HARVEST
University of Saskatchewan's Repository for Research, Scholarship, and Artistic Work
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Recent Submissions
SARS-CoV-2 pathogenesis in an angiotensin II–induced heart-on-a-chip disease model and extracellular vesicle screening
(PNAS, 2024-06) Wu, Qinghua; Rafatian, Naimeh; Wagner, Karl; Blamer, Jacob; Smith, Jacob; Okhovatian, Sargol; Aggarwal, Praful; Wang, Erika Yan; Banerjee, Arinjay; Zhao, Yimu; Nash, Trevor; Lu, Rick Xing Ze; Portillo-Esquivel, Luis Eduardo; Li, Chen Yu; Kuzmanov, Uros; Mandla, Serena; Virlee, Elizabeth; Landau, Shira; Lai, Benjamin Fook; Gramolini, Anthony; Liu, Chuan; Fleischer, Sharon; Veres, Teodor; Vunjak-Novakovic, Gordana; Zhang, Boyang; Mossman, Karen; Broeckel, Ulrich; Radisic, Milica
Adverse cardiac outcomes in COVID-19 patients, particularly those with preexisting cardiac disease, motivate the development of human cell-based organ-on-a-chip models to recapitulate cardiac injury and dysfunction and for screening of cardioprotective therapeutics. Here, we developed a heart-on-a-chip model to study the pathogenesis of SARS-CoV-2 in healthy myocardium established from human induced pluripotent stem cell (iPSC)-derived cardiomyocytes and a cardiac dysfunction model, mimicking aspects of preexisting hypertensive disease induced by angiotensin II (Ang II). We recapitulated cytopathic features of SARS-CoV-2-induced cardiac damage, including progressively impaired contractile function and calcium handling, apoptosis, and sarcomere disarray. SARS-CoV-2 presence in Ang II–treated hearts-on-a-chip decreased contractile force with earlier onset of contractile dysfunction and profoundly enhanced inflammatory cytokines compared to SARS-CoV-2 alone. Toward the development of potential therapeutics, we evaluated the cardioprotective effects of extracellular vesicles (EVs) from human iPSC which alleviated the impairment of contractile force, decreased apoptosis, reduced the disruption of sarcomeric proteins, and enhanced beta-oxidation gene expression. Viral load was not affected by either Ang II or EV treatment. We identified MicroRNAs miR-20a-5p and miR-19a-3p as potential mediators of cardioprotective effects of these EVs.
Impact of ion-neutral collisions in fluid models of plasma sheath
(2025-05-12) Mun, Jong Hern; COUËDEL, Lénaïc; MURAGLIA, Magali; AGULLO, Olivier; STAFFORD, Luc; HAGELAAR, Gerjan; PLIHON, Nicolas; SMOLYAKOV, Andrei; BOURASSA, Adam; ARNAS, Cécile; NEUFELD, Eric
In this thesis, the development of an improved one-dimensional self-consistent fluid modeling of argon plasmas in DC discharges, including the sheath regions, is presented.
Comparison of the charged species density, electron mean energy, plasma potential and ion velocity profiles with the profiles obtained by other fluid models and the profiles obtained with 1D3V (one dimension in space and three dimension in velocity) Particles-In-Cell simulations were performed.
It is shown that for moderate argon pressure ($10 \sim 10^2$ Pa), ion collisions with neutral atoms must absolutely be considered in the fluid model to accurately simulate the discharge, especially in the sheath region, and self-consistent calculation of the ion temperature profile is necessary in the whole simulation domain.
Indeed, in the cathode sheath where there is large potential fall, the ion temperature can be several orders of magnitude larger than the background gas temperature. It was found that ion-neutral collisions are responsible for a progressive spreading of the ion velocities in the directions perpendicular to the simulation axis in the cathode sheath.
The revised fluid model solves the moment equations of order zero, one and two for both electrons and ions. Also, a clear distinction of parallel and perpendicular directions to the applied electric field was observed, thus the assumption of an isotropic temperature was dropped. Instead, the problem was reduced to one dimension in the fluid model to resolve the parallel direction of the discharge. The new fluid model showed much improved agreement with the PIC results, particularly within the cathode sheath. The new model reproduced well the theoretical Paschen's curve for direct-current argon discharges. The lower pressure limit of the current fluid model was also tested, and the observations highlight the necessity of a similar analysis for the electron collisionality.
