VictorJuiz/thesis huggingface dataset:
Computational analyses of alternative splicing microarray data

Alternative splicing (AS) is the process through which exons are differentially included in mRNA. Many mouse tissues have been profiled using AS sensitive microarrays. We identify alternative exons that are differentially spliced in central nervous system (CNS) tissues. These CNS-specific AS events are highly conserved. Certain functional processes are overrepresented in these genes. A larger number of exon pairs in the same gene have highly correlated AS patterns than expected by chance. We developed regression models relating known properties of alternative exons to exon inclusion levels. Several significant predictors of AS levels were identified. These variables showed similar relationships in all tissues. Much of the variability in exon inclusion levels was attributed to variation in the average inclusion level per AS event. These models have improved prediction accuracy. These analyses allow an improved understanding of AS.
The role of parental involvement in the learning of children with Attention-Deficit/Hyperactivity Disorder

The chronic and severe academic difficulties experienced by children with Attention-Deficit/Hyperactivity Disorder (ADHD) are well documented. Previous research has not, however, explicitly examined the role of parental involvement in the learning and achievement of children with ADHD, despite a large body of normative research suggesting that it is important for children's academic success. The goals of this dissertation were to investigate: (1) factors that influence parental involvement in the learning of children with and without ADHD; (2) how parents of children with and without ADHD interact with their children in relation to their children's learning in the home; and (3) the effects of selected parenting and child variables on academic achievement. Children between 8-12 years of age (53 with ADHD, 48 without ADHD) and their parents were assessed on several measures of parenting, child behavior, and academic achievement. Parents of children with and without ADHD were compared on parental involvement variables using the Parental Involvement Project Questionnaire and the Family-School Questionnaire. Path analyses were used to predict academic achievement (Woodcock Johnston Tests of Achievement) based on an existing theoretical framework and relevant literature. Parents of children with ADHD reported lower self-efficacy in their ability to help their children academically, felt less welcome and supported by their children's schools and teachers, and perceived less time and energy for involvement in their children's academic lives. Fathers of children with ADHD, but not mothers, were more negatively involved in their children's learning compared to parents of children without ADHD. Parenting stress and controlling parental involvement were together associated with lower academic achievement through the partially mediating role of children's parent-reported inattention. Results from this dissertation illustrate the difficulties facing parents of children with ADHD in supporting their children's educational endeavors, suggesting that they may have a lack of requisite resources for effective involvement due to the combination of both child and parent factors. This research also suggests that there are multiple risk factors within the child and family that likely contribute to the underachievement of children with ADHD, highlighting the need for a systems approach, to both research and clinical practice for children with ADHD.
Preparing diverse teachers for diverse students: perceptions of linguistic identity, experiences and teaching responsibilities in a Canadian teacher education program

As the population in Canada is growing increasingly diverse, it has become critical to understand how to respond to such demographic change in the public school system and in teacher preparation programs. This thesis responds to this call by exploring perceptions of linguistic identity, experiences (participation, choices and challenges), teaching responsibilities and reported changes of future secondary teachers from diverse backgrounds in a Canadian teacher preparation program. The participants in this study include 25 linguistically diverse teacher candidates (TCs) enrolled in a 9-month intensive Bachelor of Education program and four teacher educators (TEs). Data were collected over the period of six months through interviews, questionnaires, observations and additional documents. This study draws on various sociocultural perspectives and more specifically the notion of "community of practice" (COP) (Lave Wenger, 1991). The examination of the participation, choices and challenges of TCs demonstrated the multiple, interrelated and complex issues underlying their experiences. These factors include specific COPs, instructors, peers, support in the program, age, culture, linguistic identity, personality, attitude, length of residence in Canada, curriculum and instructional practices. Findings also suggest that personal and professional experiences with ESL and diversity-related issues contribute to a higher level of empathy with English Language Learners (ELLs). However, empathy does not ensure that TCs are more likely to employ ESL-inclusive pedagogy. Explicit instruction on language education and diversity-related issues is required to help TCs develop such skills. The exploration of how TCs reported having changed as a result of the program revealed that there is evidence of both stability and change in their beliefs. The exploration of the respondents' native and nonnative self-ascription and self-assessed English proficiency, juxtaposed with the judgments of three TEs revealed the idiosyncratic and complex interplay between individuals and the social contexts in which they negotiate their linguistic identities. A six-category typology which better depicts the linguistic identities of the TCs is proposed. This inquiry reconceptualizes the native/nonnative dichotomy suggesting that linguistic identities should be viewed as dynamic, dialogic, relational, situated and multiple and thus explored in the process of their development in specific social contexts rather than as a unitary and fixed phenomenon in isolation.

