VictorJuiz/thesis huggingface dataset:
Design of a Microfluidic Based Lab-on-a-chip for Integrated Sample Manipulation and Dispensing

Microfluidic based miniature lab-on-a-chip devices integrate different laboratory functionality in microscale. Microarray technology is evolving as a powerful tool for biomedical and pharmaceutical applications to identify gene sequences or to determine gene expression levels. Preparation of samples and spotting the arrays are the two major steps required for making microarrays. The microfluidic components developed in this research would facilitate performing the above-mentioned steps by a single lab-on-a-chip. Three microfluidic modules were developed: a non-contact microdispenser, an interface connecting the microdispenser with planar Electrowetting on Dielectric (EWOD) sample manipulator and a microvalve that controls the flow at the interface. An electrostatically actuated non-contact type drop-on-demand based microdispenser was developed. The dispenser was designed using finite element modeling technique that solved electrostatically actuated dispensing process. Prototypes were fabricated and tested verifying stable droplet dispensing with error in subsequent droplet generation was less than 15% between each droplet. The frequency of stable generation was 20 Hz and the average volume of dispensed droplet was 1 nL. A closed-channel EWOD actuated interface was developed that allowed a series of droplets to merge inside at the interface converting droplet flow to a continuous flow. An innovative design modification allowed series of droplet merging inside closed-channel. The interface allows integration of pressure driven devices such as: pumps, dispensers, and valves with droplet based planar EWOD devices. A novel EWOD based microvalve was developed that utilizes a thermo-responsive polymer to block and unblock a pressurized continuous flow. EWOD actuation was used to control the positioning of the valving polymer at location of interest. The valve also isolated a pressurized flow from an integrated planar EWOD device. Valves with zero leak rates were demonstrated. Such a valve will be useful in controlling microflows in EWOD to pressure driven flows such as dispensers.

Keywords: Mechanical Engineering
Microfluidics
Microdroplet
Microarray
Electrowetting
Digital Microfluidics
Advisor: Mrad, Ridha Ben
Sullivan, Pierre E.
Defining the Roles of Oncogenic Pik3ca Mutations and Genetic Cooperation in Mouse Models of Breast Cancer

Most human breast tumors have mutations in the growth factor/phosphatidylinositol 3’ kinase (PI3K) pathway. These can occur in genes coding for receptors, adaptor proteins, catalytic and regulatory subunits of PI3K, downstream kinases, or antagonistic tumor suppressors. While each genetic change results in elevated PI3K signaling, and all major breast cancer subtypes show pathway activation, the specific mutations involved in any one tumor may play an important role in defining tumor subtype, prognosis and sensitivity to therapy. Here, I describe mouse models of PI3K-induced breast cancer. First I generated mice that express Pik3ca cDNA under control of the ROSA26 promoter, in a Cre-dependent and therefore tissue specific way. I have generated four strains of knock-in mice: R26-Pik3cawt, R26-Pik3caE545K, R26-Pik3caH1047R, and R26-Pik3caE545K-H1047R, which can be induced to express wild type, helical domain, kinase domain and double mutant forms of mouse p110α, respectively. Mice expressing mutant Pi3kca develop mammary tumors, but the phenotypic spectrum for each mutation is unique. Indeed, many E545K mammary tumors are ii vascularized, whereas H1047R tumors are not. Using these models, I have compared downstream signaling properties of E545K and H1047R. The potential for improved breast cancer treatment lies in combination therapies that target more than one oncogenic pathway. To develop such treatments, we need good mouse models, and an understanding of the oncogenic network. To this end, my Pik3caH1047R model was mated to p53 and PTEN knockout mice, and to mice with active Notch1 signaling. In each case, genetic cooperation was observed and characterized. Oncogenic PI3K cooperated with p53-loss and active Notch1 to decrease survival and alter tumor phenotype in distinct ways. Loss of PTEN cooperated with oncogenic PI3K to alter tumor type, decrease average age at end point, and increase the number of tumors per mouse. Overall, I have shown that Pik3caE545K and Pik3caH1047R are sufficient to induce mammary tumors, and that tumor characteristics differ with these mutations, and with cooperating genetic changes.

