VictorJuiz/thesis huggingface dataset:
Weighing Preaspiration: Phonetics, Phonology, Typology of a Laryngeal Phenomenon

Preaspiration is typically discussed as a rare phenomenon, with the reasons for its relative rarity compared to postaspiration being important to investigate. This approach parallels research on typologically rare segments like postaspirated fricatives (Jacques, 2011) or glottalized sonorants (Blevins, 2003), and implicitly presents preaspiration as a property of the following segment. This thesis addresses some longstanding contradictions in the phonology and typology of preaspiration, reassessing the prosodic status of this phenomenon and arguing that its traditional conception in the literature does not align with crosslinguistic phonetic and phonological patterns. Contra the commonly held assumption that preaspiration is a laryngeal property of the following segment (i.e., a “mirror image” of postaspiration), preaspiration is shown to be prosodically associated to the preceding syllable in all attested cases, typically bearing moraic weight, and thus often indistinguishable from a discrete coda [h] segment. This position is supported by a typological survey, starting from the “classic” cases of preaspiration and expanding to cases which are not traditionally described using this term, examining the phonological and phonetic evidence for the prosodic status of preaspiration in each case. This thesis also features phonetic data from North Saami, in which preaspiration is indisputably moraic but has been argued to be phonologically distinct from other coda consonants (Bals Baal, Odden, & Rice, 2012); additional data show that there is no clear evidence that this must be true. The cross-linguistic patterns observed here support a reinterpretation of preaspiration: it is not necessarily dependent on the [±spread glottis] status of the following consonant, as it may appear before both aspirated and unaspirated consonants, or before a consonant with no contrastive laryngeal specification; and it may in many cases serve as a phonological length-preserving strategy akin to compensatory vowel lengthening, or a prosodic mechanism for ensuring syllables are heavy. The typological survey also shows that preaspiration is much more widespread than generally thought, and thus a new perspective on this phenomenon may show it to not be rare at all, but rather a part of the prosodic phonology of many languages.

Keywords: moras
phonetics
phonology
preaspiration
prosodic structure
typology
Advisor: Rice, Keren D.
Rings of finite rank over integers

We study the rings and ideal classes associated to weakly divisible polynomials and other homogeneous ideals in higher projective spaces ($\mathbb{P}^{k}(\overline{\mathbb{Q}})$). To a point, say, $$P=[1:\alpha_1:\cdots:\alpha_m]\in \mathbb{P}^{m}(\overline{\mathbb{Q}}),$$ we associate a ring $$\mathbb{Z}[\alpha_1,\cdots,\alpha_m]\cap \bigcap_{i=1}^{m}\mathbb{Z}[\frac{1}{\alpha_i},\frac{\alpha_1}{\alpha_i},\frac{\alpha_2}{\alpha_i},\cdots,\frac{\alpha_m}{\alpha_i}],$$ which we show is an integral ring and is invariant under the natural $GL_{n+1}$ action. We show methods to compute its discriminant and construct objects to parameterize classes of said rings. We use these rings to improve on lower bounds on the number of number fields ordered by discriminant.

Keywords: counting numberfields
m-fine
orders
projective rings
reciprocity
rings of finite rank
Advisor: Murty, Kumar V.
Lessons Learned in Hardware-Assisted Operating System Security

Hardware security extensions are engineered to enhance software security for various purposes such as memory protection, program execution environment isolation, among others. Nevertheless, due to constrained hardware resources and the intricate nature of security goals pertaining to diverse software applications, the practical utilization of these hardware features by software developers, may diverge from those original envisioned by the hardware designers. We examine the repurposed uses of hardware features within the field of operating system security, presenting three case studies. The first involves a light-weight memory protection system designed to guard against return-oriented programming attacks, repurposing the intended use of a memory protection hardware extension. The second case presents a suite of secure OSes aimed at bolstering application security on mobile platforms, broadening the scope of the original target audience of a mobile hardware security feature. Lastly, we discuss an attack method that augments other side-channel attacks enabling them to elude detection and mitigation by manipulating processor thermal control functionality. The adapted uses of these hardware features can lead to a variety of potential consequences. While some outcomes, such as improved efficiency or innovative defense mechanisms, may be beneficial, others could inadvertently introduce security vulnerabilities. Through an exhaustive analysis of these three case studies, we gleaned the following insights: (1) A flexible approach to the utilization of hardware security extensions for different security purposes can yield partial security, resulting in lower and more acceptable overhead. (2) To accommodate new application security requirements, the design of the operating system can be adapted to cater to a broader range of users. (3) Hardware features that initially seem irrelevant could effectively counter the assumptions made by software defence that rely on hardware security extensions. This thesis underscores the importance of hardware-software collaboration for achieving optimal operating system security. Through the scrutiny of three specific examples of repurposed hardware feature utilization, the study illuminates both the potential benefits and risks inherent to these interactions. Consequently, it advocates for a more holistic and cooperative approach to navigate the challenges and intricacies of current secure computing systems.

