VictorJuiz/thesis huggingface dataset:
Per-Pixel Coded-Exposure CMOS Image Sensors

The ever-growing demand for applications of cameras necessitate research not only on improving the performance of image sensors but also on new image sensor architectures. One of the most recent image sensor architectures, based on coded-exposure pixels (CEP), allows for the programmability of exposure time at the pixel level, and allows for imaging in new ways that were not possible so far. In this thesis, first a comparison of different photo-detectors is presented to highlight their operation principle as well as their capabilities. Five photo-detector architectures are simulated to compare the most important specifications in CEP cameras, namely sensitivity and tap-contrast. Next, a first prototype, a CEP image sensor based on photogate (PG) pixels, is presented. The sensor has a total resolution of 180x160 pixels and is fabricated in 0.35um CMOS technology. Dual-tap pixels with per-tap conversion gain are proposed, where the photogenerated charges in the pixel are collected in one of the taps based on the code stored in the pixel at each interval of the exposure. The second prototype is an image sensor based on pinned-photodiode (PPD) pixels. The sensor is fabricated in a 0.11um CMOS technology with the main array consisting of 244x162 pixels. The dual-tap pixel proposed in this work has the same conversion gain for the two taps but provides per-tap adjustable gain in the readout. The array operates at a maximum subframe rate of 180Hz, which is equivalent to 4 subframes per frame at 25fps considering the overhead time of frame readout. The sensor is deployed in two different single-shot 3D computational imaging techniques. Finally, an architecture based on global-shutter PPD pixels is presented allowing the implementation of smallest CEP pixels (7um pitch) reported to date. The sensor is fabricated in 0.11um CMOS technology with a resolution of 312x320 pixels. In the proposed pixel, a pinned storage diode operates as a charge memory to pipeline the charge generation and charge sorting operations. At a subframe rate of 2.7kHz, a reasonable tap-contrast of more than 90% is measured. Finally, a few different computational imaging techniques that are demonstrated with this camera are presented.

Keywords: CMOS image sensor
computational camera
Electronics
Advisor: Genov, Roman
Kutulakos, Kiriakos N.
Full-Scale Testing and Improvements to the Design and Use of the Gapped-Inclined Bracing System

The gapped-inclined bracing (GIB) system is an innovative retrofitting device that was developed to improve the performance and prevent the collapse of reinforced concrete (RC) soft-storey buildings during earthquakes. The GIB system was designed to increase the displacement capacity of the soft ground floor without increasing the overall lateral resistance of the building. During an earthquake, the ground floor of GIB-retrofitted structures acts as an isolation layer protecting the upper floors of the building while maintaining the integrity and gravity-load-carrying capacity of the soft ground floor; this is accomplished using the geometry and gap element of the GIB system. This dissertation presents five contributions to the development of the GIB system. First, a four-phase, full-scale experimental programme of the device was completed. In the second phase of testing, the reversed cyclic response of two single storey, single bay, RC planar frames was studied: a conventional soft-storey and a GIB-retrofitted soft-storey. These frames represented the ground-floor of existing seismically vulnerable structures. The lateral displacement mechanism of the frames was governed by flexural hinging at the top and bottom of the columns, representing a common soft-storey failure. The results confirmed the improved seismic performance of GIB-retrofitted structures and revealed a stable GIB-only rocking response at extreme lateral drifts, which acts as a collapse-prevention system and a viable mechanism for post-earthquake performance. Second, these experiments were modelled using three computer software: OpenSees, VecTor2, and ATENA. Because damage of the structure was governed by flexural hinging, OpenSees was found to best represent the response of the experimental specimens. Third, the limit states of common GIB-to-structure connections were identified. Detailed finite-element analyses were performed to highlight potential failure modes and suggest strengthening options to increase the capacity of the connection. Fourth, the limits of stability for the bidirectional response of GIB-retrofitted structures were identified. Finally, with an improved understanding of the GIB system, a step-by-step design procedure for the retrofit of soft-storey buildings using the GIB system was proposed. The design procedure was exemplified for a 5-storey case-study structure. The effects of including supplemental damping in parallel with the GIB system was also investigated.

