VictorJuiz/thesis huggingface dataset:
Characterisation of ultrashort pulses
Keywords: Metrology
Ultrafast
Optics

The main topic of this thesis is the development of new characterization techniques for Ultrashort pulses with particular focus on pulses with complex spectra, often obtained with light pulse synthesisers. More in detail, I have addressed the longstanding problem of retrieving the spectral phase of a pulse which exhibits a spectral gap, i.e. a spectral null larger than any of the spectral features of the pulse. The major challenge in this scenario is attaining a reliable reconstruction of the relative spectral phase between the spectral components. I discuss the different approaches that I have employed in order to achieve this objective.
The first result has been the realisation of a low-power XFROG for the charac- terisation of a coherent pulse synthesis source developed by Prof. D. Reid’s group at Heriot-Watt University. We used it to characterise, compress, and synchronise the individual components of the source, however the relative phase remained elusive. In order to solve this problem, a radically new characterisation technique needed to be implemented. This consisted in the development of a new algorithm (MICE), which enabled the mutual characterisation of multiple fields, and in a new experimental implementation of the well-known SPIDER technique (SPICE). Both the algorithm and the new technique have been tested experimentally in a proof-of-principle experiment which constitutes the main result of this work. The appeal of these solutions for mastering light synthesisers will likely stimulate further refinements towards making it the standard technique for complex spectra.
Dynamics of Shigella intracellular replication and plasmid maintenance
Keywords: Shigella flexneri

Shigella spp. are human specific bacterial pathogens that are an important cause of diarrhoeal disease worldwide. Shigella flexneri can invade into epithelial cells, and survive within the intracellular compartment. Escape from the vacuole and replication in the host cell cytosol are critical for S. flexneri virulence. However, little is known about the basis of bacterial replication inside host cells. There are significant limitations with current methods to study intracellular replication, so fluorescence dilution, which has been developed for studying intracellular salmonellosis was applied to understand the dynamics of S. flexneri survival at a single cell level. Limitations of fluorescence dilution became apparent when it was used to examine interactions of bacteria with non-phagocytic cells.
All species of Shigella express a Type III secretion system (T3SS) which is essential for virulence and encoded on a pathogenicity island (PAI). The T3SS PAI is located on a large > 210 kb virulence plasmid, pINV, which is present as single copy in the bacterium. S. flexneri loses pINV during growth in the laboratory, but the mechanisms governing its maintenance are largely unaffected by environmental conditions except the ambient temperature. Shigella sonnei is increasingly becoming an emerging pathogen, which loses pINV at a higher rate than S. flexneri. Toxin-antitoxin systems on S. flexneri and S. sonnei contribute to the vertical transmission of pINV in Shigella populations by mediating post-segregational killing (PSK).
Single nucleotide polymorphisms in the Toxin-Antitoxin (TA) system, VapBC, from S. sonnei and S. flexneri have a profound effect on plasmid retention. Additionally, I demonstrated that the genetic background influences the ability of TA systems to mediate PSK and therefore plasmid maintenance. This is due to the different profiles of the target of VapC, tRNAfMet, in Shigella spp. and E. coli. Subtle differences in plasmid maintenance systems and the targets of TA systems can have profound effects on plasmid biology.
The influence of implementing classroom displays on student learning in mathematics
Keywords: MLT
MLT2018
Mathematics

