VictorJuiz/thesis huggingface dataset:
Compiling VDM-SL to C: A user-directed transformational approach

This work demonstrates a tool for compiling VDM documents to C in a semi-automatic way. The semi-automatic nature of the tool allows a user to guide the compilation process if desired, or leave it to act in a fully automatic way. The flexibility of this approach makes it more attractive to use VDM-SL as part of a formal development process. Complex data-types are refined by the application of data-transformers. Documents are reduced to a kernel of VDM-SL that models the C language, including direct pointer manipulation, then output as C compilation units. Annotations are used to guide the transformation pipeline, including the selection of data-transformers. Additionally, new data-transformers may be defined by the user in the concrete syntax of VDM.
Errors in phased array pulse-wave ultrasound velocity estimation systems

In the first, it was shown that the classical Doppler effect is actually an artifact and, as a result, spectral broadening in pulse-wave ultrasound velocity estimation differs from the classical approach. Using linear phased array pulse-wave Doppler ultrasound transducers, the measured maximum velocity may be in error and lead to incorrect clinical diagnosis. The primary objective of this thesis was to obtain an improved understanding of pulse-wave Doppler ultrasound systems, with the intention of determining the sources of this error and to correct for it. This was realized in a three-phase approach. The second phase consisted of an experimental investigation to determine the factors governing the estimation error for steady and pulsatile flow in a clinically relevant manner (believed to be the first for pulsatile flow). The apparatus included a tissue mimicking phantom, blood mimicking fluid, and transducer angle and position control. To estimate the maximum velocity, a new SNR independent method was developed to calculate the maximum frequency from an ensemble averaged power spectrum. When optimized for a non-steered beam-flow angle of 60°, the accuracy was found to be better than those previously reported in the literature. It was found that the effect of transducer focal depth, infra-transducer, infra-machine, inter-machine (that was tested) and beam-steering (for steered beam-flow angles less than 65°) did not significantly contribute to maximum velocity estimation errors. Instead, the primary contribution was from the dependence of the maximum velocity on the beam-flow angle. The third phase was the development of the first (to the best of our knowledge) phased array pulse wave ultrasound velocity estimation simulator. The receive gate was shown to be crucial in defining how the scattered signal from each scatterer contributes to the gated received signal. 3D sample volume simulations showed that the receive gate primarily determines the axial shape, while the focusing determines the shape in the lateral and elevation directions.
The motif of the hunt in Romantic opera

The hunt played a significant role in eighteenth- and nineteenth-century European society. It had an important pedagogical function for youth and soldiers, it was an activity that occupied the nobility on an almost daily basis, and it provided an opportunity for social interaction and diversion. Furthermore, it was an activity rich in ceremony and laden with protocol, allowing its various procedures, including its distinctive music, to become familiar and easily recognizable. The visual and aural spectacle of the hunt provided writers, visual artists, and composers with a deep source of inspiration, and the hunt appeared as a pervasive motif in painting, literature, and music. This thesis examines how the motif of the hunt was used by composers and librettists to provide meaning and dramatic structure in Romantic opera. Hunters, in the nineteenth century, were expected to demonstrate certain qualities that were understood by contemporary audiences. Thus, when a character appears in opera as a hunter, he is defined by the ways in which he conforms to the stereotype, but also by the ways in which he subverts it. The hunt, through its inherent unpredictability, also establishes a framework for furthering the plot by leading the hunter to a crucial meeting or discovery. Furthermore, the hunt was associated with other spheres of activity, namely amorous pursuit, military prowess, and the realm of the demonic. The hunting motif, therefore, could bring to a dramatic situation any of these associations or connotations, or draw on them to develop an individual's character. Finally, huntsmen formed a group representing normality and, often, the society into which the protagonist is integrated or from which he is isolated. The appearances of huntsmen could thus articulate dramatic structure by establishing the initial narrative situation, by signaling a return, in the narrative, to the state of normality, by providing a foil against which the protagonist's situation is contrasted, and by defining or even bringing about an event leading to narrative closure. An understanding of the cultural and historical implications of the hunt provides unexpected insight into the intention and significance of the works in which the motif appears.
An analysis of the interplay between telomeric factors and DNA repair proteins, in the human ALT pathway and cellular response to genomic double strand breaks