Keywords: Computer security
Hardware security
Hardware security extension
Operating system security
Software security
Advisor: Lie, David
Functional Characterization and Comparative Analysis of Trichoplax adhaerens Acid-Sensing DEG/ENaCs, Insights into DEG/ENaC Family Evolution

The DEG/ENaC superfamily comprises trimeric ligand- and mechanically-gated channels found across various animal lineages. In mammals, this superfamily includes acid-sensing ion channels (ASICs), involved in pain sensation and synaptic plasticity, and epithelial sodium channels (ENaCs), which regulate Na+ in the kidneys and respiratory airways. In invertebrates, DEG/ENaCs exhibit genetic expansions leading to pickpockets in Drosophila, mechanically gated MEC channels in C. elegans, and peptide gated FaNaCs in mollusks. In the earlier diverging cnidarians, Hydra magnipapilatta DEG/ENaCs are peptide-gated, while Nematostella vectensis homologues are proton-sensitive. The diversity of this ion channel family in gating modalities and function across animals is intriguing and prompts further exploration to understand their evolutionary history. Through extensive phylogenetic analysis, we show that DEG/ENaCs are present in nearly all major metazoan lineages, including poriferans and extend to non-metazoans with homologues present in single-celled eukaryotes. We show that all DEG/ENaCs belong to two ancient, pre-bilaterian subfamilies with distinct lineages forming proton-sensitive ion channels. Furthermore, we explored a group of channels closely related to ASICs that we dubbed Trichoplax adhaerens Na+ channels (TadNaC1-11) belonging to the early-diverging placozoan animal Trichoplax adhaerens. Using whole-cell patch clamp electrophysiology, we heterologously expressed TadNaCs in CHO-K1 cells to reveal that TadNaC6 and TadNaC2 form functional homomeric proton-sensitive channels with different gating modalities. We demonstrated that TadNaC6 conducts leak Na+ currents at neutral pH, potentiated by alkaline pH, and inhibited by extracellular protons, Ca2+ ions, and the pharmacological compound diminazene. Strikingly, the general DEG/ENaC inhibitor amiloride potentiated the TadNaC6 currents, a phenomenon previously documented for the mammalian proton-activated ASIC3. Conversely, TadNaC2 exhibited a biphasic proton-activated current with a Na+ selective early current and a late current with a higher Na+ selectivity. The channel was not inhibited by extracellular Ca2+ or diminazene and weakly inhibited by amiloride. Additionally, the identification of proton-sensitive channels in Trichoplax adhaerens lead to the characterization of novel behavioural responses to changes in extracellular pH. Together, our phylogenetic, biophysical, and structure-function analysis show that ASIC channels, TadNaC2, TadNaC6 and other proton-sensitive channels from vertebrates and invertebrates are part of phylogenetically distinct lineages that appear to have independently evolved proton sensing mechanisms.

Keywords: DEG/ENaC
Evolution
Invertebrate
Ion channel
Proton sensing
Trichoplax adhaerens
Advisor: Senatore, Adriano AS
Freight Demand Model Development and Application at the National and Urban Scale

Freight demand models are tools that are used for the analysis of the freight transportation system, exploring the impacts of potential changes to the system, and forecasting the future demand. This thesis identifies some of the limitations in freight modelling through a review of current models and addresses these gaps by developing a component of a national freight model in the US, a carrier selection model, and an urban commercial vehicle (CV) model for the Greater Toronto and Hamilton Area (GTHA). The models are then applied to examine some important issues and trends in freight transportation, namely, truck driver shortages, truck carrier market consolidation, off-peak urban truck delivery and automated trucking.The carrier selection model simulates the transportation procurement market in the US, where shippers award annual contracts to for-hire carriers to transport goods to their customers. It is based on a heuristic algorithm that iterates through a list of shippers and shipment flows and assigns carriers based on price and carrier capacity. The model generates reasonable outcomes in terms of empty truck mileage and carrier revenue, among others. Model results suggest that some carriers may gain an advantage in terms of revenue compared to others. Scenario analyses identify how empty mileage, market share and contract locations (within-state, out-of-state, etc.) may change for owner-operators, small and large carriers. The GTHA CV model is a trip-based model with three components – truck trip generation, truck trip distribution and traffic assignment. Truck trip generation is based on a set of regression models, the outcomes of which suggest that rate-based trip generation – a common approach in the operational freight models – is not appropriate for most industry categories and truck types. Two applications of the CV model are presented in this thesis – off-peak truck deliveries and automated trucking. Model results of off-peak scenarios suggest that a daily travel time savings of over 5500 vehicle-hours can be obtained in the GTHA. Automated trucking is predicted to cause more congestion during partial adoption, but substantial travel time savings will be achieved at full automation.

