritage
Qualtrics
ALSLA2021
Indigneous
English as an additional language or dialect
Semi-structured interview
Language atitudes
Mixed methods research
Aboriginal language
Country
Culture
Advisor: Murphy, V
Cancer screening programmes for refugees in Canadian primary care: A realist review

Hundreds of thousands of people are diagnosed with cancer in Canada every year; an effective way to diagnose and treat cancers earlier and to improve mortality is to carry out organised cancer screening programmes in primary care. Canada accepts approximately 25,000 refugees annually, and refugees often carry a higher risk for cancer. While Canadian physicians have committed to a vision of equitable and accessible primary care, encompassed in the vision of a Patient’s Medical Home, Canada also has a complex network of health systems, each of which have different ways to approach cervical, breast, and colorectal cancer screening. This dissertation asks: why don’t refugees in Canada participate in these cancer screening programmes? To answer this question, a realist review was undertaken to dissect the contexts, mechanisms, and outcome configurations (CMOCs) presented in the literature. A realist review comprises a literature search, construction of initial programme theory, extracting data from literature to test the initial theory, and iteratively searching, testing, and synthesising evidence. There were very few primary sources to consult regarding the specific topic of refugees and cancer screening in Canada. However, from this small body of work, it was possible to find a number of CMOCs from which to provide an explanation of why refugees do and don’t access primary care cancer screening programmes, and to point toward future research topics. Health system complexity, language and culture differences, and difficulties creating a strong relationship with a primary care provider cause a lack of understanding of the importance and immediacy of screening. However, there are models of care as demonstrated in refugee-friendly clinics in Canada that can mitigate some of the barriers refugees face to participating in cancer screening. It is clear that additional research is required to ensure that refugees in Canada are cared for appropriately and equitably through reducing cancer mortality.

Keywords: primary care
refugees
health equity
realist review
Canada
cancer screening
Advisor: Wong, G
The role of prediction error in linguistic generalization and item learning: evidence from an online eye-tracking study

The discriminative learning framework, grounded in principles of learning theory, was recently revitalized as a specific mechanism to carry out language acquisition within a domain-general, input-driven constructivist account. It specifies that language learning, rather than being guided by an innate linguistic system like Universal Grammar, could be constrained by obtaining negative evidence using prediction errors. Previous studies have tried to indirectly show the effect of prediction making on word-referent mapping by comparing the learning performance of two groups of learners who experienced language input with different input order conditions, where only one condition allowed cue competition. The current study applied eye tracking to the learning process and demonstrated direct evidence for the predictive behaviors during discriminative learning. Two learning experiments with a learning phase where cues predicted visual linguistic outcomes (labels) were conducted. Experiment 1 was a replication of an earlier word learning study – with eye tracking added – and showed that participants made predictive saccades towards positions of labels before they appeared for both high and low frequency conditions. Experiment 2 used a new cross-situational learning paradigm and did not demonstrate default fixations. Offline results showed weaker learning than previous studies and did not show above-chance accuracy for the low frequency trials. However, plot analysis of the individual variation for low frequency trials suggested that participants who failed to learn low frequency cues could have been persistently overgeneralizing in training. This overgeneralization pattern is discussed in the context of adult L2 learning.

Keywords: Word learning
Quantitative learning
ALSLA
Discriminative learning
Psycholinguistics
ALSLA2021
Learning theory
Eye tracking
Advisor: Wonnacott, E
Eva, V
Landscape memory in Arcadia

This thesis examines the topographical relationship between religious sites and sanctuaries in rural areas of Arcadia following the bronze-age collapse, and their associated mythology, to ascertain if there is any possible evidence of why population settlement in the later geometric, archaic, and classical periods favoured more urban settlement away from the rural places mentioned in the mythology of Arcadia. It relies on the assumption commonly made that since ritual practice was of paramount importance for the Greeks, that sanctuaries in rural Arcadia must have a connection to the mythology of such characters as Herakles and Artemis, as these were among the characters of mythology written about in Classical period plays; and in descriptions of the landscape by ancient writers such as Pausanias.
But settlement in the countryside was after a time changed compared to the various poleis (Cities) that began construction from the geometric period onwards through the archaic and classical. Is there evidence to be found of a change in the landscape at some point in the past that meant certain groups of people had to move away from rural areas substituting the rural gods for the polis’s protector gods, and leaving behind the traditional sites of worship and ritual memory? A natural cause perhaps such as prolonged drought, or through invasion or collapse of a dominant power? Or is the particularly Greek system of synoecism the root cause?
Crucial to unravelling the nexus of mythology, and to come to any conclusions about its relation to the everyday lives of people and how people related to the landscapes they lived in, requires careful and considered evaluation of the writings of ancient writers such as Polybius and Pausanias.
This paper aims to consider why then, in a landscape so woven with mythology and sanctuaries, did the relationship between polis settlement and rural sanctuaries become different over time? Why did the places of rural myth, and its associated religious and ritual practice, take on different meanings from where people chose to live in the geometric period onwards?