Keywords: English language, Study and teaching
English language, Ontario
Linguistic minorities, Education (Higher)
Linguistic minorities, Ontario
Minority teachers, Training of
Minority teachers, Ontario
Student teachers, Attitudes
Student teachers, Ontario
Pharmacological regulation of brain stem circuits mediating prepulse inhibition of startle in rats

The startle reflex is inhibited by moderate intensity acoustic pulses or by inferior colliculus stimulation that precede the startle-inducing stimulus by 20--500ms. This prepulse inhibition (PPI) is mediated by midbrain circuits that converge on pontine reticular formation (PRF) giant neurons mediating startle. Startle was evoked here by stimulation of the trigeminal nucleus and was recorded by an electromyographic response in the biceps femoris. To determine the transmitters and receptors influencing prepulse inhibition, the muscarinic blocker scopolamine (0.1mg/muL) and the GABAB blocker phaclofen (4.2ng/muL) were injected bilaterally in the PRF, and found to reduce PPI by means of 47% and 29%, respectively. To test further whether midbrain cholinergic neurons mediate PPI, carbachol (1mug/muL) was injected bilateraffy into the pedunculopontine tegmental nucleus, and was found to reduce PPI by a mean of 44%. These data suggest that both cholinergic and GABAergic neurons contribute to PPI.
Calreticulin and cell adhesion

An understanding of cell-cell and cell-matrix adhesions and how they are influenced is central to cell biology. Calreticulin is a multifunctional calcium binding protein of the endoplasmic reticulum of all eukaryotic cells that influences a wide variety of cellular processes including cell-cell adhesion and cell-matrix adhesion. An increase in calreticulin expression in L fibroblasts is correlated with an increase in epithelial like morphology and behaviour, while the reverse occurs for a decrease in calreticulin expression. L fibroblasts with increased calreticulin expression have increased levels of the cell-cell adhesion protein N-cadherin and its mRNA, which could account for the observed differences in adhesive behavior. There is an inverse relationship between the level of calreticulin expression and tyrosine phosphorylation, such that cells with increased levels of calreticulin expression have lower levels of tyrosine phosphorylation, and vice versa. Î²-catenin is one of the proteins underphosphorylated in calreticulin overexpressing L fibroblasts, targeting it to cell-cell junctions, and possibly contributing to the observed differences in cell-cell adhesion. Calreticulin also affects cell-matrix adhesion. Retinal Pigment Epithelial cells and L fibroblasts with increased calreticulin levels have higher levels of vinculin mRNA and protein, and make larger and more numerous focal contacts than calreticulin underexpressing or control cells. Underexpressing cells appear to adhere by a form of contact called the close contact. Calreticulin regulates fibronectin gene activity. Fibronectin is a large glycoprotein of the extracellular matrix, and is one of the substrates for cell-matrix adhesion. Calreticulin overexpressing cells synthesize, secrete and deposit more fibronectin than calreticulin underexpressing cells. On glass, calreticulin overexpressing L fibroblasts are well spread, but underexpressers are poorly spread. Plating calreticulin underexpressing L fibroblasts on a fibronectin carpet rescues cell spreading, and causes them to assemble many tensin rich fibrillar adhesions. Therefore, calreticulin overexpressing L fibroblasts adhere to a fibronectin matrix mainly by focal contacts, while calreticulin underexpressing L fibroblasts adhere mainly via fibrillar adhesions. While the mechanisms of calreticulin effects are presently unclear, they may be related to its effects on calcium homeostasis, which could then affect the activity of tyrosine kinases and/or phosphatases and protein synthesis cascades.
Least restrictive collision avoidance control

Working in crowded environments is a challenging task for mobile robotic systems as the robot may have a collision to other moving or stationary objects. One of the practical issues is that robots should not have any collision while they are performing their tasks. A general collision avoidance algorithm which can be used everywhere can be very useful. In this thesis a controller, which can avoid the collision between two vehicles modelled as unicycles, is presented and it is shown that if this controller cannot avoid collision, no other controller can do it. This controller is called a least restrictive controller. This controller is not unique and therefore we may find another controller which is least restrictive, however the set of the states, for which a collision is unavoidable, is the same for all least restrictive controllers.
Contingent work, health, and citizenship: The discursive management of stigmatising employment among temporary help agency workers