Telomeres are nucleoprotein structures that cap the ends of linear eukaryotic chromosomes and consist of repetitive telomeric DNA (T2AG 3)n as well as telomere specific proteins, such as TRF1 and TRF2. Telomeres escape detection by the DNA double strand break damage response network (DDRN), however they shorten with each successive cell division and activate the DDRN at a critical length, which causes growth arrest. Cellular immortalization requires the activation of a telomere maintenance pathway. The majority of tumors and immortalized cell lines achieve this by expression of telomerase, which adds de novo telomere repeats to the ends of chromosomes. Telomerase-negative immortalized human cells maintain telomeres by alternative lengthening of telomeres (ALT) pathway(s), which may involve homologous recombination. We find that the DNA repair protein, BLM co-localizes with telomeric foci in ALT human cells but not telomerase positive immortal cell lines or primary cells. BLM interacts in vivo with the telomeric protein TRF2 in ALT cells, as detected by FRET and co-immunoprecipitation. Transient over-expression of green fluorescent protein (GFP)-BLM results in marked, ALT cell-specific increases in telomeric DNA. The association of BLM with telomeres and its effect on telomere DNA synthesis require a functional helicase domain. We also find that inhibition of BLM expression by siRNA causes ALT-specific telomere dysfunction, as evidenced by an increase of chromosome end-to-end fusions. Our results identify BLM as the first protein to affect telomeric DNA synthesis exclusively in human ALT cells and suggest that BLM facilitates recombination-driven amplification of telomeres. In addition to describing a role for a DNA repair protein in telomere maintenance, we provide the first demonstration for the involvement of a human telomere-specific protein (TRF2), in the cellular response to genomic DNA double strand breaks (DSBs). TRF2 migrates to sites of genomic DSBs within 2 seconds post-DNA damage and is independent of other known DNA repair proteins. This migration is not dependent on its affinity for telomeric DNA or its myb DNA binding domain, but requires its basic domain. Over-expression of TRF2 attenuates the ATM dependent DNA damage response, which suggests that TRF2 is involved in the initial stages of sensing/processing genomic DSBs.
Seeking the rule of law: constitutions. amnesties and truth commissions in Chile, South Africa and Ghana

Countries in transition may choose to review their past with a truth commission and to frame their future with a constitution. Both truth commissions and constitutions are means to achieve or enhance the rule of law, but the relationship between the two mechanisms can be complicated when amnesty for human rights abusers is part of the transitional justice equation. Amnesties represent a tension in the attempt by transitional justice mechanisms such as truth commissions to achieve the rule of law in a given polity. This thesis explores the interplay between truth commissions and constitutions in Chile, South Africa and Ghana. It reviews the seeming contradiction of upholding a constitutional framework that contains a bar to accountability and suggests that the effect that transitional justice mechanisms have on one another must be taken into account in order to successfully re-entrench the rule of law in emerging democracies.

Keywords: Rule of law
Constitutional law, Chile
Truth commissions, Chile
Constitutional law, South Africa
Truth commissions, South Africa
Constitutional law, Ghana
Truth commissions, Ghana
Evolutionary genomics of Pseudomonas syringae plasmids

Plasmids are accessory DNA molecules that have been shown to enhance the fitness and adaptability of bacterial pathogens. To understand the processes driving plasmid evolution, I utilized a comparative genomics approach to examine the plasmids of the "Group 5" strains of the phytopathogenic bacterium Pseudomonas syringae. The Group 5 strains include three pathogens of Raphanus sativus (radish) and a single pathogen of Coriandrum sativum (cilantro/coriander), providing two host plants and an appropriate phylogenetic structure to assess the evolution of plasmids and their impact on host-specific virulence. To initiate comparative analyses, the five-plasmid complement of the radish pathogen P. syringae pv. maculicola ES4326 was sequenced and analyzed, revealing a predominant role for insertion sequence (IS) elements in driving plasmid evolution. This analysis also led to the identification of a new miniature transposable element that appeared to be predominantly virulence-associated and plasmid localized. I examined the role of IS elements further by comparing the three pPMA4326B-like plasmids from the radish pathogens. This analysis not only reinforced the importance of IS elements in plasmid evolution, but also revealed that this plasmid has undergone gradual deletion of the gene cluster responsible for horizontal transfer. I explored the possibility that this switch to vertical transmission was due to the presence of two virulence-associated type III secreted effectors (T3SEs), which may significantly enhance fitness and maintain the plasmid stably. One of the T3SEs, hopW1-2 confers a significant growth advantage on radish, but reduces the ability of the cilantro pathogen to grow in cilantro, suggesting the pPMA4326B-like plasmid may have once been present in the cilantro lineage but was subsequently lost. Although only one T3SE confers a measurable growth advantage, the two pPMA4326B-borne T3SEs share high sequence identity, suggesting they were derived from the same ancestral sequence. This led to the identification of a new evolutionary process, terminal reassortment, which involves the shuffling of existing T3SEs leading to the formation of gene fusions that results in chimeric T3SEs with new virulence function. As labile genomes, plasmids are sources and sinks for genetic variation, and have the capacity to significantly impact the evolution of their bacterial hosts.
"Corona" for orchestra

