VictorJuiz/thesis huggingface dataset:
Silicon Ring Modulators for High-speed Optical Interconnects

This thesis presents research contributions in the area of ring modulator modeling, design, and characterization. These include small-signal modeling of the intracavity and the coupling modulated ring modulators, optimization of intracavity ring modulator rib-to-contact distance as well as proposal, design, and fabrication of PAM-N and QAM-N modulators. Accurate modeling of the ring modulator small-signal response is essential for designing a modulator. In this thesis, a closed-form expression for small-signal response of an intracavity ring modulator is derived and verified by measurement results. The pole-zero representation of the transfer function illustrates dependency of the ring modulator frequency response upon parameters such as electrical bandwidth, coupling condition, optical loss, and sign/value of the laser detunings. Using the developed small-signal model and through measurement of the fabricated intracavity ring modulators in IME A*Star process, electrical and optical trade-offs of rib-to-contact distance are analyzed. Key parameters such as extinction ratio, insertion loss, transmission penalty, and bandwidth are compared quantitatively. We show that at 4dB extinction ratio, decreasing the high doped region distance to rib from 800nm to 350nm increases the bandwidth by 3.8Ă while increasing the insertion loss by 8.4dB. Small-signal response of the coupling-modulated ring resonator is also obtained and is compared with the intracavity ring modulator response. Based on number of poles and zeros, it is shown that unlike the intracavity ring modulator, the coupling-modulated ring resonator does not have the optical bandwidth limitation. Coupling modulation in a ring resonator is then used to present a new method for optical PAM modulation. The response of this modulator is optimized in terms of linearity for both reverse and forward-biased cases. This modulator can operate for long haul communication with its data rate only limited by the MZI bandwidth. Lastly, a compact structure for DAC-free optical QAM modulation based on the coupling modulated ring resonator is proposed and fully analyzed where various key design considerations are discussed. Output level linearity is also studied where we show that linearity among levels is achievable with two segments in QAM-16 while an additional segment may be required in QAM-64.

Keywords: Coupling modulation
PAM
QAM
Ring modulators
Silicon Photonics
Small-signal
Advisor: Sheikholeslami, Ali
Identification of Epstein-Barr virus proteins that inhibit the DNA damage response

Epstein-Barr virus (EBV) is a common herpesvirus that is the causative agent of mononucleosis and can also induce a variety of B cell lymphomas and carcinomas. To promote viral replication and cell survival, EBV is known to manipulate the cellular DNA damage response (DDR). To date there have only been a few studies on the interplay between EBV and the DDR and the functions of many EBV proteins remain uncharacterized. In this study, we screened a library of 47 EBV proteins for the ability to interfere with the formation of 53BP1 foci, a late step in the DDR, in response to etoposide-induced DNA damage. An uncharacterized tegument protein, BKRF4, was identified as an inhibitor of the DNA damage response. By studying the effect of BKRF4 on the steps of the DDR, it was shown that BKRF4 had no effect on the induction of γ-H2AX, but blocked the subsequent step at which histones H2A/H2AX become polyubiquitylated, which in turn inhibited the recruitment of 53BP1. To identify the host interactions of BKRF4, an affinity purification-mass spectrometry experiment was performed and identified histones as the most prevalent interacting partner. In keeping with this finding, an in vitro binding assay performed with purified BKRF4 and purified histone octamers showed the direct interaction between BKRF4 and histones. This interaction predicts that BKRF4 will localize to cellular chromatin, which was confirmed by both fluorescent microscopy and biochemical fractionation. BKRF4 contains a highly acidic region and this fragment of the protein was shown to be responsible for the chromatin interaction and DDR inhibition. Therefore, our results indicate that BKRF4 is targeted to cellular chromatin through a direct interaction with histones, where it can modulate at least some histone functions including the DDR.