Classroom displays are common place in primary school and even in secondary school however, there is little research to suggest the influence that classroom displays can have on students in further education settings such as a large mainstream college. This study aims to explore and contribute to this gap in literature regarding classroom displays for students aged 16+. Focusing on my own classroom practice, this study endeavours to assess the influence that introducing and implementing student-led classroom displays can have on student learning experiences such as motivation, confidence and mindset. This study attempts to answer the following research questions:
• How has student motivation and confidence in the mathematics classroom changed with the implementation of displays?
• How has student mindset changed with the implementation of displays?
• Does giving students a voice in the creation of classroom displays promote or contribute to positive learning experiences?
Questionnaires were completed before and after the implementation of the new classroom displays by 28 students and semi-structured interviews were also carried out with two students and one Education Support Worker. Findings suggest that implementing student-led and well planned displays can have a positive influence on student motivation, confidence and mindset. As a result of implementing new classroom displays, there was an overall shift of 89% from negative to positive opinions of maths. Furthermore, there was a 75% increase in students ‘liking’ or ‘loving’ maths. Significantly, pre intervention 11% of students thought the displays aided their learning compared to 96% post intervention, indicating a massive 85% change towards positive opinions.
Cheap box-ticking or effective CPD? An assessment of in-school teacher-led research as a school-wide professional development plan.
Keywords: MLT2018
CPD
MLT

There is a current rise of in-school teacher-led research taking place in English Secondary Schools. This is driven by a need to engage teachers in compelling and relevant continuing professional development at low expense; and it is under-pinned by academic literature identifying research engagement as a significant influencing factor in school improvement.
This paper sets out to assess teachers’ perceptions of in-school teacher-led research as part of the continuing professional development offering at a comprehensive school. The research evaluated the delivery of continuing professional development sessions designed to engage teachers with academic literature and partake in evidence-based practice through the implementation of action research cycles. This research utilises a mixed-methods approach within a small-scale evaluative framework.
This paper finds that although teachers have a desire the be engaged with academic literature a key barrier to this was time and space to do so. The continuing professional development innovation was effective in that it facilitated teachers’ exposure to small digestible chunks of academic literature delivered through the INSET sessions. As a consequence of these sessions, teachers were keen to implement evidence-based practice within their classrooms, and effectively reflected on these actions. This engendered a culture of collaboration and reflection within the school. However, teachers failed to effectively implement fully circular action-research cycles with time and other teaching priorities identified as barriers to engagement.
Contested pasts: improving sixth form students’ understanding of historical interpretations
Keywords: MLT2018
MLT

The study of historical interpretations is a statutory requirement but is also important in and of itself: history can only be understood with recognition that the past is contested and that interpretations are formed through the activities of the disciplinary community. Moreover, as McAleavy (2002) has argued, through studying historical interpretations, students can grasp that there are ‘no monopolies on the truth’ - a crucial appreciation for an informed citizen.
This action research project aimed to discover how an introductory taught course, supplemented by supported independent study, could improve students’ understanding of historical interpretations in the context of their A-level coursework. Student interviews and questionnaires provided baseline data, which was reviewed, with the findings used to plan the introductory lessons. These focused particularly on increasing pupil awareness of the methodology of historians and the conventions of the disciplinary community they work within. Qualitative data, such as audio transcripts and pupil work, was collected and analysed during this period. Following the completion of these lessons, a further review demonstrated that whilst pupils had advanced in their understanding, further intervention was required to better equip them with the skills necessary to pursue independent evaluation of historical interpretations, and so a second action research cycle ensued. Pupils then undertook a period of supported independent study to produce their final assignment. Collaboration with colleagues was crucial to the success of the project, particularly during the planning stages, and in communication regarding pupil progress during their independent research and writing.
The findings demonstrate that pupils progressed in their understandings of how and why interpretations differ, although some unevenness is evident in the progress achieved between individual students. Focusing on the methodology and disciplinary constraints historians work under helped pupils to move away from simple subjectivist views of academic history, and gave them a deeper understanding of the discipline which they were able to communicate in their final essays. Ultimately, the process of researching and writing academic history needs to be made more transparent to pupils, and a greater focus on meaningful interpretations work should be included throughout Key Stage 3 and 4 in preparation for the demands of A-Level.
Cultural spaces and learning identities: can engagement with museums and galleries change how sixth form students view learning?
Keywords: MLT2018
MLT