Keywords: Arcadian landscapes: Purpose of Sanctuaries. The religious topography of Arcadia, and the memory of the past use of landscapes.
Advisor: Griffiths, D
Investigating the relationship between empirical evidence and teacher practice in the use of songs in early years settings and primary school education in the UK.

Songs are a ubiquitous feature of early education, with recent surveys reporting that teachers use songs every day or often in UK and international primary school settings. However, there is little rigorously-gathered empirical evidence of songs’ pedagogical benefits. The stark mismatch between carefully-controlled research and teacher intuition lead to this mixed-methods investigation into how UK early years and primary teachers use songs. An online questionnaire (n=103 participants) explored teachers' self-reported purposes for using songs and planning behaviours. This was followed up by seven semi-structured interviews to explore teacher practice and thought processes regarding songs’ educational value more deeply. In particular, how song use varies across age groups taught within early years and primary school, teachers’ attitudes towards singing as a pedagogical tool, and their belief in songs’ educational value were investigated quantitatively through the questionnaire and qualitatively through the interview phases. Participants also suggested research they would like to see regarding song use in education. The discussion brings together research literature and teacher practice (as evidenced by participants’ self-report in this study) and suggests future research directions that might guide pedagogy.
This study’s findings indicate that teachers use songs less frequently after KS1, and less for behaviour or social purposes than for teaching content as children grow older. Despite scant research evidence, respondents report strong beliefs in the pedagogical effectiveness of songs. Key areas emerging for future research were songs’ effectiveness as mnemonics and for vocabulary acquisition. This study provides evidence that future transdisciplinary research into songs’ educational value needs to be rigorously controlled and more widely (and reliably) disseminated to practitioners.

Keywords: Young learners
ESL
Language teaching
MFL
Early years
Mixed methods research
Music
Songs
EFL
pedagogy
ALSLA
ALSLA2021
Primary education
Advisor: Murphy, V
Stochastic PDEs and weakly interacting particle systems

We study two problems relating to weakly interacting particle systems in the presence of exogenous noise. Part I presents a pathwise regularisation by noise result for McKean–Vlasov equations with singular interaction kernels. Using ideas from the theory of averaged fields and non-linear Young integrals we obtain well-posedness of the McKean–Vlasov systems, particle approximations and mean field convergence.
In Part II we study a family of semi-linear, convection-diffusion SPDEs that are closely related to PDEs coming from the theory of collision-less kinetics. We study these equations in the presence of additive spacetime white noise. In one dimension we show global well-posedness and exponential ergodicity for an equation with a cubic non-linearity and repulsive sign choice. In two dimensions we show local well-posedness for a renormalised equation.

Keywords: ergodic theory
interacting particle systems
stochastic partial differential equations
stochastic analysis
renormalisation
regularisation by noise
Advisor: Hambly, B
Chevyrev, I
Cranberry extract for symptoms of acute, uncomplicated urinary tract infection

Background
There is growing interest in using non-antibiotic treatments for common bacterial infections, such as Urinary Tract Infections (UTI). One potential non-antibiotic treatment for acute uncomplicated UTI is cranberry extract.
Methods
The existing evidence for using cranberry extract to treat acute, uncomplicated UTIs was systematically reviewed. An open-label, randomised feasibility trial was conducted to determine the feasibility of trialling cranberry extract as a treatment for symptoms of acute, uncomplicated UTI in primary care. Adult women with acute UTI symptoms were randomly assigned to one of three groups: 1) Immediate antibiotic prescription (controls) 2) Immediate antibiotic prescription and immediate cranberry capsules 3) Immediate cranberry capsules and a delayed antibiotic prescription. Two qualitative studies were embedded within the feasibility trial: The first was conducted with UTI patients (both participants and non-participants of the feasibility trial); and the second was conducted with feasibility trial recruiters.
Results
The systematic review found that the evidence base for or against using cranberry extract for treating acute UTIs was limited. Four General Practices (100% of target) recruited to the feasibility trial, with nine participants recruited per month on average. Forty-six participants were recruited (one beyond target). 89.1% (41/46) of electronic symptom diaries contained some participant entered data, and 69.6% (32/46) were fully completed. Interviewed UTI patients (n=26) and recruiters (n=8) felt that the feasibility trial addressed an important question, and generally found trial processes straightforward. Many UTI patients indicated that they would be happy to delay antibiotic treatment and try initial symptomatic treatment, such as cranberry extract, for acute UTI symptoms in certain circumstances (e.g. with milder symptoms).
Conclusions
The safety and effectiveness of using cranberry extract as a treatment for acute, uncomplicated UTIs represents an evidence gap. The present research programme demonstrates that it is feasible and acceptable to UTI patients to trial cranberry extract for managing symptoms of acute, uncomplicated UTIs. Having established the feasibility of this approach, an adequately powered efficacy trial of cranberry extract for acute UTI is indicated.