Keywords: DNA damage response
Epstein-Barr virus
Advisor: Frappier, Lori
Jin, Dong-Yan
Number Fields with Large Minimal Index

The index of an integral element α in a number field K with discriminant DK is the index of the subring Z[α] in OK. The minimal index m(K) is taken over all α ∈ OK that generate the field. This thesis proves results of the form m(K) << |DK|U for all Galois quartic fields and composites of totally real Galois fields with imaginary quadratic fields, and of the form m( K) >> |DK|L for infinitely many pure cubic fields, both types of Galois quartic fields, and the same composite fields, with U and L depending only on the type of field. The upper bounds are given by explicit elements and depend on finding a factorization of the index form, while the lower bounds are established via effective Diophantine approximation, minima of binary quadratic forms, or norm inequalities. The upper bounds improve upon known results, while the lower bounds are entirely new. In the case of imaginary biquadratic quartic fields and the composite fields under consideration, the upper and lower bounds match.

Keywords: Effective Diophantine approximation
Index forms
Minimal index of number fields
Advisor: Kim, Henry H
Acetylated Hemoglobin Bis-Tetramers: From Chemical Designs to Physiological Impacts

My research centers around the development of chemical strategies that enhance the production of hemoglobin bis-tetramers. Hemoglobin-based oxygen carriers (HBOCs) are molecules that can carry oxygen in the circulation without being contained within red blood cells. Clinical trials of early HBOCs note that the use of these materials was associated with increased risks of cardiovascular dysfunction and death. The adverse effects appear to result from removal of nitric oxide (NO), a signal required to maintain vasorelaxation. Recent pre-clinical studies show that a hemoglobin bis-tetramer do not induce such side effects. However, due to constraint on the chemical process, improved methods to produce this class of materials is necessary for further in vivo characterizations. A potential alternative route to make hemoglobin bis-tetramer is through a bio-orthogonal copper catalyzed azide alkyne cycloaddition (CuAAC) between two azide-functionalized hemoglobin tetramers and a bis-alkyne chemical linker. The efficiency of the coupling process appears to be limited by the introduction of azide-containing cross-link, which gives a mix of reactive and non-reactive azides. I developed a chemical blocking strategy to push the azide-containing cross-link to form in the reactive state. My efforts led to the formation of a novel acetylated hemoglobin bis-tetramer (BT-acHb) with up to 65% yield. In vitro characterization of BT-acHb showed that the chemical modifications did not significantly perturb the protein’s structure or oxygen carrying abilities. Further study on the nitrite reductase activity of the derivatives were carried out, as this vasodilatory feature may act as an in situ source of NO. I find that BT-acHb exhibit enhanced ability to mediate the nitrite-NO conversion. To study whether the chemical modifications necessary to improve the production of bis-tetramer affects its circulatory behavior, I examined the in vivo effects of BT-acHb in the best animal models available. Animal studies of BT-acHb indicate that HBOCs, produced using the efficient bio-orthogonal chemistry described in this dissertation, are safe and functional oxygen carriers in the murine circulation.

Keywords: Bio-orthogonal
Bis-tetramer
HBOC
Hemoglobin
Hypertension
Advisor: Kluger, Ronald
Symmetrical Elements in the Piano Music of Einojuhani Rautavaara

Einojuhani Rautavaara (1928 – 2016) is regarded as one of the most internationally successful composers from Finland since Jean Sibelius. He is widely known for his pluralistic compositions that do not follow a linear progression of stylistic development and that exhibit a synthesis of seemingly contradictory compositional styles in his mature works. Despite the rapid changes of styles, Rautavaara retains certain characteristics that set his music apart from that of others. One of these elements that remained consistent throughout his career is his fascination with symmetry. From the Three Symmetrical Preludes during his student years to his late piano miniatures, symmetrical compositional tools such as the bilateral keyboard symmetry remained a key component in his piano works. Although Rautavaara’s piano output is small compared to other genres, it is scattered throughout various stylistic periods in his life, making it possible to observe the similarities and changes in his writing. The goal of this research is to observe and study how the composer developed and utilized symmetry in his compositions through analysis of selected solo piano works from the early to the late period. As the research centers on symmetry, the works chosen for analysis will be the ones that contain significant amounts of symmetrical writings, namely the Three Symmetrical Preludes (1949–50), selections from Etudes (1969), Piano Sonata No. 1 (1969), Narcissus (2001), and Mirroring (2014). This research also provides an opportunity to study Rautavaara’s lesser-known piano works, as well as providing a first look at Mirroring, his very last work for solo piano. The concluding chapter considers the symbolisms in symmetry as well as interpretive choices and pedagogical merits of symmetrical structures in Rautavaara’s solo piano music.

