VictorJuiz/thesis huggingface dataset:
Cys2-His2 zinc-finger transcription factors in the regulation of expression of the 5S RNA and DIT genes in Saccharomyces cerevisiae

The Cys2-His2 zinc finger is a well-characterized DNA-binding domain that derives its structure from the coordination of a central zinc ion by two cysteine and two histidine residues. My thesis research addressed the role of Cys2-His2 zinc finger-containing proteins in the regulation of gene expression at two promoters in Saccharomyces cerevisiae. In Chapter 3, I describe the role of two Cys2-His2 zinc finger proteins, Rim101 and Nrg1, in the negative regulation of the DIT1 and DIT2 genes. These divergently-transcribed mid-late sporulation-specific genes are repressed during mitotic growth in a manner that depends on the Ssn6-Tup1 repressor complex and on a negative regulatory element (NRE) present in the intergenic region. The studies described in this Chapter demonstrate that Nrg1 and Rim101 bind to distinct subsites within the bipartite NRE and act as corepressors at the DIT promoter. Rim101-dependent repression through the NRE depends on an upstream RIM signaling pathway that regulates the proteolytic activation of Rim101. My studies also identify Dfg16, Ygr122w and components of the ESCRT trafficking pathway as additional regulators of both Rim101 processing and Rim101-dependent repression of the DIT genes. Chapter 2 presents my analysis of the contribution of individual zinc fingers of transcription factor (TF) IIIA to the assembly of an initiation complex at the 5S RNA gene. TFIIIA, an RNA polymerase III transcription factor that contains nine Cys2-His2 zinc-fingers, binds to the internal control region (ICR) of the 5S RNA gene as the first step in the assembly of a TFIIIB-TFIIIC-TFIIIA-DNA initiation complex. My studies highlight a critical role for zinc finger seven and for residues F50 and Y53 in the first zinc finger of TFIIIA in the establishment of a functional initiation complex at the 5S RNA gene. Versions of TFIIIA containing structural disruption of either zinc finger one or seven, or a version of TFIIIA containing simultaneous mutation of residues F50 and Y53 are unable to support in vitro transcription of the 5S RNA gene or to support cell viability. Simultaneous disruption of both zinc finger four and six also abolishes the ability of TFIIIA to support cell viability.
Concerto for oboe and orchestra

The Concerto for Oboe and Orchestra is in two connected movements. The first is an allegro that contains numerous shifts in orchestration and time signature. The entire orchestra is quite active and aggressive in this movement, and exchanges many intertwining statements with the oboe. Structurally, it is in a pseudo-ternary form, where the opening and closing sections are similar, but primary musical materials are presented in reverse order. The second movement is an adagio, although in many sections the oboe line is moving extremely fast in relation to the orchestra. There are also occasional instrumental solos within the orchestra that share this faster material with the oboe. This movement is more relaxed and lyrical than the first, but a sense of resolution is not provided until after the oboe's cadenza near the end of the piece. The primary structural building blocks in this movement are three extended descending modal passages that surround the cadenza. During their first appearance, these passages are interrupted and they are not connected together in a complete statement until the end of the movement. The second movement also contains an introduction that functions as a transition from the first movement. This introductory material has been foreshadowed at the end of the central section in the first movement. During the second movement, it returns in various guises before the oboe cadenza. The pitch materials prevalent in this work consist of three eight-note scales. The first two are octatonic scales a major third apart, while the third contains two mirroring tetrachords that start a minor second apart. These scales were developed through improvisation while contemplating oboe range and dynamics within an orchestral setting. Decisions were made regarding primary and secondary pitches that were based upon the differing characteristics of the scales and their relationship to the oboe. Each of these scales was then combined with either one or two multiphonics for the oboe. In addition to ranking pitch importance, pitch ranges in the form of glissandi were marked in order to match the out-of-tune notes that are a consistent ingredient of woodwind multiphonics. All of these materials were utilized in varying degrees throughout the composition.
Neural correlates of maternal depression in relation to child conduct problems

The neural mechanisms of cognitive impairments in depression are still poorly understood. In addition, the high prevalence of depression in women with children demands further investigation. This study examined mothers' event related potentials (ERPs) during a go/no-go error-monitoring task on the computer. EEG was recorded from 19 mothers of children who were participating in a treatment program for conduct problems, both before and after treatment. Two particular ERPs, the error-related negativity (ERN) and the error-positivity (Pe), were measured during differing emotional conditions. As predicted, mothers' depression scores decreased significantly following their children's treatment. It was found that, at first testing, those with greater depression symptoms had smaller ERN amplitudes, but greater Pe amplitudes. As well, there was a significant decrease in the Pe amplitudes following treatment. These results are interpreted both in terms of the depressed mothers' emotional over-activity and their cognitive disengagement.