Keywords: Full-scale experiments
Gapped-inclined brace
Numerical Modelling
Seismic retrofit
Soft-storey buildings
Advisor: Christopoulos, Constantin
Music for God’s Glory: The Improvisatory Organ Music of Matthias Weckmann (1616 – 1674)

The improvisatory music of German organist-composer Matthias Weckmann (1616 – 1674) has remained largely undervalued and underperformed for almost 400 years, arguably suffering a similar fate as did the works of Johann Sebastian Bach (until Felix Mendelssohn sparked a revived interest in Bach’s music during the early 19th-century). Despite Weckmann’s relative obscurity today, interest in his music is growing. Weckmann studied organ, singing and counterpoint with the famed Heinrich Schütz and Jacob Praetorius II, and was hailed as a “true virtuoso” by contemporary Johann Jakob Froberger after a legendary improvisation contest between the two musicians. This study documents the search for, and deeper understanding of, Weckmann’s improvisatory competencies through exploring the different facets of his life, relationships, and work — and ultimately how Weckmann contributed to the legacy of improvisation within the realm of North German baroque organ music. I document Weckmann’s life, his travels, the influences of his teachers and the breathtakingly beautiful instruments that shaped his artistic style and registrational practice. With a view towards 1) engendering a deeper and more comprehensive stylistic understanding of Weckmann’s music, 2) solving numerous problems of attribution, and 3) laying the groundwork for a new performer’s edition of Weckmann’s Organ Works, the dissertation provides an in-depth analysis of the Free and Chorale-based works. The study frames Weckmann’s genius in terms of his exceptional contrapuntal skill, improvisatory imagination, sensitivity to sacred texts, as well as the creative methods he implemented to maximize exploration of the expressive possibilities of the organ, thereby bringing his diverse set of powerful musical ideas to life.

Keywords: improvisation
Matthias Weckman
north German baroque
organ music
stylus phantasticus
Weckmann
Advisor: Komisaruk, Kevin
Slag Refining of Aluminum Silicon Alloys for the Purpose of Obtaining Solar Grade Silicon

The need for a reliable, cost effective method to produce solar grade silicon (>6N purity) for photovoltaic cells is imperative in the age of climate change. Boron and phosphorus are used to dope the silicon to make p- and n-junctions and require the strictest control; unfortunately, these are also the most difficult elements to remove during the purification of silicon. The relatively new path of combining of slag treatment and solvent refining is seen as a potential route to large scale and cost-effective refining of silicon. In this study, slag treatment of aluminum-silicon alloys using calcium aluminate slags with varying composition was investigated. Kinetics data was collected and used to calculate the mass transfer coefficient of B and P into the slag; a maximum of 47µm/s and 14µm/s respectively was reported at 35mol% Al2O3. Calculations showed mass transfer of boron was faster than phosphorus due to the smaller ionic radius. It was found that there was a linear correlation between the mass transfer coefficients and superheat of the slag; it is concluded that this is an artifact of the change in both slag and metal compositions as the experiment proceeds. Equilibrium data was used to compare the removal of phosphorus and boron from the alloy, showing significantly better performance for phosphorus removal as it was reduced into the slag as a phosphide ion. Boron removal, as borate ions, was less than ideal because of the very low oxygen potential provided by the slag. The maximum LB and LP reported in this study was 0.38 and 2.17 respectively at 40mol% Al2O3. Also calculated were the slag capacities for borate and phosphide ions. In addition to the fundamental data contributions to the field, a set of criteria were defined for future researchers should they want to pursue slag treatment and solvent refining. Also, a number of parameters that might prove useful when narrowing down potential alloy systems, that would benefit from slag refining, were provided and assessed.

Keywords: aluminum
calcium
silicon
slag
solar
solvent
Advisor: Barati, Mansoor
Sridhar, Ramamritham
Interprofessional Teams in the Context of Primary Care Reform in Ontario, Canada: Selection Factors and Association with Access to Care and Health Services Utilization

Background: Countries throughout the world have been exploring new models to deliver primary care. Ontario has undergone a primary care reform that includes the introduction of interprofessional teams. The purpose of this thesis was to investigate the association between receiving care from interprofessional versus non-interprofessional primary care teams and access to care and health services utilization. The first study investigated selection factors into interprofessional teams. The second and third studies compared interprofessional teams and non-interprofessional teams on access and health services utilization measures.Methods: The three studies linked provincial administrative datasets (second study included a provincial healthcare experience survey as well) to assess outcomes of interest over time. The first study was cross-sectional and the last two were retrospective cohort studies. Results: The first study identified that there are selection factors into interprofessional teams. The second study findings highlighted that as compared to Health Care Experience Survey respondents in non-interprofessional teams, respondents in interprofessional teams self-reported more timely access to care and less walk-in clinic use but no significant difference in self-reported access to after-hours care and emergency department use. The third study found that there was no difference in the change over time in Ambulatory Care Sensitive Conditions admissions and all cause hospital re-admission between interprofessional and non-interprofessional teams between the pre- and post-implementation periods. Conclusion: Ontario has made a major investment in interprofessional team-based care. The findings from this thesis indicate that there are selection factors into interprofessional teams. Interprofessional teams perform better than non-interprofessional teams on some but not all investigated processes and outcomes of care. Our findings can inform other jurisdictions aiming to expand voluntary participation in interprofessional primary care teams regarding expectations about the relationship between primary care policy, organization and delivery and patient experience and health services utilization.