Keywords: breast cancer
Pik3ca mutations
Advisor: Egan, Sean
Molecular Mechanisms of Medulloblastoma Formation: Tumor Suppressor Functions of Hedgehog Pathway Components

Hedgehog (Hh) signaling is essential for embryonic development and adult homeostasis. Aberrant pathway activity can result in various developmental disorders and cancers. The Hh receptor Patched1 (Ptc1) is a negative regulator of the pathway and acts as a tumor suppressor. Our lab and others have shown that Suppressor of fused (Su(fu)) and Kinesin family member 7 (Kif7) are major negative regulators of the pathway that function downstream of Ptc1. Medulloblastoma (MB) is the most common malignant pediatric brain tumor originating from the cerebellum. Several forms of MB have been identified, with abnormal activation of the Hh pathway associated with one major subtype. These tumors commonly show inactivating mutations in PTCH1, whereas mutations in SU(FU) are more rare. Mouse models with deletion of Ptc1 or expression of a constitutively active form of Smoothened (Smo) exhibit elevated Hh pathway activity, leading to MB formation. In this study, I examined the complex roles of Su(fu) in the formation of MB alongside the inactivation of Ptc1, Kif7 and p53 in the cerebellum. Unlike Ptc1+/- mice, Su(fu)+/- mice do not develop MB, even upon exposure to DNA damaging agents (X-ray irradiation or chemical carcinogenesis), which dramatically increases MB incidence in Ptc1+/- mutants. However, Su(fu)+/-;p53-/- mice develop MB and these MB tumor cells exhibit loss of heterozygosity of Su(fu), suggesting a protective role of p53 in tumor suppression in Su(fu) deficiency. Kif7+/- mice are not prone to tumorigenesis, even with deletion of p53. To bypass the embryonic lethality of Su(fu)- and Kif7-null mice, I generated neural stem cell-specific knockout mice, GFAP-Cre;Su(fu)f/f and GFAP-Cre;Kif7f/f. GFAP-Cre;Su(fu)f/f mice exhibit a severely disorganized cerebellum, with drastic up-regulation of p53 expression, and they survive past 1 year of age and do not develop MB. In contrast, GFAP-Cre;Kif7f/f mice appear grossly normal with only subtle cerebellar defects. These observations indicate that neither Su(fu) nor Kif7 inactivation is sufficient to drive tumorigenesis in the cerebellum. To investigate whether Su(fu) and Kif7 possess any overlapping tumor suppressor functions, I generated GFAP-Cre;Kif7f/f;Su(fu)f/f mice. Indeed, simultaneous loss of these negative regulators resulted in MB formation, which is correlated with increased Hh pathway activity as well as a lower level of p53 expression. Furthermore, I discovered a novel positive role for Su(fu) in MB development, as Su(fu) activity is required for robust formation of MB in Ptc1-deficient mice. Together, these data illustrate that Su(fu) plays a dual role in the genesis of MB, and suggest that the rare human MBs with SU(FU) mutations could be caused by simultaneous deletion of TP53 or KIF7.

Keywords: hedgehog
medulloblastoma
Advisor: Hui, Chi-chung
The Stagehands of Subversive Spaces: Site-specific Performance and Audience Labour

This dissertation develops a theory for analyzing the role of audiences as aesthetic resources in contemporary site-specific performance and relational art. Collaborating with three Canadian companies as a participant-observer, interviewer, and in some cases, documenter, I develop case studies that track flexible stage-audience relationships in public spaces. By analyzing how companies Radix Theatre Society, Bluemouth, and Mammalian Diving Reflex put spectators to work in sites like IKEA showrooms, disused warehouses, and theatres, I advance a method that attends to the doubled practice of the spectator as worker and witness. This framework, which I term bifold spectatorship, articulates how audiences constitute theatrical worlds through direct physical engagement with the cultural criticism and formal experimentation that artists stage. Folded into the event, spectators literally compose the scene of the action, and enter into what I call critical proximity with the discourses that shape the performance. As participants interact with and directly query the artistic expressions that they patron, they answer a challenge to perform that is typically reserved for professionals. Such novel participation begins with a hail that interpellates audiences into the action as subjects and even sites of performance. Adapting the concept of the casting call, or what I coin site-casting, miscasting, and central casting, I show how spectators are aligned with the exigencies of the site; “mis-placed” or miscast by artists (provoking performance anxiety in participants); or cast to play a role they already perform in their everyday lives. In addition to these critical frameworks, I challenge the established narrative of “liberating the audience” by forwarding a multi-sited genealogy of site-specific performance that confronts the romance of freeing spectators from stage conventions. In examining the ethical problems that arise when audiences are made responsible for representation, The Stagehands of Subversive Spaces extends debates within site-specific performance to wider conversations in performance studies about ethics, subjectivity, and audience reception.