Keywords: Contemporary music
Einojuhani Rautavaara
Finnish composer
Keyboard symmetry
Piano
Symmetry
Advisor: McClelland, Ryan
Transient Receptor Potential Melastatin Channel-2 Mediates Microglial Activation and Migration After Injury

TRPM7 and TRPM2 are non-selective cation channels of the Transient Receptor Potential channel superfamily and ‘melastatin’ subfamily. Each channel has gained attention for the role they play in mediating ischemic cell death in brain tissue, however their physiological expression and potential roles in the developing brain remained elusive. Real-time PCR assays revealed that TRPM7 mRNA expression peaks in the cortex 2-weeks after birth which correlates most closely with a period of rat brain development associated with neurite outgrowth. TRPM2 mRNA was most highly expressed in microglia and paralleled the perinatal expression timeline for microglial infiltration and maturation in the rat brain. These developmental expression profiles indicated a potential role for TRPM2 in regulating microglial activation. Since calcium regulation is important for cell function and migration, a specific role for TRPM2 in regulating cell migration after injury was investigated by time-lapse imaging of an in vitro model of cell migration and injury called ‘necrotaxis’. Primary microglial cells isolated from Trpm2-/- mice exhibited impaired migration, resulting in the loss of persistent directional migration. A high colocalization between Rab11 (recycling endosomes) and β1-integrin was also found in Trpm2-/- microglia, suggesting that TRPM2 affects the overall migration of microglial cells by mediating tail detachment via the trafficking or recycling of integrins. To determine whether the effects of knocking out TRPM2 on microglia persisted in an in vivo model of injury, Iba1+ immunoreactivity was assessed in wild-type and Trpm2-/- mice after inducing acute ischemic stroke. Immunohistochemistry analyses revealed a lower number of activated microglia in Trpm2-/- mice after acute ischemia compared to wild-type mice, suggesting that TRPM2 affects the recruitment of microglia to the site of injury. This study provides evidence that links TRPM2 to tail detachment via integrin trafficking/recycling which in turn affects the migration of microglial cells. TRPM2 may therefore be a good target to mitigate inflammation after stroke and other neurodegenerative diseases, when excessive microglial activation or proinflammatory processes may negatively impact brain recovery.

Keywords: Cell Injury
Cell Migration
Cerebral Development
Microglial Activation
TRPM2
Uropod
Advisor: Aarts, Michelle M
Terebiznik, Mauricio
IMMIGRANT NON-NATIVE ENGLISH SPEAKING TEACHERS IN TESOL: THE NEGOTIATION OF PROFESSIONAL IDENTITIES