This paper builds on and contributes to work in the field of museums and galleries in Education. Although a number of studies within the past thirty years have examined the relationship between these spaces and learning, there has not been a strong focus on sixth form students and the role these spaces can have for them, and their subjectivity of themselves as learners. As such, this study provides additional insights into how engagement with museums and galleries can influence how sixth form students perceive both learning, and themselves as learners. Doing so, I explore students’ experiences of visiting three cultural spaces - a combination of two museums and one gallery. This research differs from previous studies in that its preoccupation with sixth form students in this area has not been looked at previously, and through the gathering of qualitative data in an area of Education that is heavily quantitative. Moreover, in doing this it draws strongly on the work of poststructuralist thinkers: Bourdieu, Foucault and Lefebvre in bringing to light the discourses of power which (de)construct identity and subjectivities of self, as a response to experiencing museums and galleries. I argue that engaging with these spaces can impact on how students perceive learning and thus, themselves as learners.
Enantioselective synthesis of non-biaryl atropisomers
Keywords: atropisomer
phase-transfer catalysis
counterion
axial chirality
enantioselective

This thesis describes the development of novel methods to synthesise non-biaryl atropisomers enantioselectively. In Chapter 1, atropisomerism is defined and explored, with a focus on non-biaryl atropisomers and the literature stereoselective syntheses of chiral naphthamides. Chapter 2 discusses initial attempts to synthesise chiral naphthamides using phase-transfer catalysis, and the barriers to rotation of intermediate enol ethers, and benzylated and debenzylated naphthols are determined. Chapter 3 concerns investigations into the low barriers to rotation of these debenzylated naphthols. Chapter 4 builds on this work to develop an enantioselective synthesis of benzylated naphthamides via a dynamic kinetic resolution of the naphthol starting material. This reaction was tested on a wide variety of substrates to determine its scope and limitations, and the barriers to rotation of the chiral products were calculated.
Investigating the genetic basis of sleep using forward genetics
Keywords: Neurosciences
Mouse mutant
Sleep
Forward genetics

The alternation between waking and sleep is regulated by the internal circadian clock and sleep-wake history, and is also influenced by the external environment. Although our understanding of the circadian aspect of sleep regulation has increased, the mechanisms underlying sleep homeostasis are still largely unknown. Independent of the circadian clock, only a limited number of genes have been associated with specific sleep-wake properties. Forward genetics provides an unbiased approach, which seeks to identify genes involved in specific biological processes. This project has focused on the Sleepy6 mouse line which was obtained via a forward genetics sleep screen. This model has a mutation in synaptobrevin 2, which results in a decreased sleep duration. We aimed to further characterise the sleep phenotype of this line, at a molecular and behavioural level, to gain novel insights into the regulation of sleep. Using molecular techniques to evaluate neurotransmitter levels and gene expression, we found no significant differences in the neurotransmitter pathways investigated. Behavioural assays highlighted hyperactivity, with a mild learning deficit. Electrophysiology recordings from the motor (M1) and visual (V1) cortical areas revealed that Sleepy6 homozygous mice have reduced amounts of rapid-eye movement sleep (REMS) and a strong decrease in the amplitude of electroencephalography (EEG) and local field potential (LFP) signals, especially during non-REMS when traces are reminiscent of the burst suppression patterns often observed during anaesthesia, rather than natural sleep. At a local level, neuronal firing in Sleepy6 homozygotes ceased for seconds at a time during non-REMS, coinciding with very low-amplitude EEG and LFP traces. Sleepy6 homozygous mice also displayed a longer latency to switch between vigilance states. Finally, the successful adaption of an elaborated version of the “two-process” model of sleep regulation to recordings performed in mice suggests that sleep pressure decreases at a slower rate in Sleepy6 homozygotes. This result should be interpreted in light of the above findings, as the model relies on power in the slow-wave (0.5-4 Hz) range during non-REMS, which is affected by the very low-amplitude oscillations observed in this state in Sleepy6 homozygotes. This combination of in vivo and computational work using the Sleepy6 line provides new insights into the mechanisms that underlie sleep architecture and the alternation between vigilance states. It also has the potential to further our understanding of the mechanisms underpinning the generation of slow-waves and anaesthesia.
Genesis of natural fracture systems in mudrocks (Upper Cretaceous-Eocene), Jordan
Keywords: Geochemistry
Unconventional
Jordan
Mudrocks
Natural Fractures
Oil Shale