Coherence Control and Measurement at the CLS Using X-ray Interferometry
(2025-05-12) Yousefi Sigari, Yasaman; Boland, Mark James; Vogt, Johannes; Pywell, Rob; Chapman, Leroy Dean; Smolyakov, Andrei; Chang, Gap Soo; Welsch, Carsten
As synchrotron light source storage rings transition to multi-bend achromat (MBA) lattices for higher brightness and coherence, emerging challenges arise in beam diagnostic tools that accurately monitor and control the spatial degree of coherence.
MBA lattice designs in modern fourth generation light sources significantly reduce the transverse beam size, posing challenges for beam monitoring due to diffraction effects at lower energies and technical limitations at higher energies.
This work demonstrates that X‐ray interferometry can overcome diffraction limits by measuring the spatial degree of coherence.
Proof‐of‐principle double‐slit interferometry experiments were conducted on the BXDS-IVU beamline at the Canadian Light Source (CLS) to quantify the modulus of the complex degree of coherence.
The degree of coherence was measured as a function of the vertical source size.
Systematic adjustments to the secondary source size and coupling revealed changes in degree of coherence.
The method achieved sub-micron sensitivity in detecting source size variations, demonstrating that X‐ray interferometry can accurately measure small changes in degree of coherence and holds promise for measuring small beam sizes in fourth generation light sources.
To validate the results, additional supporting experiments were conducted.
The linearity of the detector was assessed as a function of incoming photon flux by gradually increasing the current of the electron beam in the storage ring.
A refined model of the linear terms of the storage ring lattice was developed by using the Linear Optics for Closed Orbit (LOCO) algorithm, minimizing the difference of the measured and modeled response matrices.
The LOCO-tuned model provides insights into the variations in the vertical beam size at different source points in the storage ring as the coupling factor is adjusted while the vertical source size was monitored by the X-ray synchrotron radiation (XSR) diagnostic beamline.
Further coupling measurements were performed using the closest-tune approach with a bunch-by-bunch feedback system.
Sublethal Effects of Pesticides on Visually-Guided Bee Behaviours
(2025-05-12) Liadi-Azeez, Basirat Taiwo; Gray, Jack R; Marchant, Tracy; Niyogi, Som; Prager, Sean
European honeybees (Apis mellifera) are abundant and effective natural pollinators contributing enormously to mass production of agricultural crops through extensive foraging. They possess visual systems that are highly sensitive to motion and rely on motion of visual elements (optic flow) to efficiently navigate their complex environment with high precision. Optic flow stimulates an innate response known as the optomotor response, which enables the bees to orient and maintain a straight course during flight. The persistent use of pesticides in seed treatments and bees’ exposure negatively impact honeybee’s ability to engage in these ecologically relevant behaviours. Previous studies showed that neonicotinoids and sulfoxaflor impaired flight performance and walking tracks associated with optomotor responses in workers. This study is investigating the responses of different honeybee castes and worker age groups to optomotor stimuli in a 360° visual stimulus arena and how nicotinic acetylcholine receptors (nAChRs) agonists – imidacloprid (IMD), sulfoxaflor (SFX) and their mixture (MIX), impair these responses. Bees were tethered on air-supported ball where I provided optomotor stimuli consisting of alternating black and white stripes rotating in clockwise and counterclockwise directions. Workers exposed to SFX exhibited significantly faster reaction times and an enhanced preference for clockwise stimulus direction, while queens in all pesticide-treated groups showed a preference for leftward orientation bias. Drones remained largely unaffected by any of the pesticide treatments. Among worker age groups, nurses exhibited slower movement and delayed responses compared to foragers and nest bees. No interactive effects between age and pesticide exposure were observed. These findings highlight potential impairments in foraging efficiency and navigation, with significant implications for pollination services and pesticide risk assessments.
ENHANCING BIOGAS PRODUCTION IN COLD-REGION WASTEWATER TREATMENT USING ULTRASONIC PRETREATMENT AND CO-DIGESTION WITH BREWER’S SPENT GRAIN
(2025-05-12) Samimi Sohrforozani, Ehsan; McPhedran , Kerry; Chang, Won Jae; Acharya, Bishnu
The abstract of this item is unavailable due to an embargo.
CHANNEL ESTIMATION TECHNIQUES FOR FASTER-THAN-NYQUIST SIGNALING
(2025-05-12) Keykhosravi, Simin; Bedeer Mohamed, Ebrahim; Liang, Xiaodong; Saadat Mehr, Aryan; Daku, Brian; Abdelrasoul, Amira; Ejaz, Waleed
The rapid growth of wireless data traffic, driven by the increasing number of mobile devices and data-heavy applications, has created a significant demand for fast and reliable wireless communication systems. Since bandwidth remains a constrained resource, enhancing spectral efficiency (SE) is a key challenge. Faster-than-Nyquist (FTN) signaling has attracted significant interest as a technique to enhance the SE of wireless systems. This approach allows for data transmission rates faster than the Nyquist rate, without requiring additional bandwidth or increased energy per bit. However, FTN signaling introduces a significant challenge, particularly in channel estimation and data detection, because of inter-symbol interference (ISI) at the receiver, which becomes more pronounced in frequency-selective and doubly-selective (i.e., time- and frequency-selective) fading channels.