Keywords: Depression in women
Cognition disorders
Emotions and cognition
Mothers, Psychology
Problem children
Mother and child
Exploring the biological correlates of post-stroke depression

This study aimed to evaluate whether the post-stroke inflammatory response contributes to the development of post-stroke depression (PSD) through stimulation of the enzyme indoleamine-2,3-dioxygenase and subsequent depletion of tryptophan (TRP) and production of kynurenine (KYN). Participants (39 non-depressed, 17 with depressive symptoms) were recruited between 5 days and 3 months of an ischemic stroke. All patients provided blood samples for the determination of plasma cytokines (IL-6, IL-10, IFN-gamma, IL-1beta and IL-18), KYN and TRP, and completed standard assessments of cognition and stroke severity. After controlling for stroke severity and time since stroke, univariate and multivariate ANCOVAs did not show a significant difference in immune activation, KYN activation and TRP depletion between stroke patients with and without depressive symptoms. If confirmed in a larger sample of patients, the role of KYN activation in the development of PSD may have important implications for the development of rational new treatment strategies.
Investigating the cotranscriptional regulation of pre-mRNA splicing and 3'-end processing

Transcriptional activators play an important role in the assembly of the transcriptional apparatus at the promoter regions of genes. We examined whether activators participate in the coupling of transcription with pre-mRNA processing, as well. Strong activation domains resulted in higher levels of splicing and cleavage compared to weak activation domains when targeted to the promoter of reporter genes. Truncation of the CTD abrogated this effect indicating that the CTD is involved in mediating the effect of strong activators on efficient processing. Further exploration of this mechanism revealed that splicing factor PSF binds preferentially to strong activation domains, and stimulates splicing and cleavage in vivo, in a CTD dependent manner. Therefore, PSF likely mediates the effect of a strong activator on efficient processing, whereby strong activators facilitate the association of PSF with the elongation apparatus. Our findings therefore implicate both transcriptional activators and PSF in cotranscriptional splicing and 3 '-end formation. The production of a messenger RNA (mRNA) is a complex process that involves many concerted steps, including the processing of the primary transcript, or precursor mRNA (pre-mRNA). Processing involves capping, 3' -end cleavage and polyadenylation, and splicing of introns from within the pre-mRNA. Pre-mRNAs are transcribed by RNA polymerase II (pol II), and it has been found that pre-mRNA processing is coupled to transcription by pol II, facilitating efficient and coordinated production of mature mRNA. Here I report the results of investigations of cotranscriptional splicing and 3'-end formation of pre-mRNAs. The carboxyl-terminal domain (CTD) of pol II is a highly-repetitive sequence unique to pol II that plays key roles in coupling gene expression events leading to the production of mRNA. We examined the CTD requirement for processing of different pre-mRNAs by exploring the effect of CTD mutations on splicing and cleavage of reporter genes in mammalian cells. We found that the length, rather than the type of CTD repeats, can be the major determinant in the efficient processing of pre-mRNA substrates. Furthermore, our results suggest that the requirement for the CTD in pre-mRNA processing is dependent on sequences within the gene itself. The degree of CTD-dependence therefore appears to be pre-mRNA specific.
Learning parts-based representations of data

Many collections of data exhibit a common underlying structure: they consist of a number of parts or factors, each with a range of possible states. For example, in a collection of facial images, every image contains eyes, a nose, and a mouth, each of which has a number of appearances. We propose a new method, Multiple Cause Vector Quantization, for the unsupervised learning of parts-based representations of data. Our technique automates the segmentation of the data dimensions into parts; while simultaneously learning a discrete model of the range of appearances of each part. We pose MCVQ as a probabilistic graphical model, and derive an efficient variational-EM algorithm for learning and inference. We present applications of this model to problems in image decomposition, collaborative filtering, and document modeling.
Rupturing the "skin of memory": bearing witness to the 1989 massacre of women in Montreal

