VictorJuiz/thesis huggingface dataset:
The LINPACK Benchmark on a multi-core multi-FPGA system

The LINPACK Benchmark is used to rank the most powerful computers in the world. This thesis is an implementation of the benchmark on a multi-FPGA system to see how the performance compares to the processor-based implementation. TMD-MPI is the MPI implementation used to parallelize the software portion of the algorithm while the TMD-MPE provides the same functionality for the hardware engines. Results show that, when using small sets of data, one FPGA can provide a speedup of 1.94 over a high-end processor running the LINPACK Benchmark with Level 1 BLAS. However, there is still opportunity to do better, especially when scaling to larger systems.
Predictors of axillary node dissection in ductal carcinoma in situ

Background. The incidence of axillary nodal metastases (AND) in DCIS is rare. Since AND may cause significant morbidity, its routine application is not recommended. Results. 727 cases of DCIS have been identified. AND was performed in 123 cases (17%). AND rates have declined from 29% to 16%. AND was associated with Type of breast surgery and year of surgery. There was significant variation in AND rates across Ontario, independent of age and tumour characteristics. Materials Methods. A retrospective study of participants of the OBSP diagnosed with DCIS between 1991--2000 has been conducted. Descriptive statistics were used. Odds ratio estimates (95% CIs) were calculated while adjusting for confounders using logistic regression. Objective. To describe the proportion of patients with DCIS who receive AND and to identify factors associated with AND. Conclusion. The rates of AND have declined over the past decade but remain high with significant variation in AND rates across Ontario.
Chromatin remodeling is implicated in negative regulation of the Caenorhabditis elegans her-1 gene during sex determination

The nematode C. elegans has two sexual fates: hermaphrodites and males. Both sexual fates are governed by a series of genes that fall into a negative regulatory pathway. The male fate is specified by her-1, a gene that produces two male-specific transcripts from two tandem promoters, P1 and P2. Genetic data have identified two sites (loss-of-function (lf) and gain-of-function (gf)) in the P1 promoter that may be regulatory sites for her-1 expression. In order to identify factors involved in the regulation of her-1, two yeast-one-hybrid screens were carried out using the lf and gf sites. The if screen identified F13G3.1, a putative DNA binding protein containing three TFIIIA-type zinc fingers. The gf screen isolated C26C6.5, the worm homologue of p66, a component of the NuRD complex. NuRD is a nucleosome remodeling and histone deacetylase complex, implying that chromatin remodeling may be involved in the negative regulation of her-1.
Understanding how age-related changes in prefrontal function affects episodic retrieval and strategic organization

The goal of the current study was to determine whether age-related decline in temporal order memory performance is due to functional changes in right prefrontal regions related to episodic retrieval processes, or, to functional changes in right prefrontal regions related to post-retrieval strategic organization processes. To achieve this goal, an event-related fMRI study was conducted in which 8 young and 9 elderly subjects were scanned while performing verbal recognition memory (R), temporal order memory (T) and reverse alphabetizing (A) tasks. A difficulty manipulation was also incorporated into the experiment to control for age-related differences in task effort. The behavioral results from this study indicated that older subjects displayed lower accuracy performance during T and difficult versions of the A tasks, compared to young subjects. Within and between group activation analyses were conducted on the fMRI data obtained from both groups. The fMRI results for young subjects indicated that right superior frontal activity was related to episodic retrieval processes since this region was only active during the performances of R and T tasks. Right middle frontal activity was related to strategic organization since it was commonly active during both A and T tasks in young subjects. The within group analysis of the older subjects indicated that the contributions of these right prefrontal regions differed with age. Older subjects engaged right middle and inferior frontal regions exclusively during episodic memory tasks. Right superior frontal (BA I0) activity was not observed in the within group results of older subjects. Older subjects also did not engage any additional right prefrontal regions during the performance of temporal order memory tasks. Instead, they engaged left middle and inferior frontal regions to a greater extent than young subjects across all tasks. Left middle frontal activity was interpreted as reflecting semantic retrieval and/or linguistic manipulation. Left inferior frontal activity was interpreted as reflecting maintenance of verbal information in WM across all tasks. Therefore, the current results suggest that older subjects had a primary deficit in right superior frontal function during EM tasks and consequently compensated by recruiting bilateral middle and inferior frontal regions to perform EM tasks and strategic organization tasks.
Effects of human milk and formula on the transcriptional regulation of cytochrome P450 3A4 in HepG2 cells