To facilitate accurate channel estimation in wireless systems, pilot symbols, which are predefined symbols known to both the transmitter and receiver, are commonly adopted. In the multiplexing pilot (MP) channel estimation method, time-division multiplexing involves inserting pilot symbols within the transmitted data stream. While this approach enables reliable channel estimation, it reduces the effective data rate and compromises the SE. To mitigate this drawback, the superimposed pilot (SP) approach has been proposed, where known pilot symbols are superimposed on the data stream. This approach overcomes the challenges of MP-aided methods, which suffer from substantial SE loss in high-mobility environments because of the requirement for more frequent pilot sequences embedded within the data. However, SP-aided methods come at the cost of introducing interference between the pilot and data symbols. Addressing the interference introduced by SP becomes especially challenging in the presence of ISI caused by FTN signaling. This thesis focuses on developing MP- and SP-aided channel estimation techniques for FTN signaling.
The first main contribution of this thesis is an MP-aided channel estimation method for FTN signaling over doubly-selective channels. This approach is built on the least sum of squared errors (LSSE) technique to estimate complex channel coefficients at pilot locations while effectively addressing the ISI caused by both FTN signaling and frequency-selective fading. The method includes the design of an optimal pilot sequence aimed at minimizing the mean square error (MSE) of channel estimation. To manage the time-selective nature of the channel, a low-complexity linear interpolation method is employed to track channel variations at data symbol locations. For FTN signaling data detection, a turbo equalizer utilizing a soft-input soft-output (SISO) MMSE algorithm is integrated. At the same spectral efficiency, simulation results demonstrate a notable enhancement—around 6 dB in channel estimation MSE and approximately 3.5 dB in the BER of FTN signaling—achieved by using the our method, in comparison to the approach of Ishihara and Sugiura (2017) over frequency-selective channels.
The second main contribution of this thesis is proposing a novel index modulation (IM)-based MP-aided channel estimation method tailored for FTN signaling in high-frequency (HF) communications. The method comprises two algorithms: pilot sequence placement (PSP) and pilot sequence location identification (PSLI). The PSP algorithm leverages the locations of pilot sequences to convey additional information, thereby enhancing SE. The PSLI algorithm enables the receiver to identify pilot sequence locations based on the specific characteristics of HF channels and the favorable autocorrelation properties of the optimal pilot sequence. Simulation results reveal that the proposed method achieves comparable MSE and BER performance in channel estimation to that of Keykhosravi and Bedeer (2023) over frequency-selective channels, while also providing improved SE. Moreover, the results demonstrate an enhancement in SE, along with approximately 6 dB improvement in the MSE of channel estimation and around 3.5 dB gain in the BER of FTN signaling, compared to the method proposed by Ishihara and Sugiura (2017) under the same channel conditions.
The third main contribution presents a novel SP-aided channel estimation method for FTN signaling over doubly-selective channels. The proposed frame structure superimposes periodic pilot sequences onto the data symbols, eliminating the overhead associated with MP methods and thereby enhancing SE. An optimal SP sequence is designed to minimize the MSE of channel estimation. To address the challenges posed by the time-varying behavior of the channel, we utilize a basis expansion model (BEM) to represent the time-varying channel tap weights as a combination of basis functions with time-invariant coefficients. Building on the proposed SP-aided estimation method, two distinct methods are developed: the SP-aided separate channel estimation and data detection (SCEDD) method, which employs a turbo equalizer for data detection, and the SP-aided joint channel estimation and data detection (JCEDD) method, which iteratively updates channel estimates during the equalization process to improve detection accuracy. Our simulation results demonstrate that, at the same SE, the proposed SP-aided SCEDD method for FTN signaling significantly outperforms the MP-aided approach presented in the works of Keykhosravi and Bedeer (2023), and Ishihara and Sugiura (2017) in terms of MSE and BER, particularly under higher fading rates on the order of 10^(-3). Furthermore, under identical SE conditions, the proposed SP-aided JCEDD method consistently achieves superior MSE and BER performance compared to these existing methods. Specifically, the techniques presented in Keykhosravi and Bedeer (2023), and in Ishihara and Sugiura (2017) are unable to effectively track rapid channel variations such as those observed in the practical high-latitude HF channel defined in the ITU-R F.1487 recommendation, characterized by a Doppler frequency of 10 Hz (fading rate of 0.004). In contrast, our SP-aided JCEDD method demonstrates reliable performance under these challenging conditions. Under very low fading rates—specifically for the practical low-latitude channel defined in the ITU-R F.1487 recommendations with a Doppler frequency of 1 Hz (fading rate of 0.0004)—the proposed SP-aided JCEDD algorithm achieves more than 2 dB and 6 dB improvements in MSE compared to the methods in Keykhosravi and Bedeer (2023), and Ishihara and Sugiura (2017), respectively. In terms of BER, while our method outperforms the MP-aided approach in Ishihara and Sugiura (2017) by over 3 dB, it maintains comparable performance to the MP-aided FTN system in Keykhosravi and Bedeer (2023), with less than 0.5 dB degradation.