This study examined how immigrant non-native English speaking teachers (INNESTs) in the field of TESOL (Teachers of English to Speakers of Other Languages) negotiate professional identities within the framework of a TESOL certification program. Three aspects of their identities were investigated: language-related identity, disciplinary identity, and teaching self-knowledge. Two groups of participants were recruited. The first group (115 in number) had already completed a TESOL program and were ESL teachers. The second group (five in number) were all registered in a full-time TESOL program to become certified to teach ESL in Ontario, Canada. A complementary, concurrent component mixed methods research design was adopted. The quantitative and qualitative data were collected through various data collection strategies. The analysis is informed by a number of theoretical concepts: identity, critical pedagogy, sociocultural theory, and teacher cognition. The main findings are as follows. First, INNESTs viewed the native speaker construct as consisting of multiple dimensions. The findings suggest that the construct is complex, contextual, dialogic, dynamic, ideological, intersecting, multifaceted, negotiable, relational, situated, and shifting as a developmental process as opposed to a fixed unitary state. Despite that, INNESTs continue to experience mostly conventional realizations of the construct. Second, institutional certification serves as a symbolic discourse of de-professionalization for INNESTs applying for certification. INNESTs reacted to such discourse in different ways, accepting and internalizing or questioning and resisting it. The certification process did not distinguish the experienced INNESTs from their novice native-born teacher candidates; but it did provide them with recognition, acceptance, and legitimacy in the professional TESOL community. Third, the majority of the INNESTs reported a high level of confidence by presenting a generally positive self-image. The findings highlight the importance of self-image in negotiating teaching knowledge in the TESOL community. Moreover, INNESTs’ cognition is influenced by conflicts they experience reconciling their new teaching context, their past learning experiences and teaching beliefs, as well as their instructional decisions. Implications regarding ways to facilitate positive identity construction and professional integration are discussed.

Keywords: Canada
Immigrant Teachers
Non-Native English Speaking Teachers
Professional Identity
Teacher Certification
TESOL
Advisor: Gagné, Antoinette
The Development and Application of Global Proteomic Approaches to Quantify Protein Oxidation

ROS and ROS-induced protein oxidation are involved in a variety of physiological and pathological conditions. Methods that can globally detect and quantify protein oxidation are important for studying redox signaling pathways. I developed/optimized two MS-based approaches to detect protein oxidation, one is specialized to monitor classical PTP oxidation and the other detect oxidation of reactive cysteines more generally. Using these two approaches, I identified PTPN12 and PKM2 oxidation in FH-deficient hereditary leiomyomatosis and renal cell carcinoma (HLRCC) cells. PTPN12 oxidation leads to ABL1 activation, which is important for HLRCC cell proliferation and survival, whereas PKM2 is likely to be a redox sensor and its oxidation lowers oxidative stress in HLRCC cells. Overall, globally detecting and characterizing protein oxidation help us to understand the pathobiology of HLRCC and to identify potential therapeutic interventions to treat this cancer.

Keywords: ATS
HLRCC
PTP
PTPN12
q-oxPTPome
ROS
Advisor: Neel, Benjamin G
Low-cost Sensor Array Devices as a Method for Reliable Assessment of Exposure to Traffic-related Air Pollution

The exposure to air pollutant mixtures is a well-known risk factor for inducing and increasing the severity of diseases. Combining low-cost sensors in arrays holds great potential for real-time monitoring of pollutant exposure because of versatility and aptitude for tracking multi-pollutant exposure. While many low-cost air pollution monitoring devices have been proposed, several underexplored opportunities remain, including sensor-derived pollution indices, source analysis and exposure assessment. A thorough investigation of different low-cost commercial gas and particulate matter sensors from 5 manufacturers has been conducted and best-performing sensors were identified. A device for monitoring air quality has been developed and tested. Each device consists of an array of commercially available metal oxide semiconductor for monitoring NOx and O3, CO, CO2 and optical sensors for monitoring PM2.5. Level of pollutant exposure has been characterized at different locations in Toronto over 3 different campaigns between 2013 and 2016. These deployments allowed long-term sensor performance to be evaluated under different meteorological conditions as well as different ranges of pollutant concentrations. Analysis of a large range of gas sensors revealed several key challenges, including high intra-sensor variability, interference from temperature and nonlinearity. Air quality health index estimation from sensor readings was successfully demonstrated. Three aspects of device reproducibility were evaluated: drift over time, impact of interferences and impact of site-specific mixtures. Three categories of approaches for improving sensor accuracy and reproducibility were tested: nonlinear calibration models, variable transformations and training data selection. Model reproducibility, ability to adjust for multiple combinations of interferences and ability to resolve sites was improved when devices were calibrated at multiple sites. Analysis showed that both short-term and long-term temporal patterns could be resolved and compared at different sites. Background subtraction helped further emphasize the differences and rank sites in terms traffic-related pollution.