Keywords: Access to Care
Health Services Research
Health Services Utilization
Primary care
Primary Care Reform
Advisor: Glazier , Rick
Reconstructing Maritime Networks in the Bronze and Iron Age Eastern Mediterranean: A Diachronic Analysis of Canaanite and Phoenician Maritime Transport Containers

This thesis provides a diachronic overview of the evolution of Canaanite and Phoenician Maritime Transport Containers (MTCs) produced in the Levant from the Early Bronze Age (EBA) II/III to the terminal Iron Age (IA) II. The focus is on the morphological development of these ceramics and how this relates to maritime function, standardization for international markets and technological innovation. Through an examination of the spatial distribution and provenance of these ceramics, as well as EBA precursor and Iron Age successors, this study will elucidate their essential relationship with eastern Mediterranean maritime (and terrestrial) exchange networks. Their morphological development reflects growing specialization as an MTC and the transport of bulk liquid staples like oils, resins, and wine, characteristic of production in the Levant. Littoral patterns are apparent, with exemplar MTCs common to coastal centres, but with evidence for dendritic patterns of exchange connected to hinterland production. This study reveals expansions and contractions in long-distance trade during the Bronze and Iron Ages, with some continuity in patterns stemming from coastal emporia, which interfaced with other economic centres via long-distance maritime activities. A basic typological framework for the development of Levantine MTCs is presented, covering a period of nearly two millennia, but revealing appreciable continuity. With the growth of incipient EBA long-distance maritime routes, so too occurred the innovation of new ceramic technologies in the form of MTC prototypes (MTC #1), further refined in the Canaanite Jars (MTC #2) of the Middle Bronze Age (MBA), and with the expansion of international networks in the Late Bronze Age (LBA) IIB, producing what may be the earliest purpose-built MTCs (MTC #3). Despite the disappearance of this distinctive, standardized type with the transition to the Iron Age, likely due to contraction in long-distance trade, there is continuity in the production of this carinated jar tradition along the Phoenician coast (MTC #4). The Phoenician MTCs of the Iron I-II relate to similar processes, with evidence that international trade continues during the Iron I (particularly with Egypt and Cyprus), and that it proliferates during the Iron II when MTC #5 is similarly standardized for international markets and provides evidence for deposition in contemporary shipwrecks. These Phoenician MTCs display further continuity with amphorae produced into the later Persian, Classical, and Roman periods.

Keywords: Amphora
Canaanite
Levant
Maritime Networks
Maritime Transport Containers
Phoenician
Advisor: Harrison, Timothy P.
The Transcriptomic Heterogeneity in Prostate Cancer

Prostate cancer affects millions of people worldwide. The current risk stratification and disease management strategies are not sufficient. Understanding the molecular basis of prostate cancer can help address these clinical needs. While the genome is extensively investigated, the transcriptome of prostate cancer is much less well characterized. I have worked to unravel the transcriptomic heterogeneity in prostate cancer. I investigated the transcriptome of primary tumors with ultra-deep total RNA-seq and identified widespread RNA circularization in prostate cancer for the first time: the average tumor expressed 7,232 distinct circular transcripts and circRNAs showed a highly tissue specific expression pattern. The parental genes of circRNAs showed distinct characteristics and the circular transcriptome harbors unique prognostic information. The degree of circRNA production is directly correlated to disease progression in multiple patient cohorts. Loss of function screening identified 11.3% of highly abundant circRNAs as essential for cell proliferation; for ~90% of these, their parental linear transcripts were not essential. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth partially through regulating microRNA miR-181. In two side projects, I interrogated the tumor transcriptome from two different aspects: First, I tackled the intra-tumoral heterogeneity at single cell resolution and identified multiple transcriptomic reprogramming associated with tumor progression in primary tumors (Appendix I). Second, I worked to outline the transcriptional regulatory mechanism of the histone demethylation protein LSD1 on the pioneer transcription factor FOXA1 in prostate cancer (Appendix II). Together, my work reiterated the importance of transcriptomic study in prostate cancer: it provided novel insights into prostate cancer biology, offered multiple opportunities for future investigation and pinpointed actionable targets for advanced tumors.

