VictorJuiz/thesis huggingface dataset:
Brain Biometrics under Auditory Stimulation for Human Identity Recognition

The demand for security and user authentication has recently become an essential part of all aspects of our lives thus increasing the popularity of biometric recognition. As this technology becomes more common, the potential of spoofing attacks is of rising concern. For instance, conventional biometric traits, like face or fingerprints, are highly vulnerable to presentation attacks as these traits are exposed and can be easily replicated. This urges the scientific community to investigate other biometric modalities that are less prone to such attacks. Biomedical biometrics is an emerging technology that adopts vital signals acquired from the human body for biometric recognition. Such biosignals inherently provide liveliness detection and robustness to circumvention against presentation attacks as these modalities are difficult, if not impossible to replicate. Among various biomedical biometrics, the feasibility of the electrical activity of the brain, or Electroencephalogram (EEG), has been extensively examined for human identification tasks. This thesis proposes a new acquisition protocol to establish an EEG-based biometric system. The acquisition protocol adopts auditory stimulation to elicit a special class of brainwaves known as steady-state Auditory Evoked Potentials (AEP). AEPs, as neural responses share the same advantages of biomedical biometrics in terms of circumvention prevention and liveliness detection. Besides, steady-state AEPs share unique advantages that do not apply to other biosignals; being modular (i.e., stimulus-dependent) steady-state AEP supports cancellable biometrics, additionally, it can be linked to a user-selected PIN to implement a two-step authentication system. However, one of the most challenging aspects of deploying brainwaves in biometric systems is the high time-variability of the EEG signals. This study addresses this issue by investigating two different approaches: 1) exploiting BCI-spatial filtering techniques for target identification to maximize the intra-subject repeatability of the task-induced responses, 2) addressing inter-subject variability using a new training procedure for deep learning to improve the time-permanence of AEPs. Additionally, the feasibility of enhancing the collectability of EEG signals was also examined by reducing the acquisition time and the number of EEG electrodes. Overall, this thesis provides a framework that enhances the cross-session repeatability of brainwaves under auditory stimulation allowing the possibility of employing the AEP signals in biometric recognition.

Keywords: Auditory Evoked Potentials
Biomedical Signal Processing
Biometric Authentication
Biometrics
Brainwaves
Machine Learning
Advisor: Hatzinakos, Dimitrios
Revisiting the History and Practice of Congregational Organ Accompaniment in the Dutch Reformed Churches of the Seventeenth and Eighteenth Centuries

The history of seventeenth-century Dutch Reformed church music presents us with a compelling paradox. On the one hand, we see a proliferation of massive, new organ installations exhibiting vibrant spectrums of tonal colours, which had a powerful influence on compositions and instruments throughout Europe, including those of Buxtehude and Bach. On the other hand, we also see the simultaneous emergence of the Reformed church’s apparent (though inconsistently applied) prohibition of accompanied congregational singing, one which would seem to preclude the building of these very instruments. To what can we attribute this inconsistency, and why has it been largely overlooked in published research? More compellingly, why does Calvin’s prohibition remain strongly uncontested in today’s contemporary Reformed practice? In this dissertation, I assert that by more critically examining a) the text of John Calvin’s 1543 Preface to the Genevan Psalter, b) primary sources on organ construction and tonal design, as well as c) seventeenth- and eighteenth-century treatises on the organist’s role in the church service, a more nuanced understanding of the circumstances, broader context, and underlying objectives behind Calvin’s perspective may justify exercising an expanded and more creative use of the organ. Central to my argument is Calvin’s uncontestably favourable attitude towards the human voice, and that his perspective was represented in the attempts of Dutch organ builders to recreate vocal sounds in their instruments. Ultimately, I argue that Dutch Reformed churches viewed the organ as a vocal tool rather than an instrumental one. Viewed through this lens, the flood of massive organ installations that occurred in these historic churches stands in no conflict with Calvin’s theology. Moreover, it is thus likely that present-day Dutch Reformed practice disfavours the use of the organ beyond what may be historically justifiable.