Keywords: Freight modelling
Transportation modelling
Travel demand forecasting
Advisor: Roorda, Matthew J.
Brain Injury and Pain Exposure are Associated with Alterations in Structural Connectivity and Neurodevelopment in Very Preterm Infants

Preterm infants undergo neonatal intensive care during a period of maturation of structural brain networks, which may be affected by clinical illness and exposures such as brain injury and pain. This thesis explores (1) the impacts of brain injury and pain on development of structural connectivity and neurodevelopmental outcomes, and (2) whether aberrations in structural connectivity are an important mediator of outcomes. A prospective cohort of very preterm infants underwent early-life and term-equivalent age brain MRI to assess brain injury and structural connectivity. Exposure to pain was quantified as number of invasive procedures. Neurodevelopmental outcomes were assessed at 18 months corrected age with the Bayley Scales of Infant and Toddler Development, Third edition. Brain injuries were segmented to quantify volumes and develop voxel-wise lesion-symptom maps to assess relationships between brain injury size and location with neurodevelopmental outcomes. These data were combined with data of structural connectivity to develop voxel-wise disconnection-symptom maps that assessed relationships between brain injury size and location with aberrations in structural connectivity and neurodevelopmental outcomes. These maps revealed that brain injury involving tracts passing through the basal ganglia, thalamus and pons were associated with poorer neurodevelopmental outcomes. This highlights the importance of considering brain injury relative to white matter tracts when predicting neurodevelopmental outcomes. Greater early-life pain was associated with poorer neurodevelopmental outcomes, and potentially mediated by alterations in neonatal structural connectivity. Specifically, greater invasive procedures were associated with widespread reductions in structural brain connectivity, and reduced connectivity was associated with poorer neurodevelopmental outcomes with specificity for the striatum. The relationship between greater early-life pain and adverse neurodevelopmental outcomes was modified by duration of morphine exposure. However, morphine exposure was not associated with neonatal structural connectivity suggesting that morphine may modify neurodevelopmental outcomes through alternative mechanisms. Finally, associations observed between pain and brain injury, aberrant connectivity within the striatum, and neurodevelopmental outcomes highlight a potential vulnerability of this region to clinical illness and exposures during early brain development in very preterm infants. These data also suggest that the striatum may play an important role in neurodevelopment in this population; this warrants further study.

Keywords: Brain injury
Brain networks
Neurodevelopment
Neuroimaging
Pain
Prematurity
Advisor: Miller, Steven P
Ibrahim, George M
Adhesive Conductive Membrane Relieves Atrial Fibrillation: Feasibility, Efficacy, and Mechanism

Atrial fibrillation (AF) is the most common form of cardiac arrhythmia, significantly contributing to public health care expenditure and cardiovascular disease-related mortality.Due to the lack of efficient long-term treatment, AF remains one of the major public health burdens, especially in the aging population. Targeting the electrophysiological features of biological tissues, conductive biomaterial has emerged in recent decades with promising potential. We have focused on studying the novel conductive biomaterial in cardiac applications to facilitate the propagation of the electrical signals between cardiomyocytes that are physically separated due to structural and functional electrical blockages. In this study, I synthesized the adhesive conductive membrane, gelatin-based polydopamine (Gel-PDA), with conductivity to facilitate the propagation of the electrical signals between cardiomyocytes and the adhesiveness to enhance the biomaterial-to-tissue contact and ease the implantation procedure. I performed in vitro analyses and confirmed its biocompatibility and bio-conductivity. In my in vivo study, a cardiac-specific LKB1 KO mouse was selected to be the PersAF model. Gel-PDA was used as a novel treatment for persistent stage AF. Here, the Gel-PDA membrane was implanted directly onto the right atrial surface. Upon Ge-PDA implantation, PersAF mice showed immediate AF burden relief reflected by more evenly distributed RR intervals and re-appearance of the p waves. In the 28-day-long term monitoring, I found that Gel-PDA treated mice had a restoration of diastolic and systolic functions, maintenance of connexin 43 expression, and prevention of further atrial enlargement and fibrosis. From the ex vivo multielectrode array (MEA) test, I found that when Gel-PDA was added to the system, the conduction inhomogeneity index was reduced to a closer-to-WT level and from the ex vivo two-heart-system study, I have proven that Gel-PDA can pass the electric signal generated by one heart to another and dominate its rhythm. Overall, this study on the application of conductive biomaterial provides an alternative approach for long-term AF treatment.

