VictorJuiz/thesis huggingface dataset:
Open-loop Temperature-compensated Digital Predistortion for Power Amplifiers

Cable communication standards are migrating to multicarrier modulation schemes with wider bandwidths and high-order constellations. However, stringent linearity specifications, aggressive transmit bandwidth requirements and higher-order modulation schemes necessitate inefficient power amplifier operation. The proposed digital predistortion scheme employs several strategies to save power, thus enabling low-power operation of the amplifier without linearity degradation across a bandwidth that is almost double the largest bandwidth encountered in predistortion literature. The digital predistortion scheme accounts for temperature and board variations by virtue of temperature compensation techniques and per-board coefficient calibration. The effectiveness of the proposed digital predistortion scheme is demonstrated on a DOCSIS 3.1 upstream power amplifier supporting simultaneous bandwidths of 200MHz. The proposed strategy overcomes novel challenges specific to DOCSIS 3.1 upstream applications: digital passband input signals and spectral overlapping of intermodulation and harmonic distortion products. The proposed technique reduces net power consumption by 25% while suppressing distortion by 11.7dB in the best case and -0.4dB in the worst case.

Keywords: docsis
linearization
memory
power amplifier
predistortion
temperature
Advisor: Gulak, Patrick G.
Social and Environmental Factors Influencing Reproductive Success in a Cooperatively Breeding Primate

Cooperative breeding is a system where non-breeding individuals care for another individual's offspring. In primates, cooperative breeding is only found in the family Callitrichidae. Leontopithecus chrysomelas (the golden-headed lion tamarin) is an endangered callitrichid that is facing high rates of habitat loss and fragmentation. For this study, I analyzed the influence of social, parental and environmental variables on reproductive success in L. chrysomelas, using data previously collected during the first long-term study on a wild population of this species. I found that infant survival was negatively associated with group size, but this was tempered by the presence of multiple adult males. The use of secondary forest was associated with high body condition, as well as high resting and reproductive rates, indicating that it can act as a good quality habitat under certain conditions. In addition, secondary forest use and the presence of multiple males were associated with faster infant growth and higher adult weights.

Keywords: Cooperative breeding
Habitat use
Infant success
Primate
Reproduction
Social behaviour
Advisor: Raboy, Becky E
Estimating the Direct Lifetime Health Care Costs of Patients with Schizophrenia in an Ontario Tertiary Care Centre

The direct lifetime health care cost of schizophrenia was estimated in patients treated at an Ontario tertiary care institution. Using methods related to incidence- based cost-of-illness studies, an estimate of lifetime costs were estimated using data from the largest mental health institution in Canada. Inpatient, outpatient and emer- gency visit information were obtained between fiscal years 2007â 2012. A probabilistic sensitivity analysis was used to test the cost assumptions used in the analysis. The direct lifetime health care cost for patients with schizophrenia was estimated to be $2.6 million CAD per patient in 2012. Hospitalizations were a major cost driver, ac- counting for up to 90% of costs. Between 2007â 2009 there was a significant decrease in the number of hospitalizations leading to a large reduction in costs. Policies and initiatives that focus on prevention of schizophrenia relapse resulting in hospitalization may be critical to effective patient management and cost containment.

Keywords: Burden
Canada
Cost
Illness
Lifetime
Schizophrenia
Advisor: Papadimitropoulos, Manny
Towards the Inclusion of Trans* Identities: Making Space and Creating Change in Postsecondary Institutions

This thesis examines the current climate of colleges and universities for trans* students in Canada. In accordance with poststructural theory, it is argued that meaning is constructed and maintained within the postsecondary social structure. An assessment of the language employed in administrative procedure, student documentation, and discrimination policies within thirteen Canadian institutions will show how the identities of trans* students must be recognized and respected to avoid systemic erasure. It will also illustrate how the gendered division of space serves to restrict access and render trans* bodies invisible. There is a dire need for linguistic and structural change in order to ensure the acknowledgement of trans* identities in all aspects of postsecondary life. This thesis calls upon postsecondary establishments to work towards the affirmation and inclusion of trans* identities while simultaneously working to address the underlying binarist, heterosexist, and cissexist structures that shape the institution.