Keywords: air pollution
exposure
sensors
spatial
temporal
traffic
Advisor: Evans, Greg J
Innovative by Design: How Organizations Can Sustain Continual Innovation in Highly Competitive Markets

Almost every contemporary organization operating in competitive markets is pressed to come up with novel concepts that create new experiences or meaningfully transform product typologies. For most organizations, this is a quest for survival and continued relevance in rapidly changing markets. The intuitive solution is “act,” more like a startup, playing fast and loose to disrupt established rules and conventions. Research shows however that the entrepreneurial mindset is short lived, giving way to the routines and structures that founders initially rebelled against, as companies scale and persist over time. More often than not, this leads organizations to disproportionately exploit existing knowledge at the cost of exploring for new ideas and ways of solving problems. This raises a fundamental question: how can creative organizations, whose value and vitality are derived from consistently generating novel concepts, do so reliably and over time, without becoming predictable in their output? My research, based on a yearlong ethnographic study at a world renowned architectural firm in New York City and interviews with designers across the United States, points to the criticality of project-based organizational structures, which serve as the framework for balancing the twin tasks of learning between projects and unlearning within projects — which is vital to productively breaking with past experiences and expectations. This organizational typology is in many instances necessary to drive innovation within a company, however not sufficient to explain its continuation and nonconformity with past outputs. I argue that it is the presence of company specific predispositions to ways or modes of responding to situations, and not particular acts, that enables highly innovative organizations to continually move forward explorations into the unknown, to generate genuinely novel concepts. I argue that to successfully drive continual innovation, three distinct areas of a creative-project based organization’s approach rely on predispositions for moving forward explorations, including team coordination, exploration, and constructing ideas.

Keywords: Design
Exploitation
Exploration
Innovation
Practice
Project-Based Organization
Advisor: Schneiderhan, Erik
Mechanically Robust, (Super)Hydrophobic Surfaces

In this doctoral study, applied and fundamental research on mechanically robust, (super)hydrophobic surfaces was performed. On the applied front, a simple electro-codeposition process was developed to fabricate non-wetting metal matrix composite coatings with exceptional hardness and resistance to degradation of non-wetting characteristics from abrasive wear compared with a commercial superhydrophobic surface coating. The composites were made of ultra-fine grain / nanocrystalline nickel matrix with embedded hydrophobic particles: polytetrafluoroethylene (PTFE) or rare earth oxide (i.e. cerium oxide) distributed throughout the thickness of the composite coating. Various characterization techniques, including wetting property measurements, electron microscopy, microhardness measurements, and abrasive wear testing were performed to develop the structure – property - performance relationships for this new class of non-wetting material. On the fundamental side, the inherent wettability of rare earth oxides was investigated, as there is currently an active debate in the literature as to whether these ceramics are hydrophobic or hydrophilic. To develop a better understanding on the wettability of rare earth oxides, a study of single crystals with near perfect surfaces was carried out. Epitaxial films of CeO2 and Er2O3 were grown on low Miller index oriented yttria stabilized zirconia single crystal substrates by a pulsed laser deposition technique. Through this study, the crystal orientation – surface energy - wetting property relationships for rare earth oxides were established. Fresh REO epitaxial films were hydrophilic, the water contact angle (WCA) strongly depending on the crystallographic orientation; WCA(111) > WCA(110) > WCA(001), which reflects the differences in surface energy (SN); SN(111)

Keywords: composite coating
electrodeposition
non-wetting
pulsed laser deposition
rare earth oxide
structure-property relationships
Advisor: Erb, Uwe
Azimi, Gisele