Keywords: performance and place
theatre
audiences
site-specific performance
relational art
contemporary Canadian performance
Advisor: Copeland, Nancy
Understanding the Source of Emotions: Anxiety, Emotion Understanding Ability, and Risk-taking

Can only a subset of individuals – those higher on the ability to understand the sources of emotions – determine whether to disregard or allow the effects of emotions when making decisions? I test two central predictions. First, I test whether individuals high on emotion understanding ability (EUA), one of the key dimensions of emotional intelligence, are less affected by incidental anxiety when making decisions involving risk than their lower ability counterparts. The rationale for this prediction is that individuals who have high EUA are able to correctly identify their source of anxiety and, based on perceived irrelevance, disregard incidental anxiety when making risky decisions, whereas individuals who have low EUA are confused about the source of anxiety and are more influenced by incidental anxiety when making risky decisions. Second, I test whether individuals high on EUA are more affected by integral anxiety when making risky decisions than their lower ability counterparts. The rationale for this prediction is that individuals who have high EUA are able to correctly identify their source of anxiety and, based on perceived relevance, use their integral anxiety to inform their risky decision making whereas those who have low EUA misattribute their anxiety and are less likely to incorporate their integral anxiety into their decision making. In Experiment 1, incidental anxiety reduced risk-taking among individuals with low EUA, but not among their higher ability counterparts. In Experiment 2, the interactive effect of EUA and incidental anxiety on risk-taking was eliminated when I identified the irrelevance of anxiety to the present decision, but it remained when the irrelevance was not identified. To explore the role of EUA in using the adaptive function of emotion in decision making, Experiment 3 assessed whether emotionally intelligent individuals who have high EUA incorporate integral anxiety, as measured by skin conductance responses, into their risk-taking, compared to those with low EUA. Contrary to expectations, the results of Experiment 3 showed that, when EUA was high, there was a negative effect of integral anxiety on risk-taking that was not significant. When EUA was low, there was a significant positive effect of integral anxiety on risk-taking.

Keywords: emotional intelligence
decision making
Advisor: té, S
The North Caucasus in the Second Half of the Sixteenth Century: Imperial Entanglements and Shifting Loyalties

The present dissertation seeks to present and analyze the hitherto poorly understood first encounter between the Ottoman Empire and the Tsardom of Muscovy in the North Caucasus from the Muscovites’ annexation of the nearby Khanate of Astrakhan in 1556 and subsequent penetration into this region, to their expulsion from it by the Ottomans in 1605. The study relies on both Ottoman and Muscovite sources, both documentary and narrative, as well as archival and published. The main archival documentary sources are the Ottoman mühimme defters (registers of orders issued by the Imperial Council [Divan-i Hümayun]) and the Muscovite posol’skie knigi (registers of diplomatic documentation, including ambassadorial reports, diplomatic correspondence, and other documents administered by the Ambassadorial Office [Posol’skii Prikaz]). The main narrative sources are sixteenth-century Ottoman and Muscovite chronicles. On the basis of the Ottoman and Muscovite documentary sources it is possible to determine what Ottoman and Muscovite policies in the North Caucasus were, to what degree they were well-formulated, and how they evolved during the aforementioned time period. It becomes clear that Ottoman and Muscovite policies in the Pontic-Caspian steppes and specifically in the North Caucasus had some superficial similarities, but were in essence fundamentally different. Taking into account that it was only after Muscovy’s expansion into the North Caucasus that the Ottomans decided to take an active stand in the north, the dissertation also shows the ways in which Muscovite steppe policy not only affected the political structures on the frontiers but also influenced Ottoman northern policy, and specifically in the North Caucasus. However, this dissertation is not solely a study of an imperial rivalry in a contested frontier zone. The Ottoman and Muscovite involvement brought about changes to the internal dynamics of the polities within the North Caucasus. Lastly, during the first round of this imperial clash, Ottoman and Muscovite presence and sway in the North Caucasus underwent several extreme and unexpected shifts. These shifts and resulting new strategies that the Ottomans and Muscovites had to develop in the North Caucasus played an important role in their future encounters in the northern Black Sea region.