Keywords: gender identity
inclusion
postsecondary
student
trans
transgender
Advisor: Bialystok, Lauren
Functional Enzyme Discovery by LC-MS Metabolomics in Yeast

In pursuit of novel enzymes, I have carried out a systematic analysis of gene function in the budding yeast, Saccharomyces cerevisiae. I used LC-MS metabolomics to profile metabolite levels for 120 prototrophic mutants carrying deletions in uncharacterized candidate enzyme-encoding genes. Methodology I developed in this study was successful in capturing metabolomic phenotypes for 26 candidate enzyme deletion mutants. Furthermore, I explored the function of a set of mutants deleted for genes not previously known to have a role in metabolism. I showed these mutants have altered levels of NAD+ biosynthetic intermediates. New phenotypes, here discovered, will lead to dissection of biochemical functions of uncharacterized genes and determination of their contributions to metabolism. I have also uncovered biologically-derived compounds that are uncharacterized and may be new metabolites. Overall, my work underscores LC-MS metabolomics as a powerful tool for functional genomics in its ability capture the metabolic functions of uncharacterized genes.

Keywords: Enzyme
Metabolism
Metabolomics
Yeast
Advisor: Caudy, Amy A
Application of a Novel Di-substituted 1,4-Benzodiazepine 2,5-Dione Library for the Stabilization of p53 Through Inhibition of HDM2

The HDM2 protein plays a critical role in the inhibition and degradation of p53, a key mediator of cell cycle arrest and apoptosis. The inactivation of p53 is known to be oncogenic, therefore the inhibition of HDM2 promotes apoptosis in cancer cells. In this study we describe a second round of structural activity relationship optimization on a directed library of 1,4-benzodiazepine 2,5-dione inhibitors of HDM2 for the treatment of acute myeloid leukemia. First the rational and synthetic route of the library is described. The cytotoxicity of library members is then assessed in several cell lines in the effort to establish selective activity in p53 wild type cancer cells. The biological activity of the lead compound was then evaluated by Western blot analysis for biomarkers of the induction of p53 activity.

Keywords: benzodiazepine
HDM2
p53
Advisor: Gunning, Patrick T
Development of a New Mulitcomponent-Multicatalytic Reaction of Vinyl Pyrazine Utilizing Orthogonally Reacting Boron Coupling Reagents

Multicomponent-Multicatalyst Reactions (MC)2R, which utilize multiple metal catalysts to form multiple bonds under a single set of reaction conditions, are an emerging area of research in the Lautens group. They represent a method for rapidly generating complexity and increase time and cost efficiency due to the elimination of isolation and purification of intermediates. Building on previous work from our group, a new strategy of (MC)2R using vinyl pyrazine has been developed. This new strategy merges the Hayashi-Miyaura reaction with a base-mediated SNAr and a Suzuki coupling in a one pot-one step process forming three new bonds under a single set of reaction conditions. The robustness of the process has been shown through the synthesis of a compact library of compounds (18 examples, 52-88% Yield). The key feature of this strategy is the utilization of an unprecedented pair of orthogonally reacting boron coupling reagents which allows for the excellent selectivity and yields observed.

Keywords: Dual Metal Catalysis
Multicomponent
Organoboron
Palladium
Rhodium
Advisor: Lautens, Mark
Taylor, Mark
Differences Between Domestically Violent and Non-violent Fathers' Perception of their Children in a Three Minute Interview

The present study examined the differences between domestically violent and non-violent fathers' brief perceptions of their child. Based on prior research on male batterers, a coding scheme was developed to assess fathers' ability to perceive their child. It was hypothesized that domestically violent fathers would make more self-referential comments in relationship to their child after accounting for potential confounding sociodemographic factors. The sample included 85 fathers; 40 who had domestic violence charges, and 45 with no self-reported history of perpetrating domestic violence. Children, about whom fathers reported, ranged in age from 3 to 16 years. Results indicated that domestically violent fathers made more self-referential comments, consistent with clinical descriptions of male batterers. These findings suggest there is a parenting deficit in perceiving the child as an intentional being, and the mechanisms of father maltreatment may differ. Contributions of other variables, such as father's age and child contact, are discussed.