Keywords: Adhesive Biomaterial
Atrial Fibrillation
Conductive Biomaterial
Electrophysiology
Stereometry
Transgenic mouse
Advisor: Li, Ren-Ke R.L
Practical Considerations of Discrete Multitone Modulation for High-Speed Wireline Links

To overcome the severe losses beyond 28 GHz in low-cost electrical channels, 4-level pulse-amplitude modulation (4-PAM) wireline links targeting 112 Gb/s incorporate resource- or power-intensive equalization schemes such as decision-feedback equalizers (DFEs) with many taps. Alleviating the timing constraints that cause DFEs to balloon in size and power, discrete multitone (DMT) modulation involves independent sub-channels that can be equalized in the frequency domain without feedback. DMT allows flexibility in assigning bits to each sub-channel, thereby potentially avoiding lossy parts of available frequency spectrum. This document presents behavioural modeling and experimental results on DMT transceivers. One set of simulations aimed to study various impairments shows 200-Gb/s operation at a bit error rate (BER) of less than 10^{−5} over an IEEE P802.3ck channel with 21 dB of loss at 50 GHz and assuming 150 fs_{rms} of jitter, 1.26 mV_{rms} of noise at the receiver’s input, and 7-bit 80-GS/s data converters. The estimated power and area of the associated digital signal processing are comparable to those of DFE. We also present experimental results achieving 61.6 Gb/s at a BER of 8.6×10^{−4} over a physical channel with severe magnitude response notches that is very challenging for 4-PAM. Furthermore, because there is considerable variability in the use of bit loading and power loading in DMT for wireline applications, this document also elucidates the relative benefits of these loading mechanisms. After comparing various loading scenarios in simulations, we propose a method for dynamically adjusting bit and power profiles based on the bit error distribution across sub-channels. A second set of experimental results demonstrates 75-Gb/s DMT operation with a spectral efficiency of 2.5 b/sample over a channel with a smooth magnitude response exhibiting a loss of 26 dB at half the sampling rate and 33 dB at 1/4 the data rate (the Nyquist rate of a 4-PAM signal at the same data rate). The proposed dynamic bit and power allocation method helped get a BER of 2×10^{−5}, lower than the BERs reported by other recent DMT implementations for high-speed wireline links, including some with lower channel losses than that compensated in our setup.

Keywords: communication circuits
digital modulation
discrete multitone
DMT
OFDM
wireline
Advisor: Chan Carusone, Anthony
The Impact of Ammonia Combustion on Soot Emissions Formation in Compression Ignition Engines

The impact of ammonia (NH3) co-firing with diesel on the greenhouse gases (GHG) and soot emissions of compression ignition (CI) engines is a current concern in large-scale agriculture, marine transportation, and shipping applications for which NH3 is proposed as a near-term decarbonization solution. In this thesis, the addition of NH3 to hydrocarbons combustion is studied in laminar diffusion co-flow C2H4 flames and through port injection in a dual fuel diesel engine. The effect of NH3 combustion on soot formation is investigated numerically and experimentally using measurements of: (1) the soot volume fraction and mass yield, (2) the average primary particles diameter and number concentration, (3) the graphitization of the soot nanostructure, and (4) the soot surface nitrogen content. Engine GHG, NOx, and unburnt NH3 emissions are also measured. The results show a suppressive chemical effect for NH3 cofiring with hydrocarbons on soot inception and growth in flame and engine combustion. The chemical bonding of nitrogen to the soot surface is found to increase soot graphitization leading to less carbon bonding. In addition, the nitrogen content of the soot surface is found to increase indicating an increased potential for nitrogenated PAHs formation with NH3 addition.

Keywords: Ammonia
Diesel
Emissions
Engine
Nanostructure
Soot
Advisor: Thomson, Murray J.
Application of Microwave Imaging in Identifying Valuable Minerals/Metals in Ore Sorting

Ore sorting is a pre-concentration technique used in mineral processing to reject low-grade ore particles from the feed material at coarse particle sizes. Modern ore sorting technology employs sensors to distinguish between the properties of different rocks. This study aims to investigate if microwave imaging (MWI) can be used to distinguish rocks that contain valuable minerals or metals from those that do not, for potential application in sensor-based ore sorting as a new sensing method. Compared to more established sensors, such as XRT and XRF, MWI has the potential to penetrate deeper into ore particles and to be used as a supplementary method for analyzing those ores with high contrast in electromagnetic (EM) properties between valuable minerals/metals and gangue minerals. Microwave scattering simulations and experimental measurements are performed on both gold ore cores and gold ore particles with irregular shapes. A MWI algorithm and a sorting algorithm are proposed to form images of rocks and to make the accept/reject sorting decision, respectively. Both simulation and measurement results suggest the feasibility of using MWI to identify the presence of valuable minerals or metals in ores.

Keywords: electromagnetic scattering
microwave imaging
ore sorting
Advisor: Bobicki, Erin
Hum, Sean