This thesis has been written through the aftershock of the 1989 murder of fourteen women at Ecole Polytechnique in Montreal, Quebec, an event known commonly as the "Montreal Massacre". Taking a feminist position that this was not the act of a "madman", I argue for careful consideration of how to remember this event and in what relation to other acts of violence against women. I propose the massacre may be understood as an event of "historical trauma": both because it broke the frame of what was normal and expected for women attending university in Canada, and because it surfaced a sense of the horror that is already known and unbearable in the lives of those subject to more everyday assaults and violations. By way of explicating the nuances of this argument, the thesis is developed along three intersecting dimensions. First, I work with my own memories of violation--a history of incest that I began to remember through the event of the massacre. Second, I draw from post-Shoah (Holocaust) theorizings to introduce a language of witnessing and to contemplate the impacts of trauma, not only on individual "survivors", but also for social integrity. Third, I perform the writing as itself a site of bearing of witness, marked by the disturbances of rupture, incomprehensibility and visceral impact. Substantively, the thesis develops through a series of engagements with feminist memorial responses to the Massacre of Women, including art, song, installation, memorial vigils, and monument--drawn from my annotated bibliography of English-language feminist response (1990-1995). Each of the selected works is approached through two central questions: Which calls to witness are inscribed in memorial responses to the massacre? What are the implications of bearing witness to these responses, when one comes to witnessing already traumatized? The close analysis of responses is organized in part through an interest in attending to and conceptualizing the pedagogical effectiveness of memorial practices. The work will be of interest to those working on philosophies of witnessing; relations between history, traumatic memory, and pedagogy; autobiographical theorizing: and, cultural practices in response to violences against women.

Keywords: Mass murder, Québec (Province)
Sex discrimination against women
Women, Crimes against
Feminist theory
Consumption stereotypes and self-perception: Does choosing to eat a healthy or an unhealthy food affect mood and views of the self?

Previous research has shown that people make negative judgements about others based on what they eat (this has been termed "consumption stereotypes"). It is possible that people may pass judgements on themselves based on what they choose to eat. The effects of consumption stereotypes on self-perception were examined. Females were either assigned to eat or chose to eat an apple or a chocolate bar. Subjects rated themselves on mood, state self-esteem, and a set of bipolar adjectives after being assigned/choosing their snack and again after eating their snack. Results showed that subjects who chose the apple had higher self-esteem after choosing their snack and a better mood after eating their snack, compared to all other experimental groups. A second experiment was performed in order to replicate the findings from previous studies on consumption stereotypes and person-perception. The results did not confirm findings from previous studies; raters did not perceive targets who chose the chocolate bar more negatively on the bipolar adjective scale. However, we did find that on the mood and state self-esteem measures, in which raters were asked to put themselves in the shoes of the target, raters perceived the target who chose the chocolate bar as having the best mood and the highest self-esteem.
An evaluation of computer-aided learning in orthodontics

Introduction. Both objective and subjective outcomes have been widely documented in the literature, however to date, there does not appear to be a study that attempts to correlate these two outcome measures. Methods. The main objective outcome measured was performance on a written test covering material found in the ODET administered to 92 fourth year undergraduate dental students. The main subjective outcome measured was a 12 statement questionnaire to elicit students' perception of the ODET and CAL as teaching modalities. Results. When analyzing male and female subgroups, a statistically significant difference in mean lecture test scores favouring females (72.46%) over males (67.08%) was observed (p=0.05). Nevertheless, this difference was not observed for mean ODET test scores (p=0.52). Although responses to the questionnaire were for the most part positive, students are not prepared to replace lectures with CAL tutorials. Responses revealed that male students preferred self-instruction as a mode of learning more than female students did (p=0.05). When linking objective and subjective outcomes, mean ODET test scores demonstrated a statistically significant (p=0.025), but weak, positive correlation (r=0.243) with self-reported time spent reviewing the ODET but not with any other statement in the questionnaire. Conclusions. Despite a difference in lecture test scores between male and female students there was no difference in mean ODET test scores between the two subgroups which may be explained by gender differences with male students preferring self-instruction more so than female students did. Improved performance on the ODET test was noted for students that reported longer times spent reviewing the tutorial. Because students are not prepared to replace lectures with CAL tutorials, from their perspective the ODET should continue to be used in conjunction with traditional modes of learning.
Investigations of remote memory for topographical and autobiographical information: evidence from functional magnetic resonance imaging and amnesic patients