Keywords: Abuse
Domestic Violence
Fathering
Maltreatment
Reflective Functioning
Trauma
Advisor: Scott, Katreena
Design and Evaluation of an Evaporator for a 1 kW Organic Rankine Cycle System

A 1 kW organic Rankine cycle (ORC) was designed, produced and evaluated. The system used an organic working fluid to generate power from a low temperature heat source. Considering both safety and performance, R-245fa was selected as the optimum organic fluid for the application. The necessary evaporator coil sizing was calculated and a standard air handler burner was modified to provide a heat source. An exhaust gas dilution system was developed to reduce the evaporator heat transfer temperature and protect the working fluid from thermal decomposition. A kinematically rigid scroll expander produced 334 W of electrical power, while the ORC system achieved a cycle efficiency of 1.9%. It is hypothesized that the reduced power output was due mainly to pump delivery issues leading to an instable refrigerant mass flow rate. Moreover, the pump did not provide the desired amount of pressure head, resulting in off-design operating conditions throughout the cycle.

Keywords: cogeneration
efficiency
energy
organic
rankine
Advisor: Wallace, James S
Understanding Maltreatment: A Secondary Analysis of the 2008 Canadian Incidence Study of Reported Child Abuse and Neglect

Little work to date has been done to understand perpetrators of maltreatment within Canadian families. This is especially true for biological fathers and stepfathers. The current study utilized data from the 2008 Canadian Incidence Study of Reported Child Abuse and Neglect to determine perpetration patterns in two parent, single caregiver, and blended family households. The study also examined risk factors associated with maltreatment. Results suggest that parents come to the attention of child welfare services for different reasons; fathers tend to be investigated for exposing children to domestic violence and mothers for physical abuse. While mothers were identified as perpetrators of neglect more often than fathers, the majority of neglect investigations involved both parents as co-perpetrators. Mothers and fathers showed different risk profiles. Specifically, fathers were more likely to abuse substances but less likely to have mental health issues or poor social support. Implications for policy and practice are discussed.

Keywords: Abuse
Children
Fathers
Maltreatment
Perpetrators
Risk Factors
Advisor: Scott, Katreena
Study on the Phagocytosis of Asbestos Fibers and the Mechanisms for its Frustrated Phagocytosis in Macrophages

Asbestos is a group of mineral silicates with fibrous morphology, which cause various respiratory diseases, including mesothelioma. Fiber toxicology has evolved a paradigm to explain the toxicity of asbestos fibers. It states that fibers >15 um cannot be completely engulfed by alveolar macrophages, thereby aborting phagocytosis in a process called frustrated phagocytosis. To study the mechanisms that cause this phenomenon, we investigated the phagocytosis of asbestos by confocal microscopy in cultured murine and human macrophages. Our findings showed unexpected differences in asbestos phagocytosis between murine and human cells. While murine macrophages completely engulfed fibers >15 um, albeit through a process that deviated from the canonical phagocytic pathway, phagocytosis arrested at the phagocytic cup stage in human macrophages. Strikingly, we restored phagocytosis in human macrophages by indirectly opsonizing fibers, which directed their uptake via Fcy-receptors. Altogether our results indicate that phagocytic receptors for asbestos determine its frustrated phagocytosis.

Keywords: Asbestos
Fibers
Macrophage
Phagocytosis
Advisor: Terebiznik, Mauricio R
Regulation of Argonaute Proteins and Small RNA Pathways in Caenorhabditis elegans by CHORD Domain Protein-1 (CHP-1)

Caenorhabditis elegans CHP-1 (CHORD-domain containing protein 1) has been shown to be required for embryogenesis and germline development. I observed that CHP-1 interacts with certain Argonaute (AGO) proteins and may play a role in related small RNA pathways. Recent research suggests Hsp90 and co-chaperones may regulate small RNA pathways; CHP-1 homologues have also been identified as Hsp90 co-chaperones. There has yet to be a mechanism identified for how chaperone proteins and CHP-1 may function to regulate AGO function in C. elegans. In this thesis, I will provide evidence of an interaction between CHP-1 and the C. elegans Hsp90 homologue DAF-21, as well as the existence of a CHP-1/DAF-21/AGO complex. Additionally, I will show that loss of CHP-1 has differential effects on AGOs and small RNAs across multiple small RNA pathways. Together, these studies constitute the first report of chaperone-mediated regulation of small RNA pathways in C. elegans.