Caffeine is eliminated nearly 3-fold faster in formula-fed infants. As cytochrome P450 3A4 (CYP3A4) is a major caffeine metabolizer and as its expression is primarily regulated by the human pregnane X receptor (hPXR), we postulate that formula induces CYP3A4 expression through hPXR activation. The human liver-derived cell line, HepG2, was tested for CYP3A4 mRNA expression after incubation with undigested human milk and formula. A reporter construct containing CYP3A4-PXR binding elements were transfected into HepG2 cells and examined for activation by milk. CYP3A4 mRNA was increased 2--3 fold and reporter activity was mildly induced after all milk treatments. hPXR expression plasmid co-transfection modestly augmented reporter activity only with bovine-based formula. These results suggest that CYP3A4 induction by formula does not account for differences in caffeine elimination between breastfed and formula-fed infants. Furthermore, PXR-mediated regulation most likely does not play a major role in the transcriptional induction of CYP3A4 by milk.
Collagen structure and preferential assembly explored by parallel microscopy and bioinformatics

Although its self-assembly is ubiquitous for most animals and has been extensively studied for decades, collagen remains a rather enigmatic protein. The preferential assembly process of one particular collagen construct, fibrous long spacing collagen formed with added alpha1-acid glycoprotein, is detailed. Stable intermediate structures are resolved by atomic force microscopy, demonstrating for the first time the onset of the periodic surface protrusions separated by 270 nm that are characteristic of this form of collagen. A preliminary fibrillogenesis mechanism is proposed on the basis of this data, but the ongoing problem of the lack of a high-resolution structure for the collagen monomer makes detailed analysis difficult. Therefore, a diversion into bioinformatics styled analyses is presented. In the first analysis, the collagen triple-helix is parameterized using all available high-resolution crystal structure data. This provides a general framework for prediction of any triple-helical peptide structure and is shown using a nonredundant data set to generate a prediction agreeing exceptionally well with the highest resolution structure solved to date. From a preferential assembly standpoint, only the terminal atoms of each residue are important--it is these that modulate supramolecular assembly through either attractive or repulsive interactions. However, the large size ( sim;3150 amino acids) of the collagen monomer makes prediction of all side chain atoms undesirable. Following the success of backbone dependent rotamer libraries, a second statistically derived parameter set is developed. It allows prediction of terminal side-chain atom positions given only a polypeptide backbone. This is validated by comparing numerous predictions to experimental structures for a large set of protein structures, showing excellent potential as a general predictive method for efficiently positioning side-chains. Combining the two parameter sets, any triple-helical structure may be readily predicted. A model of the human type I collagen monomer is introduced and its utility is demonstrated through correlation with atomic force microscopy data. This allows both the interpretation of height data, and the clarification of the preliminary assembly mechanism proposed towards the beginning of the Thesis for fibrous long spacing collagen.
Before the company: English perceptions of India in the sixteenth century

This thesis examines a number of the epistemological frameworks that the inhabitants of England used to comprehend the lands loosely denoted by the term India in the sixteenth century. It argues that in contradistinction to the experience of Europeans in the New World, the intellectual inheritances of both Antiquity and the Middle Ages provided these people with flexible and resilient structures that at once served to stimulate intense interest in the region but also furnished them with a series of overlapping but culturally comprehensible cognitive categories for the assimilation of new particular geographical intelligence. The introduction begins with a broad survey of the most important classical and medieval sources accessible to readers in England in the sixteenth century that treat India in any depth. It then turns to describe the more significant attempts of English adventurers to reach these lands over the course of the century, situating them against developments on the continent. Chapter one is divided into two sections. It begins with a chronological assessment of sixteenth-century texts that treat the subject of India at length before turning to appraise sixteenth-century notions of geography . In so doing, it argues that space was often conceived as heterogeneous with specific places functioning as cognitive categories with predefined characteristics into which empirical observations could be assimilated. Taken together, these categories amount to a metageography for the ordering of spatial intelligence. After a review of the competing modern approaches to the problem of the east in the sixteenth century, chapter three investigates the first of these metageographies, that derived from scripture. It argues that not only did the eastern wealth described by scripture serve as a powerful lure, but contemporary exegetical practice meant that there were powerful theological reasons to maintain much of the fantastic hitherto associated with the region. Chapter four addresses the same issues but from the perspective of natural philosophy and secondary causes. It argues that regions might be construed as subsistent entities with defined characteristics based upon their location relative to the cardinal extremes. As such, those created things proper to India share an array of well-known diagnostic characteristics.
Characterizing the effect of beta1 adrenergic blockade on the physiological responses to hemodilution in rats: Evidence for organ-specific tissue hypoxia