Eco-Friendly Non-Thermal Inactivation of Escherichia coli in Wheat Flour Using Cold Plasma Technology
(2025-05-12) Lee, Jeongmin; Baik, Oon-Doo; Korber, Darren; Abdelrasoul, Amira; Tabil, Lope; Zhang, Lifeng
This study investigated the application of atmospheric cold plasma (ACP) for reducing Escherichia coli in wheat flour and explored its effects on various quality attributes. Initially, response surface models (RSM) were developed to optimize ACP treatment for E. coli inactivation using three different gases: nitrogen, air, and argon. The analysis identified sample mass and treatment time as critical factors, with nitrogen gas proving the most effective, achieving a maximum reduction of 5.55 log CFU/g under optimized conditions. Subsequently, the study assessed the impact of ACP treatment on microbial dynamics, dough ripening, rheological properties, and sensory quality of wheat flour. Using optimized RSM parameters, ACP treatment resulted in a 3.10 log CFU/g reduction in E. coli without inhibiting the growth of lactic acid bacteria, suggesting a synergistic effect for pathogen control. Fungal growth was significantly reduced, corroborating ACP's efficacy in microbial inactivation. Dough fermentation times remained unaffected, while texture profile analysis (TPA) indicated that adjustments in moisture content could modulate changes in dough texture. Sensory evaluations revealed no significant consumer-perceived differences in pancakes made from treated versus untreated wheat flour, implying only subtle alterations in dough properties. This research highlights ACP as a promising non-thermal technology for enhancing food safety in wheat flour while maintaining its baking functionality. Future work should focus on scaling up the technology through the development of a dielectric barrier discharge (DBD) system for indirect treatment under vacuum conditions, aiming for efficient, homogeneous processing of large flour quantities, as preliminary designs and tests have indicated potential improvements in treatment efficacy and uniformity.
Investigation of polyphenol diversity among lentil species (Lens spp.) using mass spectrometry-based metabolomics guided by photodiode array detection
(ScienceDirect, 2025-03) Purves, Randy W.; Khazaei, Hamid; Elessawy, Fatma M.; Munro, Roger; Shurmer, Bryn O.; Vandenberg, Albert
Polyphenol diversity was investigated among seven lentil species, including Lens culinaris (cultivated lentil), L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans, using photodiode array detection coupled with liquid chromatography - mass spectrometry (LC-MS). Principal component analysis showed that most species grouped individually, except L. tomentosus and L. odemensis, which overlapped. The LC-MS data from both negative and positive electrospray ionization modes were used to identify 85 polyphenols observed in the UV–vis spectra, which included 27 proanthocyanidins, 17 flavonols, 15 flavones, and 12 hydroxybenzoic acids. An untargeted (comprehensive) analysis of the LC-MS data using Compound Discoverer software identified additional polyphenols (231 total), including numerous overlapping proanthocyanidins that contribute to a broad peak in the UV–vis spectra. The software analysis uncovered some notable differences among polyphenol profiles and intensities within the flavones, flavonols, and phenolic acids present in the species. This result indicates natural variation among the lentil wild relatives, which in part, is attributed to structurally isomeric compounds. A hierarchical clustering analysis, and a differential analysis using volcano plots used to look for statistically significant differences in polyphenols, illustrated significantly lower relative levels of polyphenols in L. culinaris compared with the wild types, especially within the proanthocyanidins and flavones. Our results highlight the potential of lentil wild relatives to enhance lentil seed quality.