Keywords: urinary tract infection
vaccinium macrocarpon
primary health care
family practice
systematic review
qualitative research
clinical trial
Advisor: Butler, C
Heneghan, C
Boylan, A
Tonkin-Crine, S
Vietglish: translanguaging in Vietnamese and English

This dissertation investigates the translanguaging patterns of five Vietnamese-American individuals residing in the state of California, focusing on the attitudes, motivations, and insights of these participants on their use of Vietnamese as a heritage language. Since the beginning of large-scale immigration from Vietnam to the United States following the sociopolitical events of the 1970s, overseas Vietnamese communities have had extensive contact with the language and culture of the new host countries to which they had emigrated. This study specifically investigates the translanguaging practice of combining Vietnamese and English within conversations and utterances for daily, vernacular use, informally dubbed “Vietglish”.
In the first phase of the research project, natural-speech audio files were extracted by five participants through hands-off recordings of conversations in the home. These recordings were transcribed and analyzed for meaning and translanguaging occurrences. In the second phase of the research project, participants were remotely interviewed using discourse-based interview questions as well as stimulated recall measures. These interviews were also transcribed, and the transcripts were analyzed for instances of translanguaging and dynamic language use across Vietnamese and English based on content as well as form.
The findings suggest that these five inhabitants of Orange County, CA, U.S.A. are highly motivated to maintain the use of Vietnamese and English in their community and families. These participants also monitor and regulate their language use in order to convey respect and deference to both their immediate superiors or elders, as well as to express respect and emotional ties to abstract concepts and events. While participants varyingly reported negative emotions about the use of Vietglish, all interviewees indicated that they use Vietglish daily, nearly everyday, or otherwise regularly.

Keywords: qualitative research
transcription
discourse analysis
translanguaging
ALSLA
interviews
sociolinguistics
Vietnamese
Viet Kieu
ALSLA2021
Vietglish
conversation analysis
immigrant speech practices
code-switching
bilingualism
remote data collection
multilingualism
stimualted recall
Advisor: Rose, H
Sleep-control circuits in Drosophila melanogaster

Sleep is conserved across the animal kingdom, and it is essential for cognitive and physical wellbeing. Therefore, understanding the biological basis underlying sleep homeostasis is of critical importance. In Drosophila melanogaster, a small number of neurons with projections to the dorsal fan-shaped body (dFB) in the brain function as a homeostatic switch that controls sleep according to sleep need. During wake, these neurons are in an electrically silent (OFF) state and, as sleep pressure builds up, they switch to an electrically excitable (ON) state, promoting sleep. Dopamine signalling into the dFB neurons controls the switch from the ON to the OFF state, waking flies up. However, the relevant dopaminergic neurons that convey the arousal-promoting signals to the dFB are unknown, and so are the mechanisms and rules that govern their activity. In this study, I have identified and gained genetic access to a restricted subset of wake-promoting dopaminergic neurons with projections to the dFB. The accumulation of mitochondrial reactive oxygen species (ROS) increases the excitability of the dFB neurons and promotes sleep through the modulation of the plasma membrane Shaker channel β-subunit, Hyperkinetic. Here, I hypothesised that lipid peroxidation by-products link mitochondrial ROS to the modulation of Hyperkinetic. Accordingly, supplementing Drosophila’s diet with lipid peroxidation- resistant D-PUFAs resulted in a decrease in sleep. In addition, I evaluated the influence of ROS in tissues other than the dFB neurons in promoting sleep. Using an innovative inducible ROS-generating chemogenetic system based on the D-amino acid oxidase enzyme, I observed that inducing ROS in gut enterocytes (MyO1A-GAL4 cells) increases sleep. Interestingly, I also found that dietary composition significantly altered sleep amount, further highlighting the gut as a potential target where diet, ROS, and sleep may intersect.

Keywords: sleep
lipid peroxidation
dopamine neurons
drosophila
gut
reactive oxygen species
Advisor: Miesenboeck, G