Keywords: Argonaute
C. elegans
CHORD domain protein
DAF-21
Hsp90 co-chaperone
Small RNA
Advisor: Claycomb, Julie M.
Maternal and Infant Variables Associated with Critical Volumes of Breastmilk in Very Low Birth Weight Infants During the First Month of Postnatal Life

This study investigated the variables associated with the initiation, duration and exclusivity of breastmilk feeding in very low birth weight (VLBW) infants. Maternal and infant correlates associated with the provision of a critical dose, ¡Ý50 ml/kg/d, of mother¡¯s own milk in the first 28 days of life was also determined. Data including socio-demographic and health characteristics were collected prospectively for 115 mothers and infants. Ninety-six percent of infants received some mother¡¯s milk during hospitalization. Sixty-eight percent of infants received some breastmilk at discharge and 48% fed exclusively mother¡¯s own milk. Maternal Asian background (p=0.005), birth weight ¡Ý1000 g (p=0.008), gestational age ¡Ý28 weeks at birth (p=0.01), and SNAP-II Score

Keywords: breastfeeding
breastmilk
preterm infants
very low birth weight
Advisor: O'Connor, Deborah
Characterization of the Dependence of Src:ND2 Binding on Phosphorylation and Intramolecular Src Interactions

The role of the nonreceptor tyrosine kinase Src in up-regulating NMDAR activity via phosphorylating the carboxyl-terminal domain of NMDAR is well-known. The interaction between the intrinsically disordered regions of Src and an anchoring protein, ND2, is known to be essential in this up-regulation. However, the molecular mechanism underlying this docking remains elusive. We have demonstrated that the Src:ND2 interaction is phosphorylation regulated, resulting in an enhancement from no detectable binding to sub-micromolar binding, especially with Thr37/Ser75 phosphorylated. Moreover, we have discovered that the presence of SH3 domain increases binding affinity significantly from sub-millimolar to sub-micromolar. These results indicate how electrostatic interactions and intramolecular Src interactions influence the Src:ND2 interaction. Our findings expand knowledge of the regulatory possibilities of disordered proteins in general, and will be valuable for the development of therapeutic agents that target the Src:ND2 complex to treat the patients suffering from chronic pain.

Keywords: intrinsically disordered protein
ND2
NMDAR
Src
tyrosine kinase
Advisor: Forman-Kay, Julie
Identification and characterization of adhesive proteins in freshwater mussels towards the development of novel bioadhesives

The European freshwater mollusk Dreissena bugensis (quagga mussel) adheres to a variety of underwater surfaces via the byssus, a proteinaceous “anchor”, from which threads are secreted. The threads terminate in small, disc-shaped adhesive plaques which have adapted to turbulent conditions with remarkable adhesive strength for their size. Top adhesive candidates that demonstrated evidence for an adhesive role were identified via LC-MS/MS and relative quantification of proteins between the mussel plaque and adhesive interface. For the first time, a top candidate for adhesive activity (Dbfp7) was isolated directly from the quagga mussel. We aim to incorporate relevant protein motifs from these proteins into peptide mimics and to recombinantly express Dbfp7, leading to the development of novel bioadhesives for medical and dental applications. Understanding the molecular mechanisms and proteins responsible for adhesion in freshwater mussels will provide a paradigm for medical adhesives which function reliably on wet tissue surfaces with minimal inflammation.

Keywords: bioadhesion
byssus
DOPA
mussel adhesive proteins
Advisor: Sone, Eli D
The effect of bisphenol A on pro-opiomelanocortin and circadian clock gene expression in POMC-expressing hypothalamic neuronal models