'CORONA', a single-movement work for medium-sized orchestra like its namesake, the surface of the sun, renews and re-invigorates itself through the upsurge of new material. The organic growth of foreground thematic material through developmental procedures, although present, is not the primary underpinning of the musical unfolding. Of greater importance to the musical argument is the ongoing process of the narrative constantly moving forward and articulating large-scale symphonic form through the outburst of new material, the process of unfolding providing coherence. There are three primary sections in the piece, marked fast-slow-fast which, on the surface, appear to embody an A B A' structure; however, the proportions of the sections do not reflect the prototypical form, in which the two A sections are generally of the same length. The dimensions of the three major formal divisions can be reduced to a ratio of roughly 1:2:3, corresponding to the quantity of chronological time, and to the number of measures in each section. Major areas in the piece are informed by a sense of harmonic and thematic stability, where the work obstinately insists on musical matter only to discard it in favour of a new and contrasting one. It is in these stable sections that the inverse relationship between foreground and background becomes apparent, as the foreground slows its rate of change and fixates on its thematic content, the background structure telescopes outwards, expanding in time. In between these ephemeral moments of stability lie sudden shifts between combinations of diatonic, hexatonic, octatonic, and chromatic collections. These shifts create a heightened sense of immediacy, of the piece constantly erupting and exploding forward as the music replenishes itself creating dramatic musical contrasts through the abandonment of previous material, while the prolongation of sections through thematic fixation alters the proportions of the overall form, creating a unique structure quite unlike an A B A' form.
Developmental changes in pitch perception: Distinguishing up from down

We examined the pitch-discrimination abilities of musically untrained children and adults. Participants in five age groups (5-, 6-, 8-, and 11-year-olds, and adults) identified the direction of displacement (i.e., up or down) of the second tone in a sequence of three tones. The first and third tones were always identical (440 Hz) but the middle tone was shifted upward or downward in pitch by 4, 2, 1, 0.5, 0.3, 0.1, and 0.05 semitones. Pitch-discrimination accuracy improved from 5 to 8 years of age. There were no further improvements after age 8, which implies that some aspects of pitch perception may be mature by this age. Importantly, we were able to use a pitch-discrimination procedure successfully with very young children, even though the experimental task involved relational concepts. Compared to previous efforts, the present study represents a more ecologically valid examination of the development of pitch perception.
An investigation of the effect of display augmentation with instantaneous movement information on telemanipulation performance under visual-motor mismatch

A review is presented of the well documented difficulties in performing manual control tasks under visual-motor mismatch. In that light, a new display concept is proposed, where additional visual information about a telemanipulated instrument's direction of instantaneous movement is graphically superimposed at the instrument tip's location in a camera image. An experimental platform is developed to evaluate the new display concept in a pointing task, under various camera misalignments and path constraints. Both global and dynamic measures are used to evaluate recorded movement trajectories, including a novel analysis of distributions of bivariate time and space domain parameters. The reported performance decrement is consistent with the literature; however, the global and dynamic measures analyses suggest that the proposed display concept offered no significant improvement over the case of no additional visual information in the experiment reported.
Myc and apoptosis: identifying key regulators and target genes