Keywords: Constantijn Huygens
Dutch Reformed
John Calvin
organ voicing
pipe organ
vocality
Advisor: Komisaruk, Kevin
Sisyphus Overture

Sisyphus Overture is a retelling of Albert Camus’ Myth of Sisyphus through the prism of his novel The Plague. It has a running time of approximately ten minutes and is a single movement, through-composed symphonic  piece. Sisyphus Overture  is not meant to be a programmatic piece, or scene by scene extract of Camus’ stories, rather, the piece explores the literary themes of Absurdism and Existentialism through music.  The music probes the Absurd Hero’s rebellion and struggle for meaning in the Absurd modern world as understood by Albert Camus.  To accomplish this, Sisyphus Overture prominently explores the historical usage of polytonality, the octatonic modes, tone-rows, and quartal harmony to transform and reinvent themes presented at the start of the piece, which will come to embody the Absurd, and serve as the leitmotif of the piece.  There is an additional exploration of underlying scale collections within the octatonic mode, as well as chordal/vertical representations of this scale, and unique chord voicings.  In addition to an exploration of harmony, the concept of Euclidean Rhythms is touched upon in one of the groove-based sections of the piece, and an exploration of tone color and extended techniques is also undertaken.

Keywords: Music
Orchestra
Overture
Symphonic Poem
Advisor: Rapoport, Alexander
Unsupervised machine learning for hypothesis discovery and representation learning in biological image and sequence analysis

High-throughput screening technologies, such as robot-controlled microscopes and whole genome sequencing, have led to an increasing volume of unbiased biological data. An open question is how we can best support hypothesis discovery from these datasets. While we expect some of the data to contain cryptic patterns like novel phenotypes in images or motifs and molecular features in protein sequences, that may lead to new hypotheses about regulation or function, manually sifting through millions of images or protein sequences is too time-consuming and subjective. In this thesis, I will demonstrate how representations, which convert raw images and sequences into computationally comparable measurements, can form the basis for efficient and objective exploration of big biological datasets. I will show how representations can be combined with unsupervised clustering to discover new functions of proteins from an integrative study of almost 400,000 microscopy images of yeast cells. I will describe new computational methods that reduce barriers in effort and expertise in converting images and sequences into representations, by exploiting self-supervised deep learning, where models autonomously learn effective representations of biology through self-posed puzzle-solving tasks. These models develop their own independent conception of data unbiased by prior expert conceptions: I show that by interpreting the features learned by models trained on protein sequences, we can discover sequence features that may be functionally relevant. Finally, I will outline open challenges in out-of-sample generalization in representations, to illuminate future directions for producing representations that capture biological signal in data invariant of noise.

Keywords: Hypothesis discovery
Intrinsically disordered regions
Machine learning
Microscopy image analysis
Representation learning
Self-supervised learning
Advisor: Moses, Alan M
Village Society and the Holocaust in the General Government: The Case of Kreis Debica