Beta1 blockade in perioperative patients leads to increased cerebral injury by unknown mechanisms. This study assesses the effect of beta1 blockade on the compensatory cardiovascular and neurohormonal responses to acute blood loss and fluid resuscitation (hemodilution) and its impact on vital organ oxygen tension (brain and kidney). Rats were randomized to receive a beta1 blocker or saline before undergoing 50% hemodilution. beta1 blockade significantly blunted the cardiac response but did not alter neurohormonal levels following hemodilution. Hemodiluted rats demonstrated a decrease in renal tissue oxygen tension while cerebral oxygen tension was maintained. In beta1 blocked rats, cerebral tissue oxygen tension was significantly reduced after hemodilution. These results demonstrate that beta1 blockade impaired cerebral oxygen delivery following hemodilution by limiting cardiac output and cerebral blood flow. This data may explain the observed increased stroke rate in beta 1 blocked perioperative patients.
Neural activity in traumatic brain injury: Complexity as a model for disordered awareness

Traumatic Brain Injury (TBI) is characterized initially by loss of consciousness due to distributed damage to neural interconnectivity. Here we examined neural complexity, a measure which has been used to study consciousness and which reflects neural information processing capacity, in TBI. We calculated multiscale entropy (MSE) for magnetoencephalography signal during a feature-integration task and related it to performance in patients and controls. MSE quantifies complexity at varying time scales. Behavioral performance was equivalent between groups. We found lower complexity in medial posterior regions in TBI patients, indicating less ability to integrate information in these areas. For both groups, higher complexity predicted less variability in performance. This relationship was expressed at coarser time scales which may reflect long-range neural communication. The relationship was expressed significantly more in TBI patients and may represent a mechanism of compensation for distributed damage. No relationship was found to speed of performance except in motor areas.
Feasibility study: research efforts to identify and reach portuguese-speaking women who are underscreened for cervical cancer

The value of secondary prevention of cervical cancer by screening with the Pap test is well-recognized, but women at greatest risk for cervical cancer (older, poorer, not speaking an official language) continue to be least well-screened. This study investigated the use of quantitative and qualitative research to identify and reach Portugese-speaking women who are underscreened with respect to cervical cancer. Traditional epidemiologic approaches were seriously constrained, but conceptual synthesis using qualitative approaches provided a resolution. The project was developed, implemented and reviewed, in iterations, with Portuguese-speaking women and those who care for them in Toronto, Ontario. Many approaches to identify and reach underscreened women were considered; two approaches (health events and physicians' offices) were evaluated. Questionnaires, surveys and physicians' logs revealed misclassification of “eligibility for screening”, “interval since last Pap test”, and “intentions regarding Pap tests”. Not all underscreened women identified by their doctors or friends wished to attend health events or have Pap tests. A pilot trial of appointment scheduling (now versus later) and brochure language (Portuguese versus English and Portuguese) showed that randomization, consent forms and follow-up interviews were largely acceptable to participants, but data validation (requested on follow-up) was not. Barriers and facilitators of Pap testing were categorized using the PRECEDE (Predisposing, Reinforcing, and Enabling Constructs in Educational/Environmental Diagnosis and Evaluations) model. A theoretical model integrates elements of others, including the Health Belief Model, and social learning theory. This “Two Streams” model explains perceptions of need and value for Pap testing in the context of the test and understandings (including myths) about cancer and health care. This model explains how age, fear, and lack of symptoms impede screening Pap tests. Time, contact and communication are proposed to develop trusting relationships and understandings about health behaviour and health outcomes. Public health's role in developing and implementing strategies for improving screening to prevent invasive cervical cancer is affirmed. Recommended strategies, which should contribute to social marketing, include: scheduling appointments for prevention counselling, dispelling myths (e.g., Pap tests are for young and sexually active women) with their complements, and developing narrative or dramatic scenarios to model patient-provider interactions.
A study of a voyage: Developing archival descriptive standards in Canada from 1987--1996

This qualitative study investigates the development of archival descriptive standards in Canada and provides a comprehensive narrative of this development as it occurred from January 1987 to February 1996. Through the use of data analysis of primary sources and interviews a story of the development of the Rules for Archival Description (RAD) emerges. The development included many challenges as the Planning Committee on Descriptive Standards (PCDS) and nine working groups drafted and circulated chapters for comment by the archives community. The study's findings explore the process of developing RAD as well as influences on the project; the questioning of foundational principles; the development of relationships; and the rewarding and challenging aspects of the participants' experience. The author argues that that although RAD's development is documented in the literature, it is only documented by members of the PCDS and presents only part of the story, that from the PCDS's perspective.