Keywords: North Caucasus
Ottoman Empire
Muscovy
Safavid Iran
Astrakhan Campaign
Ottoman-Safavid War 1578-1590
Advisor: Ostapchuk, Victor
“A Foolish Adventure" in a Country that went Mad: Healing Psychosocial Suffering in Post-genocide Rwanda

Abstract There is a scarcity of programs addressing psychosocial suffering in post-genocide Rwanda. The locally-initiated models are understudied and lack legitimate support to strengthen their interventions. This study addresses this gap by exploring the Healing of Life Wounds (HLW) program and its context of implementation. HLW is a community-based program that was introduced in Rwanda in 1995 by a Rwandan, Dr. Simon Gasibirege, to facilitate mutual healing among members of the groups involved in the 1994 genocide. Using a critical ethnographic approach, a multi-method data set was obtained from two groups of participants from two separate organizations applying HLW model. One group of twenty-three community participants from one local association shared their experiences as they participated in HLW. The other group included seven experienced HLW facilitators who provided their perceptions about using HLW from an international organization operating in Rwanda. The data also included HLW documents and reflexive notes. Dialogic performance analysis was the overarching analytical approach of the different data sets. Data collection, analysis and interpretation were guided by principles of critical theories, indigenous methodologies and narrative inquiry. The findings indicate that healing psychosocial suffering in the post-conflict global South requires innovative approaches that critically address on-going psychosocial issues affecting the marginalized by giving them voice and working with them to integrate contextual healing techniques. This study suggests that healing psychosocial suffering through HLW is a consciousness-raising process by which participants gain voice, acquire new understanding of issues affecting them through the sharing of personal stories, and develop mutual support and humane identities. This development contributes to individual, group and community healing. Openness and willingness to share stories of brokenness in a trustful and supportive environment enhance HLW outcomes. The study contributes to theories of knowledge and healing practices in cross-cultural settings, and to critical interdisciplinary and transnational research.

Keywords: mental health
Rwanda
genocide
healing
suffering
trauma
program
intervention
community-based
narrative
psychosocial
culture
brokenness
Advisor: Sakamoto, Izumi
Stereoselective Synthesis of Nitrogen Containing Compounds from Hydroxy Allylic Azides

This thesis describes research conducted since September 2006 in Prof. Robert Batey’s laboratory. The thesis is divided into four chapters. Chapter one presents a general introduction of domino reactions, sigmatropic rearrangements, and the allylic azide rearrangement. Several factors affecting the allylic azide rearrangement along with some respective examples are presented. Chapter two describes an efficient synthesis of azido unsaturated ester compounds using a microwave-assisted domino allylic azide / Johnson-Claisen rearrangement. The domino rearrangement reaction proceeds to give the azido ester compounds in good yield and excellent diastereoselectivity. The synthesis of vinyl epoxides and hydroxy allylic azides starting materials are also presented. In addition, other variants of Claisen rearrangements are briefly discussed. Chapter three describes a microwave-assisted domino allylic azide / Overman rearrangement process. The scope of the domino rearrangements, including an example involving an enantioenriched compound, is presented. The product of the domino rearrangements can be used as precursors to 1,2-vicinal diamines. Several functional group transformations and potential application of the product of the domino rearrangement are also described. Chapter four provides the synthesis of cis-2,5-disubstituted pyrrolidines from domino reduction / cyclization of γ-azido-α,β-unsaturated ketones. The overall process involves hydrogenation of the alkene and the azido group, followed by intramolecular cyclization and loss of H2O to form an imine, which is further reduced to give cis-2,5-disubstituted pyrrolidines. The reaction proceeds cleanly to give the products in high yield and with a very high diastereoselectivity ratio. In addition, the formation of pyrrolidinones via domino reduction / cyclication of γ-azido esters are also reported