This dissertation is a microhistory of a phase of the Holocaust in German-occupied Poland characterized by widespread police manhunts for fugitive Jews (Judenjagd) from mid-1942 to late 1944, which followed the violent deportation Aktions directed at ghetto populations. It is a case study of one rural county, or Kreis, of Debica, located in the eastern half of District Kraków of the General Government. The study identifies 1,257 Jews who evaded the mass killing operations and took shelter on the territory of Kreis Debica, 75% of whom were subsequently killed and 25% survived. It provides a fine-grained reconstruction of the social dynamics and processes that informed the participation of locals in the persecution of Jews for a period of almost three years. The data is drawn primarily from postwar legal proceedings against individuals accused of collaboration on the basis of the Decree of August 31, 1944. The dissertation integrates the Judenjagd with parallel processes aimed at other groups by means of a thick description. It places the findings within two theoretical frames of reference. First, it treats the nexus of local structures co-opted by the occupation authorities as a critical meso level of the process of genocide in the General Government. Those with institutional ties to the system of indirect German rule over the Polish countryside became bound by a self-regulating dynamic of mutually reinforcing fears among its members, which did not necessitate the presence of the uniformed police. Second, it views local dynamics as a response to ongoing security dilemmas. The aftershock of German state violence against locals for the shelter of Jews provided a combustible social atmosphere, in which Polish fear of Jewish exposure upon capture set off a chain reaction of pre-emptive violence against Jews in hiding. The study situates the question of Polish agency within these structures and dynamics. It finds that the occupation authorities had essentially unleashed a sociology of state collapse upon Poland’s multiethnic society. These conditions lowered the threshold for participation in persecution and violence against targeted groups. This account stands in contrast to interpretations that explain Polish participation in genocide as stemming primarily from ideology and personal convictions.

Keywords: Dębica county
District Kraków
General Government
German-occupied Poland
Judenjagd
peasantry
Advisor: Wróbel, Piotr J.
Biophysical Regulation of Endothelial Functions by the Spectrin Cytoskeleton

Endothelial cells perform critical homeostatic functions at the interface between the blood and surrounding tissues. The endothelium regulates the hemodynamic characteristics of the vascular environment by modulating vascular tone and maintaining blood fluidity. During inflammation, it also coordinates the step-wise egress of leukocytes from the circulation.These responses require the appropriate regulation of the organization and stability of several functionally important plasma membrane molecules. In this dissertation, I identify a previously unappreciated spectrin cytoskeleton at the apical (luminal) surface of the endothelium. In chapter 3, I describe how this network tethers transmembrane protein pickets to limit the mobility of selectins, critical adhesion receptors that orchestrate leukocyte migration to inflamed tissues. I detail how spectrins thus induce the apical accumulation of selectins and promote their clustering within caveolae to coordinate leukocyte-endothelial interactions. In chapters 4 and 5, I outline how spectrin stabilizes extracellular and intracellular polymer networks to coordinate normal endothelial responses to shear stress. Moreover, I demonstrate that spectrins control the stability of caveolae in the luminal plasma membrane. Crucially, I relate the stability of these cellular components to the viscoelastic properties of the endothelium. This work establishes the functional importance of spectrin networks in the vasculature. It also contributes to our understanding of how, by influencing molecular movements and mechanically coupling cellular structures, the cytoskeleton acts as a major regulator of cellular signaling.

Advisor: Grinstein, Sergio
Reactive Intermediates in Secondary Organic Aerosol and Oxidative Potential

Secondary organic aerosol (SOA) contributes a significant fraction of particulate matter (PM), which has important impacts on climate change and public health. Reactive intermediates in SOA are compounds with relatively high reactivities, whose environmental fate can significantly influence the physicochemical properties of aerosol. The present thesis characterizes the reactive intermediates in OA by evaluating their potential role in atmospheric chemistry and human health. Organic peroxides are highly reactive components detected in a variety of organic aerosol systems. The current work investigates the reactivity of organic peroxides towards SO2 through laboratory measurements of bulk-phase and heterogeneous reaction kinetics. Results indicate that this interaction is important for particulate sulfate formation and other aerosol characteristics. Furthermore, organic peroxides can serve as a significant source of reactive oxygen species (ROS) and exhibit high oxidative potential (OP) as observed in OA from cooking emissions. Among OA from various emission sources, the OP of polycyclic aromatic hydrocarbons derived SOA is the highest while the evolution in the atmosphere remains obscure. Using naphthalene SOA (NSOA) as a model system, secondary ozonolysis and oligomerization was found to enhance the OP of NSOA while chelation with transition metal (Cu2+) reduces the OP. Photochemical aging can initially enhance and then decrease the cytotoxicity of NSOA. Post-translational level results from proteome-wide analysis show that quinones and other unsaturated carbonyls are responsible for the toxicity of NSOA during atmospheric aging. This work contributes to our understanding of the dynamic evolution and potential health impacts from organic aerosol in the atmosphere.