Impact of Single Substitution Mutations in Conserved N-Terminal Residues of FtsI on Penicillin Binding and FtsW Interaction in Neisseria gonorrhoeae
(2025-05-09) Oladele, Oluwatobi Emmanuel; Dillon, Jo-Anne R.; Wachter, Jenny; Stone, Scot; White, Aaron; Thomassin, Jenny-Lee; Davies, Christopher
Background: Penicillin-binding protein 2 of Neisseria gonorrhoeae (PBP2/FtsINg) is an essential cell division protein and the major target of β-lactam antibiotics. As a transpeptidase involved in bacterial cell wall synthesis, its C-terminal domain mutations are well-known for their role in chromosomally-mediated β-lactam resistance. However, the function of the N-terminal domain remains poorly understood. This study investigates the conservation and functional roles of N-terminal FtsI residues across proteobacterial species, their impact on penicillin-binding in N. gonorrhoeae, and their effect on FtsWNg interaction to determine its role in the functionality of FtsINg.
Methods: FtsINg protein sequences and homologs from proteobacterial species were retrieved from the NCBI database and aligned to identify conserved residues. Site-directed mutagenesis was performed on FtsINg to introduce single amino acid substitutions at the identified conserved residues. Recombinant histidine-tagged wild-type and mutant FtsINg were analyzed for structural integrity using size exclusion chromatography multi-angle light scattering (SEC-MALS), dynamic light scattering (DLS), and circular dichroism (CD). The effects of mutations on penicillin-binding were ascertained by isothermal titration calorimetry (ITC). Bacterial two-hybrid (B2H) assays evaluated the impact of these mutations on FtsINg-FtsWNg interaction.
Results: Four amino acid residues (R75, R167, G180, and E193) were 100% conserved in the N-terminus of FtsI from 2132 Proteobacteria species and 19 Neisseria species. DLS and SEC-MALS methods demonstrated that wild-type and mutant FtsINg were monomeric, monodisperse, and free from aggregation. CD analysis confirmed the structural integrity of these proteins. ITC revealed increased penicillin-binding affinity (apparent Kd) for R75A, R75G, R167A, R167G, and by 2.6-fold, 4-fold, 2.9-fold, 2.1-fold, and 2-fold, respectively, compared to wild-type FtsINg (p < 0.05). B2H assays showed that alanine and glycine substitutions at R75, R167, and E193 disrupted FtsINg-FtsWNg interaction, with residual β-galactosidase interaction levels ranging from 56% to 95%.
Conclusions: This study identifies four conserved N-terminal residues in FtsINg as potential allosteric modulators of penicillin binding and FtsWNg interaction, highlighting their roles in antibiotic resistance and cell division. Conservation of these residues across Proteobacteria raises intriguing possibilities about horizontal gene transfer and provides potential targets for novel antimicrobial strategies.
Essays in Cryptocurrency
(2025-05-09) Rajapaksa, Danusha; Shao, Enchuan; Chaban , Maxym; Pollak, Andreas; Mamun, Abdullah
This thesis examines key aspects of the cryptocurrency ecosystem, focusing on Bitcoin mining, transaction
fees, and the structural relationship between Tether and Bitcoin. The first chapter provides an overview of
how these studies are interconnected.
The second chapter examines the welfare implications of entry barriers in Bitcoin mining, extending
a monetary search framework to incorporate entry costs. The analysis shows that barriers to entry lead
to moderate welfare gains by reducing competition, which lowers mining costs. These gains stem from
cost savings rather than improvements in transaction settlement times, highlighting the trade-offs between
competition and efficiency in maintaining the network’s security and value.
The third chapter investigates the determinants of Bitcoin transaction fees, focusing on the strategic role
of miners and the dynamics of competition. Empirical evidence demonstrates that increased competition
among miners reduces average fees but raises total fees by confirming more transactions. Additionally, as
block rewards decrease, users offer higher fees to compensate for lost miner revenue. The study emphasizes
the significance of endogenous factors, such as waiting times and mining costs, in shaping the fee structure
and provides insights into the complex interplay between miner behavior and the economics of the Bitcoin
network.
The final chapter explores the relationship between Tether and Bitcoin, analyzing Tether’s price volatility
and the impact of arbitrage on stability. The study identifies triangular arbitrage as a crucial mechanism
maintaining Tether’s price peg. It reveals that demand shocks in Tether markets can drive up Bitcoin
prices in the short term and, unexpectedly, shows that the circulating supply of Tether responds more to
Bitcoin market price differentials than to conditions in its own market. Together, these chapters provide a
comprehensive view of the economic mechanisms governing cryptocurrency ecosystems, offering new insights
into market structure, miner behavior, and stablecoin dynamics.