Organic-rich mudrocks are of great importance to the petroleum industry, potentially acting as source rocks, cap rocks or unconventional reservoirs. The analysis of natural fractures in mudrocks is crucial for the evaluation of their impact on fluid storage and flow. This research focuses on the investigation of natural fractures in organic-rich mudrocks, using integrated core, borehole image, field, petrographic, and geochemical techniques. The aim is to obtain a better understanding of the development of natural fracture systems in mudrocks, regarding their stratigraphic distribution, timing and formation mechanism. Natural fractures are abundant in the Upper Cretaceous-Eocene Belqa Group of Jordan. Distribution analyses of fractures resulted in an informal division of the stratigraphic section into three units; upper and lower highly fractured units and a middle weakly fractured unit. The host lithology represents an important factor influencing fracture distribution and formation; calcite-filled veins were observed in calcareous mudstone and carbonate intervals, and silica-filled veins were observed in chert intervals. Bitumen is present within natural fractures, either as macroscopic deposits, or as inclusions in the fracture cement, suggesting that hydrocarbons were present throughout and after the opening of fractures. Fractures are commonly associated with concretions in the Upper Cretaceous strata, implying that fracturing is sensitive to diagenesis. Open fractures in the succession are often confined to specific beds minimizing the potential leakage risk due to the high fracture intensities within the upper and lower caps which can be posed where fracture networks are connected. Mechanical stratigraphic controls on fracture distribution, relationship to compaction and early cementation, as well as the presence of bitumen within fractures, suggest that fracturing was affected by different processes and has different timings. Fracture formation mechanisms can be summarized as fluid pressuring (bedding-parallel veins), early diagenesis (folded calcite veins and silica veins) and late tectonic processes (planar calcite veins and joints, and gypsum veins). Petrographic and geochemical analyses show that fractures have developed at two main stages; (1) early diagenesis (calcite veins, ~40-30 Ma, were folded by sediment compaction), followed by fracturing during burial diagenesis, and (2) late fractures (~25-20 Ma) formed during uplift and extension, or fault reactivations.
Search for a low-energy excess of electron neutrinos in MicroBooNE
Keywords: microboone
oscillations
neutrino
sterile neutrino

The Micro Booster Neutrino Experiment (MicroBooNE) is a Liquid Argon Time Projection Chamber (LArTPC) designed for short-baseline neutrino physics at the Fermi National Accelerator Laboratory. The main physics goal of MicroBooNE is to address the low-energy excess of electron-like events observed by the MiniBooNE experiment and, if confirmed, clarify its nature. The MiniBooNE experiment is a Cherenkov detector and this technology does not allow to distinguish between electrons and single photons in the final state. LArTPC detectors, instead, offer excellent granularity and powerful separation between electrons and photons. For this reason, they represent an ideal technology for the detection of electron neutrino interactions. This thesis presents the first fully-automated electron neutrino selection in a LArTPC. The selection looks for charged-current electron neutrino interactions with no pions and at least one proton in the final state. It is applied on a sub-sample of the data acquired by the detector in the Booster Neutrino Beam, corresponding to 4.34 x 1019 protons-on-target. A validation of the analysis is performed on two orthogonal side-bands, enriched with neutral-current and charged-current muon neutrino interactions, respectively. The uncertainties on the neutrino cross sections, flux, and detector simulation are evaluated. The MicroBooNE detector is placed off-axis with the Neutrinos at the Main Injector (NuMI) beam. An independent dataset of events acquired by triggering on the NuMI beam is employed to measure the significance of the detection of electron neutrinos in the beam using the selection presented here. The sensitivity of the MicroBooNE experiment to the MiniBooNE low-energy excess of electron-like events is evaluated. The efficiency and background-rejection power necessary to achieve 5σ sensitivity are also quantified.
Gene expression and regulation in the yeast metabolic cycle
Keywords: Metabolism
mRNA degradation
Protein turnover
S. cerevisiae
YMC
Translation
cell cycle
ultradian rhythm
UGRR
circadian rhythm
Gene Expression
Yeast Metabolic Cycle