Keywords: Aerosol
Air pollutants
Haze
Health impacts
PM
Advisor: Chan, Arthur W.H.
Bluegreen Ecstatic Grey

My DMA Thesis Composition, Bluegreen Ecstatic Grey, is a large ensemble work for woodwind quintet (flute doubling on piccolo, oboe, clarinet in B flat, bassoon doubling on contrabassoon, and french horn), percussion quartet, string quintet (first violin, second violin, viola, cello, and double bass), piano solo, and electronics. Bluegreen Ecstatic Grey is a personal musical exploration and metaphor for the process of uncovering and healing latent grief. Held within this metaphor is the idea that the human qualities of love and truthful self-expression are the keys to and rewards for healing one’s grief.The composition is approximately 18 minutes in duration and has two parts, the first running ‘attacca’ into the second. This structure reflects the guiding metaphor of the piece: part one expresses what life is like before the uncovering of repressed grief, as well as the process of uncovering, while part two expresses the process of feeling and healing this grief. A significant change in instrumentation, from the full ensemble in part one to the extended piano solo writing in part two, enhances the metaphor — the piano leaves the other instruments much like pretense is discarded when one ventures into a truthful, unfiltered expression of previously repressed emotion. My DMA Thesis Composition is also linked to my research into field recording as well as live-electronic composition and performance practise. Bluegreen Ecstatic Grey merges acoustic instrumental writing with the live-triggering of forty-seven pre-recorded electronic audio cues. These cues were created with various electronic instruments as well using my own field recordings of nature and bird sounds. These sounds are used with the utmost care and serve to enhance the musical metaphor. For example, the second half of the work prominently features the sounds of a single Blue Jay I recorded in my backyard. The Blue Jay holds meaning for me as a symbol for love, communication, and truthful self-expression since my wife and I were fortunate to see one at our wedding site on the day we were married.

Keywords: contemporary classical
electronics
grief
large chamber ensemble
new music
piano solo
Advisor: Hatzis, Christos
Muscle Matters: Understanding how Muscle Function Contributes to Reactive Stepping Performance

Muscle weakness and balance control are two important predictors of fall risk. The main objective of this work was to determine how leg muscle function contributes to reactive stepping performance – a strategy used to recover balance. Studies 1-3 were conducted in young, healthy adults and study 4 was performed in individuals with chronic stroke. The first study demonstrated that force plate measures used to estimate foot-off and swing times of the stepping limb following a loss of balance had good to excellent between-session reliability. The second study highlighted unique function-specific increases in muscle activity following larger balance perturbations. Namely, the timing of muscle activation suggested that the modulation of medial gastrocnemius and biceps femoris was likely important for reducing forward momentum, propelling the swing limb forward, and applying braking forces at foot contact. In addition, increased muscle activity of the vastus lateralis and tibialis anterior likely contributed to earlier foot-off times and restabilization of the centre of mass following foot contact. The third study found that while most measures of muscle strength and explosive force were not related to reactive step timing, knee extensor explosive force was correlated with swing time. The last study revealed strong correlations between the average number of steps required to recover balance and knee flexor and extensor concentric peak torque in chronic stroke. Overall, the findings of this work suggest that muscle function contributes to reactive stepping performance, with the knee extensors having an important role particularly during restabilization. Variability in strength and balance control due to aging or neurological injury may accentuate these correlations to a greater extent and warrant further investigation.