Bisphenol A (BPA) has been linked to obesity. However, the direct effect of BPA on hypothalamic pro-opiomelanocortin (POMC) neurons, which regulate energy homeostasis, remains unexplored. We describe here the effect of BPA on immortalized POMC-expressing cell models, mHypoA-POMC/GFP-2 and mHypoE-43/5. BPA increased the mRNA levels of Pomc at 1 and 4 hours. BPA altered the expression of Bmal1, Per2 and Rev-Erba circadian clock genes. BPA increased the expression of inflammatory markers Nfkb, Il6 and Ikba, and steroid receptors Esrrg and Pparg. BPA decreased the expression of steroid receptors Esr2 and Gpr30. Pre-treatment with GnRH, PS1145, and T0070907 abrogated BPA-mediated Pomc induction. BPA increased Pomc mRNA levels in the mHypoA-Bmal1KO cell line. BPA treatment for 20 minutes increased relative aMSH secretion. Bisphenol S did not alter Pomc expression. In conclusion, BPA may have direct effects on hypothalamic POMC neurons, with implications for understanding the role of BPA in the arcuate nucleus.

Keywords: Cell biology
Endocrine-disrupting chemical
Feeding-regulation
Metabolism
Neuronal cell lines
Neuropeptide
Advisor: Belsham, Denise D
Design of a Polymer Transducing Pad as a Replacement for Commercial Ultrasound Gel in Low-Income Countries and Resource-Scarce Settings

A polymer pad has been formulated and tested to act as a conductive element between an ultrasound transducer and the human body during external ultrasound examinations. This pad acts as a replacement for commercially-available ultrasound gel, which is often difficult to acquire in low-income, resource-scarce, geographically inaccessible, and conflict areas, in addition to any type of zone with disrupted distribution channels for medical equipment. As ultrasound examinations are safe, portable, and relatively affordable, they are an important diagnostic imaging tool; a lack of ultrasound gel hinders the use of this technology. This polymer pad replaces the need for commercial ultrasound gel. It is composed of 4 chemical component groups: a divinyl backbone, acrylic acid and acrylate monomers, and an oligomeric poly(ethylene glycol). Certain formulations of this polymer pad can be used to produce ultrasound images that are comparable to those acquired using ultrasound gel and suggest prolonged reusability.

Keywords: absorbent polymer
couplant
hydrogel
ultrasound imaging
Advisor: Santerre, J. Paul
Salmon, Margaret
The Role of Acid Sphingomyelinase in Murine Placental Development

Sphingolipids are a diverse class of bioactive signaling lipids that control an array of fundamental cellular processes. Recently, dysregulation of sphingolipid metabolism has been observed in placentas from complicated pregnancies. In the present study, we demonstrate that acid sphingomyelinase (Smpd1), an enzyme involved in sphingolipid metabolism, is critical for normal placental development, and that its deficiency results in fetal/intrauterine growth restriction (IUGR). Smpd1-/- placentas display several structural abnormalities, including a reduced labyrinth compartment and increased thickness of the fetal-maternal interhemal membrane. In addition, Smpd1-/- placentas exhibit a three-fold decrease in sphingosine-1-phosphate (S1P), a sphingolipid important for promoting angiogenesis. Finally, we observed several hallmarks of defective autophagy and lysosomal impairment in Smpd1-/- placentas, which could contribute to the IUGR phenotype. This study proposes Smpd1-deficient mice as a novel model of IUGR, and can aid in the understanding of molecular events which lead to IUGR and placental pathologies in humans.

Keywords: acid sphingomyelinase
autophagy
fetal growth restriction
placenta
sphingolipids
Advisor: Jurisicova, Andrea
Enhancing the Generation of Progenitor T-cells from Hematopoietic Stem Cells

T-cells are an essential component of the adaptive immune system that responds to pathogens and provides surveillance against cancerous cells. In vivo, T-cells develop from hematopoietic stem cells (HSCs) in a specialized organ called the thymus that provides unique and stage specific cues to developing T-cell progenitor (proT) cells. The development of robust in vitro systems for generating proT-cells from HSCs would enable new clinical therapies for treating cancer and immunological disorders. Current assays that are amenable for clinical translation are inefficient and do not generate cells in sufficient quantities for therapeutic use. I hypothesized that incorporating molecules present in the thymus into in vitro assays would better recapitulate development and improve proT-cell generation. I identified synergistic effects between inflammatory cytokines and showed that this effect is mediated through the positive regulation of T-lineage developmental genes. This work provides new strategies for engineering systems for generating proT-cells for clinical therapies.

Advisor: Zandstra, Peter W