Keywords: Cataloging of archival materials, History
Cataloging of archival materials, Canada
Descriptive cataloging, History
Descriptive cataloging, Canada
Descriptive cataloging, Planning
Descriptive cataloging, Canada
Pushing the boundaries: Canadian women's experiences in World War II

This thesis contextualizes the use of oral narratives with the academic and popular literature written during World War II and since 1945. The work focuses upon the experiences of various Canadian women during the war. The thesis illustrates how the circumstances of the war provided many women with new found opportunities which were created from the disruption and loosening of numerous social conventions which defined the gender order. Expanded freedom allowed some women to push the boundaries relating to their mobility, their living spaces, and the regulation of their sexuality. The experiences of the interviewees demonstrates the nature of femininity and the structure of gendered and non-gendered roles of women during this period. As well, the interviews illustrate that through the disruption of the gender order shifts were created which allowed some women to make important advancements towards gender equality.

Keywords: World War, 1939-1945, Women
World War, 1939-1945, Canada
Women, Social conditions
Women, Canada
Women's rights, History
Women's rights, Canada
Sex role
Meloxicam and preterm birth

Preterm birth that occurs before 37 weeks gestation, complicates 5-10% of all pregnancies and represents a significant obstetrical challenge which imposes a large burden on the Canadian health care system. 70% of all neonatal deaths and up to 75% of neonatal morbidity is associated with preterm birth (1-8). Various tocolytic drugs have been employed in the treatment of preterm labour. However, currently there is no drug available on the market that can stop preterm labour and improve neonatal outcome. Although effective at blocking labour contractions, most tocolytic drugs were associated with significant maternal and fetal side effects. The purpose of this thesis was to test a new potential tocolytic drug, meloxicam, for the treatment of preterm labour and to examine the effects of meloxicam on the cyclooxygenase enzymes important for prostaglandin production involved in the labour process and uterine activity during induced preterm labour contractions. We investigated these effects in parallel experiments using an in vivo chronically catheterized pregnant sheep model, and an in vitro human amnion and placental cell culture model. We hypothesized that meloxicam would be an effective tocolytic, blocking preterm labour contractions without serious maternal or fetal side effects observed with other tocolytics. In our ovine model meloxciam successfully reversed induced preterm labour contractions to their pre-labour type for a 48 hour period, without affecting maternal or fetal physiological parameters, fetal lower-body regional blood flow, fetal urine production and osmolality and maternal and fetal blood osmolality. Furthermore meloxicam decreased prostaglandin concentration in maternal and fetal blood, and cyclooxygenase-2 protein levels in intrauterine tissues (Study 1) without affecting the cyclooxygenase-1 isoform (Study 1 and Study 2). This effect was dose and time dependant. In cell culture models meloxicam also decreased prostaglandin concentration and cyclooxygenase-2 protein levels but spared cyclooxygenase-1 protein. The results obtained in this thesis using meloxicam as a new potential tocolytic are very encouraging, as meloxicam was able to reverse uterine labour contractions without serious side effects. However, we suggest that in human clinical trials meloxicam should be administered for a short period of time to avoid potential side effects caused by downregulation of cyclooxygenase-2 synthesis.
Atomic force microscope and electron microprobe study of calcite and apophyllite

The cleavage planes of calcite and apophyllite in thermodynamic equilibrium with water were examined at atomic resolution using an atomic force microscope (AFM). The average two dimensional fast Fourier transform of the calcite images exhibits a rectangular unit cell 0.74(5)nm by 0.48(2)nm, and that of the apophyllite images exhibits a square unit cell 0.93(3)nm on edge. Apophyllite images were consistent with the non-silicate layer of the structure, and this suggests counter-ion adsorption onto the silicate layer at the inner Helmholtz plane of the mineral-water interface. For periodic surfaces, averaging of images in Fourier space improves image quality without loss of information. Digital Fe Kα, Mn Kα and Mg Kα X-ray maps of sections cut from a calcite crystal were collected using a Camebax s%50 automated electron microprobe. Features as small as ≈25 μm were resolved, as were changing growth forms, inter- and intra-sectoral zoning and dissolution events. The maps also allow reconstruction of qualitative changes in growth solution composition and the Miller indices of growth forms.