The myc oncogene is frequently deregulated in a wide-variety and large number of cancers and is a potent activator of both cellular proliferation and apoptosis. As a nuclear transcription factor, Myc is believed to drive these disparate cellular activities through direct regulation of gene expression. However, Myc target genes have been only partially defined and the rate-limiting step downstream of Myc activation along the apoptotic pathway is unclear. Our results indicate that in the presence of apoptotic agonists, Myc regulates an important aspect of Bax activation to induce cytochrome c release from mitochondria, thus potentiating the apoptotic response. However, Myc does not appear to regulate this activity through a direct interaction with Bax. Therefore, the point at which Myc acts to regulate Bax activity must lie further upstream. To identify target genes regulated by Myc during apoptosis that may play a role in Bax activation, we performed cDNA microarray analysis to profile Myc gene regulation in response to two mechanistically distinct apoptotic agonists, taxol and doxorubicin. In contrast to previous studies wherein Myc target gene analysis has been conducted primarily under growth conditions, we conducted our expression analysis under both growth and death conditions to investigate whether different cellular inputs could direct different programs of Myc gene regulation. Our analysis revealed a sustained repression of Myc-repressed target genes that were bound directly by Myc under both growth and apoptotic conditions, where these genes were expressed at high levels in the absence of Myc in response to these same stimuli. Importantly, our data supports a model wherein the repression of any single gene does not constitute the mechanism by which Myc sensitizes cells to undergo apoptosis. Instead, we suggest a more global model wherein Myc repression of a cohort of genes establishes a program of gene regulation that imposes a block to the normal response to cellular stress. The knowledge gained by these studies has contributed to our overall understanding of Myc molecular function and role during apoptosis, and further defines the molecular pathways that can be exploited to harness Myc activity in tumours.
Effects of nocturnal lifestyle on the visual morphology and flight behaviour of nearctic moths

The diverse lifestyle adaptations of Lepidoptera likely arose after the evolution of echolocating, insectivorous bats. I examine the adaptations of two lifestyles that characterize most moths. The first is nocturnality, the degree of which varies between species and families. All Nearctic, nocturnal moths share a second lifestyle of being subject to bat predation. Using estimates of eye surface area, I found that eyesize in moths is positively correlated with degree of nocturnality; a lifestyle adaptation that I believe increases resolution, sensitivity, and field of view. Eyesize is not related to auditory state, suggesting earless moths do not visually detect bats. I found that earless moths fly less than eared moths, suggesting that they have behaviourally adapted to avoid bats. This may limit reproductive success in earless moths, which is supported by a survey of moths from a natural community in which earless moths are larger, less abundant, and less diverse than eared moths.
Mainstreaming indigenous peoples and indigenous knowledges into the public school system: A case study of Tubo Tubo Elementary School in Bataan, Philippines

This study is about a Filipino indigenous tribe called the Aetas and their experience of coping and survival in the public education system that is a product of over four hundred years of colonization of the Philippines. Amidst the loud cry by other indigenous groups in the Philippines for a culture-based education or the recognition and implementation of the indigenous education system, the Aetas in Bataan, oblivious to these efforts, have no other choice but to integrate into the mainstream system of education. In the process, they are faced with various factors that enable or disable their participation, performance and survival in the said system. These factors range from the students themselves, to the teacher, their parents, school and supporters. Culture proved to be an insignificant factor to the Aetas' education, however, the majority of the Filipino IPs think otherwise.

Keywords: Aeta (Philippine people), Education (Elementary)
Aeta (Phillippine people), Science
Aeta (Phillippine people), Attitudes
Ethnoscience, Phillippines
Public schools, Phillippines
Factors that influence front-line managers' perceptions of comparative reports of hospital performance: design and test of a conceptual model

Although efforts to measure hospital performance continue to grow, the extent to which these performance data are perceived to be useful and are actually used remains unclear. Drawing on the feedback literature from organizational behavior, Huberman's (1994) research dissemination model and existing improvement literature, this study involves the design and test of a conceptual model of the factors that influence front-line and mid-level hospital managers' perceptions of usefulness of hospital performance data. Findings indicate that both data characteristics variables including data quality, relevance and report complexity as well as organizational factors including dissemination intensity and improvement culture explain significant amounts of variance in perceptions of usefulness of comparative reports of hospital performance. In addition, improvement culture was found to moderate the relationship between data relevance and perceived usefulness; with a very strong improvement culture, line managers perceive performance reports to be useful even though they may not be perceived as having much relevance. The contribution of this research is to advance knowledge of how to structure performance measurement initiatives in a way that maximizes the likelihood that data can be used to bring about improvements in the processes and outcomes of care. Organizations and those who fund and design performance reports need to recognize that both report characteristics and organizational context play an important role in determining line managers' response to these types of data.