Keywords: organic chemistry
azide chemistry
domino reaction
sigmatropic rearrangement
allylic azides
Advisor: Batey, Robert A.
Human B Cell Responses to Infection with Pathogenic and Commensal Neisseria Species

The Neisseria genus includes pathogens, Neisseria gonorrhoeae (Ngo) and Neisseria meningitidis, as well as commensals. Ngo, the cause of gonorrhea, induces massive inflammation but a surprising lack of adaptive immune responses. We have observed that Ngo can inhibit both T cell activation and dendritic cell maturation through interaction with the host expressed co-inhibitory receptor carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). Therefore, I wondered whether B cells may also be affected in this manner. Herein, I examine primary human B cell responses to infection with Ngo, as well as the other Neisseria species. B cells infected with Ngo show no sign of inhibition, regardless of their ability to bind CEACAM1, instead responding to gonococci with robust activation and proliferation. There are distinct subsets of B cells found in the periphery and, intriguingly, the IgM memory B cell subset expand and produce polyreactive IgM in response to goncoccal infection. These cells are innate in function, producing low affinity, polyclonal IgM that is protective against bacterial and fungal dissemination. This effect was broadly specific for Neisseria sp., as B cell infection with all commensal Neisseria species examined induced innate B cell responses. Curiously, meningococcal strains avoid inducing the innate B cell responses, making it enticing to hypothesize that its avoidance of such an ancient immune response may contribute to its ability to cause disease in humans. Finally, I tested whether gonococcal Opa protein binding to CEACAM1 affects primary human B cell activation, and show that no inhibition was observed. This absence of co-inhibitory function of neisserial-bound CEACAM1 may reflect inherent differences between distinctive cell types. Combined, the results in this thesis contribute new insight regarding the poorly characterized human IgM memory B cells, as well as to the function of CEACAM1 in lymphocytes.

Keywords: neisseria
IgM memory
innate
B-1
commensal
CEACAM1
human
B cell
lactamica
gonorrhoeae
meningitidis
Advisor: Gray-Owen, Scott
Contextualizing Value: Market Stories in Mid-Victorian Periodicals

This dissertation examines the modes, means, and merit of the literary production of short stories in London periodicals between 1850 and 1870. Shorter forms were derided by contemporary critics, dismissed on the assumption that quantity equals quality, yet popular and respectable novelists, namely Charles Dickens, Anthony Trollope, Elizabeth Gaskell and Margaret Oliphant, were writing and printing them. Navigating discourses about literature and writing to delineate and ascertain the implications of the contextual position of certain short stories, this study characterizes a previously unexamined genre, here called the Market Story. Defined by their relationship to a publishing industry that was actively creating a space for, demanding, and disseminating texts based on their potential to generate sales figures, draw attention to a particular organ, author, or publisher, or gather and hold a captive audience, Market Stories indicate their authors’ self-aware commentary on the relativity of literary and generic value, and ultimately constitute a discourse on value. Following an outline of the historical field in which market stories were produced, Chapter One reads Trollope’s six “Editor’s Tales” as intensely comic and interrogative of extant conceptions of cultural and literary value; Trollope glories in the exposure and dismantling of seemingly-reliable externality. Chapter Two considers “Somebody’s Luggage” as Dickens’s argument for the contrivance of literary genre insofar as it constructs an exaggerated system of exchanges whereby the short story generates unprecedented income. Chapter Three moves to Gaskell’s “Cranford Papers” to argue that their diligent tracing of the careful consumption of small wholes and cultivation of irregular habits constitutes an insistence on the plurality of appropriate models of consumption and value. Shifting the discussion from content to form, Gaskell’s text throws the shape of the market story into relief. Finally, Chapter Four considers Oliphant’s “Dinglefield Stories” as a figurative argument that generic and literary value is always inextricably contextualized. As literary works and cultural products, these stories embody the tensions between the utilitarian and the ‘purely’ artistic that underwrote much nineteenth-century discussion of art and culture, and these authors were unmistakably aware of the external conditions enabling and affecting the production and valuation of literary work.

Keywords: Victorian Literature
Advisor: Matus, Jill