Hippocampal amnesia is characterized by loss of recent spatial memory, but more systematic study of remote spatial memory in the amnesic patient K.C. had indicated a largely preserved cognitive map of an environment learned long ago. By contrast, memory for topographical details, such as houses, was lost, which may relate to K.C.'s inability to retrieve autobiographical details from any time in his life. Findings of spared performance may reflect the function of brain structures outside of the hippocampus that are intact in K.C. and that have been implicated in spatial cognition, whereas impaired memory for spatial and autobiographical details may reflect a more general visual imagery or strategic retrieval deficit. To explore these possibilities, the network of brain structures supporting remote spatial memory was examined in fMRI experiments of healthy adults (Chapter Two), in behavioural studies involving an Alzheimer's disease patient (S.B.) who was once a taxi driver (Chapter Three), and in combined lesion and fMRI investigations of patient K.C. (Chapter Four). Tasks believed to place different emphasis on the neural correlates of spatial representations were used, including: (1) landmark recognition, involving a sector of occipitotemporal cortex, (2) allocentric distance judgments, governed by parahippocampal and retrosplenial cortex, and (3) egocentric route navigation, within posterior parietal regions. As predicted, remote memory recruited the topographical neural network based on the processing demands of each task in the fMRI studies and was dissociable based on S.B.'s lesion profile, with impaired landmark recognition but intact allocentric and egocentric processing. Moreover, in line with the preservation observed in S.B., no hippocampal activity was evident in K.C. though he has part of his hippocampus still remaining. Chapter Five investigated whether K.C.'s profound deficits in house recognition and autobiographical memory are symptomatic of widespread damage to medial occipital and frontal cortex, rather than loss of hippocampal tissue. However, performance was normal on visual imagery testing, and autobiographical memory did not benefit from a retrieval support manipulation, contrary to what would be expected if respective medial occipital or frontal lesions were responsible. Taken together, this research informs theories of hippocampal and neocortical contributions to remote memory.
Modalities of gender and nation in the mid-Victorian novel

This dissertation analyses constructions of English masculinity in four mid-Victorian novels, arguing that the modalities of gender and nation are not external to one another but mutually constitutive. A theoretical introduction, which establishes this double analytic, critically engages theories of gender identity and questions the subversive power of hybridity. Chapter one provides a reading of the collocation of flogging and fascination in Charles Dickens's David Copperfield, addressing Victorian understandings of the will as configured in arguments about corporal punishment and discourses of mental physiology. It focuses on the difficult work of producing the self as a discrete subject and opens up the topic of the colonial framings of English masculinity. Like Dickens, Elizabeth Gaskell in Cranford is engaged in revising models of manhood, and she also invokes flogging to characterise the kind of manhood that needs reformation. In this novel, Orientalised masculinity mediates the problems of men and modernity for the Cranford community of ladies. Chapters three and four develop these themes ...

Keywords: English fiction, History and criticism
English literature, History and criticism
Essays in the economics of technology and innovation, and development economics

In this thesis I study two fields in economics. While my focus is on issues of knowledge and technology diffusion, my work also investigates the proletarianization of attached workers in agrarian economies. Each chapter constitutes a free-standing contribution to the field of the economics of technology and innovation or to development economics. In Chapter 2, I theoretically explore why firms leading a research and development (R D) race sometime choose freely to disclose valuable technology. Disclosing basic knowledge only helps rivals far behind the lead to compete more strongly against the leader's closer and more threatening rivals, thus lowering the latter's incentives to perform R D; with greater competition, the expected profits of these firms decreases. If disclosure harms close rival more than the leader, technology disclosure benefits the leader. Finally, in Chapter 3, I propose a theory of the proletarianization of attached labour in agrarian economies. Where farm owners need to motivate worker effort with contingent payments but no institution exists to prevent farmers from cheating workers from these payments, workers may be paid with the use of subsistence plots. This facilitates contracting when farmer reputation is valuable; subsistence plots decrease the farmers' benefit of cheating workers relative to the cost workers may impose in retaliation. Proletarianization occurs as the price of the farmers' principle crop rises and farmers can commit to make more of the contingent payment in cash. The model also predicts workers become pure wage earners instantly once their rights are enforced. Both predictions are consistent with observations of the proletarianization of attached labour. In Chapter 1, I empirically compare the pattern of knowledge flows associated with university patents to those of firm patents. Specifically, I explore the change in how more broadly university knowledge disseminates to subsequent patent holders and how more broadly patented university innovations draw from different prior art owners. The findings are that university knowledge flows concentrated substantially over the 1980s to resemble more the knowledge flows of firm patents. Moreover, I find the concentration of flows is caused mainly by universities experienced in patenting, suggesting these phenomena are unlikely to dissipate with experience.