This study examines how contingent workers hired through temporary help agencies conceive of and experience their work. Contingent employment---short-or fixed-term contracts, part-time, casual/on-call, self-employment, seasonal, and temporary agency work---has re-emerged in the context of the globalisation of trade, investment, production, and intensified competition. Its expansion has raised concerns about the health effects for workers. Efforts to assess these effects have however been hampered by conceptual and definitional disagreements and by methodological challenges. While researchers in the area of contingent work and health have examined the experience of workers, much of this research has (i) tended to adopt a particular perspective with the result that alternative aspects of workers' experience are not considered; (ii) employed an objective or quantitative approach, which cannot adequately capture the complexities of differences in work arrangements and worker experiences. As a result, research findings have been largely inconsistent and/or inconclusive and the relationship between contingent work and health remains unclear. I propose that examining contingent work via workers' experience and by means of a qualitative methodology might cast light on, or further our understanding of this relationship. Using a combination of social constructionist theoretical perspective and an interpretive, qualitative, analytic approach, this interview based study of the experiences of 23 day labourers and clerical workers employed through temporary help agencies (i) describes the dual discourses that these workers use to portray their experience of contingent work; (ii) accounts for these discourses in terms of general perceptions of contingent work as inferior or stigmatising work and in terms of the broader socio-political and economic contexts in which they are located; and (iii) considers the health implications of these discourses. The study found that workers conceive their work in terms of discourses of advantage and disadvantage and it argues that these individual-level discourses are shaped by and mirror neoliberal rationalities. The study also argues that workers, who are conceived as active agents, use these discourses to resist, counter, and reconstruct the social, structural, symbolic conditions of stigmatised work and to (re)present themselves as active neoliberal citizens. The implications of this discursive management of contingent work are discussed.
Predicting the tensile modulus and strength of single and hybrid natural fibre reinforced thermoplastic composites

Natural fibre reinforced thermoplastics (NFRT) are used in a variety of commercial applications, but there is little theoretical modeling of structure/property relationships in these materials. In this thesis, micromechanical models available in the short-fibre literature were adapted to predict the tensile modulus and strength of some NFRT formulations. Hemp, 20 and 40-mesh hardwood, rice hulls and E-glass fibres were blended into HDPE to produce single and hybrid composites. Changes in fibre density and moisture content that occur during composite manufacturing were included in the micromechanical models. To account for fibre densification, the Young's modulus of the natural fibres was determined on a cell wall basis. A modified hybrid rule of mixtures (HROM) equation that uses experimental data from single NFRT was developed and found to adequately predict the tensile modulus of the hybrid composites. The tensile modulus for both the single and hybrid composites was found to linearly increase with an increase in fibre loading. The failure mechanism for all composite specimens was due to fibre pullout followed by matrix failure. Consequently the tensile strength of the NFRT was predicted using a ROM strength equation, which was modified with a derived semi-empirical fibre clustering parameter. The clustering parameter correctly predicted that as fibre loading increased, the average fibre stress would decrease. By assuming no contact between different types of fibres it was possible to use a modified HROM strength equation to predict the tensile strength of the hybrid composites. As a result parameters taken from the respective single fibre systems could be applied directly to the HROM equation. The modified ROM and HROM strength equations adequately predicted the tensile strength of various single and hybrid fibre reinforced composites over a wide range of composite loading. In this study experiments were conducted to shed light on the effect of a coupling agent (maleic anhydride) on the tensile strength and stiffness of various NFRT. Coupling agents, which alter the interfacial shear strength between the fibre and matrix, were determined to have a minimal effect on composite stiffness but produced increases in composite strength.
The effects of vanadium on bone quality in rat models of diabetes and postmenopausal osteoporosis

Vanadium-based drugs lower glucose by enhancing insulin's effects. Oral vanadium drugs are being tested for diabetes treatment. Vanadium accumulates in bone, though its effects on bone are unknown. The purpose of this study was to determine if incorporated vanadium affects the quality of bones in normal, diabetic and osteoporotic rats. Sham-operated, streptozotocin-induced diabetic or ovariectomized rats were treated with bis(ethylmaltolato)oxovanadium(IV) (BEOV), a vanadium-based anti-diabetic drug. Bone mechanical, mineral and remodeling parameters were examined. In normal rats, BEOV increased bone formation, bone vanadium content, mineralization and cortical toughness. In diabetic rats, BEOV improved diabetes-induced decreases in mechanical properties, mineralization and crystal length by improving the diabetic state, but also increased bone formation and bone vanadium content. In osteoporotic rats, BEOV increased bone vanadium content, but did not affect other bone quality parameters. These results suggest that BEOV has direct actions on bone cells and bone mineral in normal and diabetic bone.
An examination of issues surrounding fund-raising in Ontario public education