Biological oscillations such as the circadian rhythm are central to physiology of organisms ranging from humans to bacteria. By coupling cellular processes to a periodic oscillator or "clock", cells can pro-actively coordinate their behaviour with periodic changes in their environment such as cycles of the Earth and the Moon. Defects in these processes can lead to diseases ranging from diabetes to cancer and improving these processes has the potential to enhance yields from crops and bioreactors. As such, a thorough understanding of the mechanisms underlying biological rhythms is critical for medical, agricultural and industrial applications.
The yeast metabolic cycle is a model ultradian rhythm that can be induced in prototrophic S. cerevisiae cells under nutrient-limiting conditions. However, very little is known about either the role of post-transcriptional gene-regulation in maintenance of metabolic cycling or the extent to which protein levels cycle. In order to better understand these processes, this study examines the effects of disruption of RNA degradation pathways on transcript cycling and uses polysome profiling, RiboSeq & proteomics to assess the impact of cycling transcripts on the proteome of the yeast metabolic cycle. We find that low rates of protein turnover effectively suppress transcriptional cycling at the protein level and argue that the role of cycling mRNA levels in the yeast metabolic cycle is to control steady-state rather than dynamic protein levels, coupling gene expression to growth rate and nutrient availability.
'I'm classic now': Byron's engagement with antiquity
Keywords: Byron's  classical translations and compositions
Byron's Latinity

Against the background of current debate within the academy about a less rigid demarcation between British Neoclassical and Romantic writing generally, and about the place of Rome among the Romantics specifically, this thesis examines Byron’s engagement with antiquity.
It reveals Byron as a sophisticated reader and inventive re-imaginer of classical texts and approaches. A significant component of his literary aesthetic was the extensive, and often highly creative, substratum of classical intertextuality in his writings throughout his life. By contrast, his exploitation of ancient texts as formal models fell largely into two periods, with an intense engagement in his apprentice years until 1812 and again in his artistic maturity from 1818, but a comparative hiatus during his ‘Years of Fame’ when he published Childe Harold’s Pilgrimage and the Oriental tales. His instincts in this regard were not academic or antiquarian. The value of the classical to Byron was not primarily to recover the past, but to illuminate the present and to enrich the reading experience.
A key contention of this thesis is that, notwithstanding Byron’s libertarian support of Greek independence from Turkey and a Hellenophilic culture in Britain in the early nineteenth century, his Hellenism—in the sense of being influenced by ancient Greek culture—and his expertise in ancient Greek have in general been over-emphasised. Conversely, the influential role of Latin texts and the Roman world in his self-construction and literary development has been under-appreciated. There is a preponderance of Latin source material in Byron’s classical translations and ‘imitations’, forms largely confined to his early years. Moreover, Roman writers emerge as central to the great works of his maturity in satire, epic and even tragedy, where the thesis argues that the principal classical dramaturgical influences on Byron’s three, professedly Greek, closet dramas of 1820–21—Marino Faliero, Sardanapalus and The Two Foscari—were in fact the tragedies of the contemporaneously unfashionable Roman writer, Seneca.
As revealed by his poetry and letters, what is most striking about Byron’s engagement with classical literature, once he left behind the enforced requirements of school and university, is his predominant Latinity.