Keywords: circRNA
FOXA1
Prostate cancer
scRNA-seq
transcriptional regulation
Transcriptome
Advisor: He, Housheng H
Channel Estimation in TDD and FDD-Based Massive MIMO Systems

There are three parts to this thesis. In the first part, we study the channel estimation problem in frequency-selective multi-user (MU) multi-cell massive multiple-input multiple-output (MIMO) systems, where, a time-domain semi-blind channel estimation technique is proposed. Compared to frequency-domain, the time-domain channel estimation requires fewer parameters be estimated. Importantly, the time-domain estimation has enough samples for an accurate channel estimate. Given this many samples in the time-domain, the proposed channel estimation technique obtains a better estimate of the channel. Here, there is no assumption on orthogonality of users' channels, knowledge of large-scale fading coefficients, and the orthogonality between the training symbols of the users in all cells. The second part of the thesis studies the channel estimation problem in correlated massive MIMO systems with a reduced number of radio-frequency (RF) chains. Leveraging the knowledge of channel correlation matrices, we propose to estimate the channel entries in its eigen-domain. Due to the limited number of RF chains, channel estimation is typically performed in multiple time slots. Using the minimum mean squared error (MMSE) criterion, the optimal precoder and combiner in each time slot are aligned to transmitter and receiver eigen-directions, respectively. Meanwhile, the optimal power allocation for each training time slots is obtained via a waterfilling-type expression. In the final part, we study the downlink channel estimation for frequency-division-duplex (FDD) massive MIMO systems. Acquiring downlink channel state information in these systems is challenging due to the large training and feedback overhead. Motivated by the partial reciprocity of uplink and downlink channels, we first estimate the frequency-independent channel parameters, i.e., the path gains, delays, angles-of-arrivals (AoAs) and angles-of-departures (AoDs), via uplink training, since these parameters are common in both uplink and downlink. Then, the frequency-specific channel parameters are estimated via downlink training using a very short training signal. To efficiently estimate the channel parameters in the uplink, the underlying distribution of the channel parameters is incorporated as a prior into our estimation algorithm. This distribution is captured using deep generative models (DGMs). The proposed channel estimation technique significantly outperforms the conventional channel estimation techniques in practical ranges of signal-to-noise ratio (SNR).

Keywords: Channel estimation
Deep generative model
Frequency division duplex
Hybrid Beamforming
Massive MIMO
Waterfilling
Advisor: Adve, Raviraj
ShahbazPanahi, Shahram
Advancing Photodynamic Therapy via Targeting and Nanomedicine

Photodynamic therapy (PDT) is a cancer treatment modality that relies on a combination of non-toxic photosensitizers, oxygen, and light to generate cytotoxic reactive oxygen species. PDT traditionally has been used in superficial cancers, but with the advent of fiber optic technologies and laparoscopic surgical techniques it has become feasible in a variety of deep-seated tumours. Despite these technological and clinical advancements, PDT has several limitations that prevent it from becoming a mainstay clinical modality. First, clinical PSs lack tumour specificity, which results in prolonged photosensitivity in patients as well as suboptimal PS tumour accumulation. Secondly, PDT combination with systemic therapies such as chemotherapy, remains underexplored, which restricts PDT indications. This thesis seeks to address these limitations by advancing PS design and investigating PDT in combination with systemic chemotherapy.Chapters 3 and 4 of this thesis describe the development of two porphyrin-based prostate-specific membrane antigen (PSMA)-targeted PSs with complementary phototherapeutic and imaging properties. These PSMA-targeted porphyrins demonstrated excellent specificity and favorable tumour accumulation, which translated into potent PDT. Furthermore, it was discovered that the inclusion of a 9-amino acid D-peptide linker between the porphyrin molecule and the targeting ligand is a robust strategy to improve pharmacokinetics, particularly half-life, of a targeted PS that further enhanced its tumour accumulation. This dissertation also explores whether the use of porphyrin supramolecular interactions within nanoparticles could yield phototheranostic agents with tunable properties. Specifically, Chapter 6 of my thesis probes the effects of different porphyrin conjugates on the resulting nanoparticle’s imaging and phototherapeutic properties. While photodynamic therapy can be effective as a stand-alone modality, its combination with other mainstay clinical techniques such as chemotherapy is extremely promising as it expands the range of cancers it can be applied to. Chapter 5 explores the use of subtherapeutic photodynamic treatment as a priming strategy to modulate the tumour microenvironment and enhance delivery of various nanoparticles including clinically approved nanomedicines. Overall, this dissertation pursues several research avenues for PDT advancement, which will hopefully aid the development of next generation clinical photosensitizers and more precise and versatile PDT protocols.

Keywords: cancer
lipoprotein
nanomedicine
photodynamic
porphyrin
PSMA
Advisor: Zheng, Gang