Public education in Ontario has undergone several political changes over the last few decades with the promise of improving our education system. However, none of these changes has reduced the lack of contentment with the state of affairs in public education. In fact, publicly funded schools now find the pursuit of private sources of revenues, commonly referred to as fund-raising, essential in order to provide basics such as textbooks, classroom supplies and library books (People for Education, 2002; Fine, 2001; and Tymko, 1996). Interviewed principals stated that fund-raising was an activity that would never cease in schools, even with the insertion of extra revenue. Even more disturbing are the findings of Molnar (2000; 2001; 2002; 2003) in which he states that schools in the United States are attempting to raise these supplementary sources of revenues by engaging in activities that undermine their curricular message and, in some cases, promote unhealthy lifestyles for students. The purposes of this paper are to provide insight into the policies, degree, level, pattern, motivation, perception, amount, typology, and effects of fund-raising in publicly funded elementary and secondary schools across Ontario by focusing on certain schools in southwestern Ontario as case studies. This study uses a mixed method research approach in the form of qualitative and quantitative comparisons among multiple or comparative case studies involving the use of interviews, questionnaires and public documents. The relationship between fund-raising revenues and the overall government expenditures is explored in this study, which provides an in depth look at fund-raising in southwestern Ontario publicly funded schools. The results indicate that the government has very little involvement in the regulation and control of fund-raising in publicly funded schools. In fact, the government has left the responsibility for regulating school fund-raising in the hands of school boards of Ontario. The school boards in turn, have passed the majority of the responsibility of regulation and control of fund-raising onto the principals of each school. Each board has developed policies relating to the collection of supplementary resources within schools. However, these policies vary considerably in their depth and breadth.
Flame propagation in natural gas fueled direct injection engines

Natural gas has shown promise as an alternative fuel for diesel engines. Research has shown that natural gas requires assistance to ignite in a diesel engine chamber. This results in a single site of ignition from which the flame must propagate to other jets in the injection pattern. The goal of this work was to determine what factors affect how the flame propagates from this initial ignition site to the remaining unburned mixture. The combustion of natural gas jets under diesel engine conditions was studied over a range of temperatures, pressures, equivalence ratios, and glow plug shield designs using a rapid compression device. Ignition was provided by a shielded glow plug. The results show that of all the factors considered the geometry of the injection pattern, chamber, and glow plug shield are most dominant in controlling combustion rates and efficiency.
Investigation of cystic fibrosis disease mutations and cis elements associated with pre-mRNA splicing

Cystic fibrosis (CF) is a common, autosomal recessive disease in Caucasians, characterized by pulmonary disease, pancreatic insufficiency, male infertility and elevated sweat electrolytes. CF is caused by mutations in the cystic fibrosis transmembrane-conductance regulator (CFTR) gene which encodes a chloride channel located at the apical membrane of epithelial cells. Splicing is catalyzed by the spliceosome, a large ribonucleoprotein complex that recognizes short and poorly conserved splice site consensus sequences. Recognition of these sequences is controlled primarily by cis elements (enhancers or silencers) bound by trans-acting splicing factors. A purine-rich sequence in CFTR exon 13 was investigated and shown to function as an exonic splicing enhancer (ESE). A series of disease mutations positioned in and around the ESE caused skipping of the first 195 or 248 nucleotides of exon 13. Moreover, over-expression of splicing factors, hTra2alpha and SF2/ASF, which are known to bind purine-rich ESEs, altered the levels of the aberrant splice variants. The effect of another mutation (R553X) on the splicing of CFTR exon 11 was investigated and shown to cause exon skipping through the creation of a putative exonic splicing silencer. R553X-associated exon skipping was found to be modulated by over-expression of the splicing factor SC35. These results indicated that nucleotide changes that interfere with splicing regulatory elements should be considered as possible causes of loss of function of CFTR. Alignments of CFTR genomic sequences from eight mammalian species were performed to identify intronic splicing regulatory elements. A T-rich motif was found in conserved sequences immediately downstream of CFTR 5' splice sites. This motif was also found in 2.5% of introns (>176,000) of all protein-coding human genes between nucleotides +6 and +30. Further, silencing of the related factors TIA-1 and TIAR, which bind T-rich sequences, decreased the inclusion of a subset of alternatively spliced exons followed by the T-rich motifs. These motifs represent a common intronic splicing enhancer and were found to be conserved downstream of exons that are alternatively spliced in human and mouse species. The investigation of splicing regulatory elements provides targets for disease mutation screening and also leads to deeper understanding of splicing mechanisms.