Advisor: Mathur, Sunita
Mansfield, Avril
Mixed-signal Processing Techniques for RF Transmitters

The design of high performance integrated radio frequency (RF) transmitters (TX) able to meet the constant demand for faster, “greener”, and more cost-effective wireless communication links, is driving innovation on all fronts: device, circuit, and system level. Recent advances in advanced CMOS process nodes are pushing for more “digital-intensive” architectures, yet certain aspects of analog integrated circuits (ICs) cannot be easily replaced by digital functions. This thesis aims to take a fresh approach at the circuit and system level by proposing two designs that lie at the border between digital and analog domains. The first part of the thesis focuses on the design of a wireless TX front end based on the concept of time-variant passive signal processing. The digital-to-analog converter (DAC) is merged with a higher order passive switched-capacitor filter (PSCF) and so the functionalities of digital-to-analog conversion, baseband filtering, and signal upconversion are implemented by a passive switched capacitor (PSC) network. The resulting passive switched-capacitor DAC (PSC-DAC) offers a versatile architecture that fully benefits from CMOS scaling. The front end was integrated in a 65nm CMOS technology and can support various channel bandwidths simply by adjusting the switching frequency for the PSC network. Thanks to its third-order reconfigurable filter, it maintains a thermal noise floor better than −156 dBc/Hz at a power dissipation of 45 mW. The measured prototype achieves an alternate adjacent channel leakage ratio (ACLR2) of −57 dB and an error vector magnitude (EVM) of −31 dB for a 20-MHz 64-QAM OFDM and a 20-MHz 16-QAM signal,respectively. In the second part, quantized analog (QA) signal processing is applied for the first time in RF power amplification culminating in the concept of the quantized analog power amplifier (QA-PA). By allowing the signal to virtually exceed the supply, the QA-PA leads to an improvement in the output dynamic range that is not possible by conventional analog techniques. Simulations of a 65nm CMOS design show good agreement with the presented theory and predict up to 18dB improvement in both EVM and adjacent channel leakage ratio (ACLR) compared to an analog class-A poweramplifier (PA) for a 256-QAM, 100MHz 5G signal.

Keywords: CMOS
PSC-DAC
PSCF
Quantized Analog
RF transmitter
wireless
Advisor: Liscidini, Antonio
Experiential Learning for All! An Institutional Analysis of How University Administrators Responded to the Ontario Government’s Call to Action

Governments in Western liberal democracies, such as Ontario, have increasingly used policy tools to influence university priorities and actions, despite the literature suggesting that policy tools are limited in their ability to shift institutional behaviour. As institutional theory posits, institutions require legitimacy to remain prominent in society and they may respond to government policy tools in superficial ways that mask non-compliance. Universities are autonomous institutions rooted in their small, liberal arts traditions and structures of decentralization, collegial governance, and academic freedom, and this institutional context makes institutional change difficult. This study explores the gap between the intention of government policy tools and their implementation by institutions. By leveraging the Ontario government’s experiential learning (EL) call to action in 2016-2019, a multi-case study design is used to explore how five universities interpreted and responded to the government’s EL call, as a way to explore this gap between policy tool goals and institutional responses. In particular, this study focuses on the experience of 21 university administrators who sit below the President and Provost, and at the juncture of strategy and implementation (i.e. Vice-Provosts, Assistance Vice-Provosts, Directors, Managers, and Registrars) to explore how administrators balance government calls for accountability and transparency with university structures and cultures. Using theoretical and conceptual constructs from institutional theory, this study contributes to our understanding of policy tools and institutional change by highlighting characteristics of the political and institutional contexts that influence institutional actions. First, the findings suggest that a process of layering is occurring, where the Ontario government is arguably introducing new priorities without the authority to replace existing structures and priorities. Second, the findings highlight the role of central university administrators as rule facilitators—critical actors who work with their institutional structures and cultures to respond to government policy tools in ways that maximize institutional legitimacy. Lastly, the findings echo existing propositions in the literature that suggest there is a relationship between alignment and compliance, where government policy tools that do not align with institutional priorities encourage strategic responses that mask non-compliance.

Keywords: Administration
Experiential Learning
Governance
Institutional Change
Institutional Theory
Policy tools
Advisor: Wheelahan, Leesa