HARVEST
University of Saskatchewan's Repository for Research, Scholarship, and Artistic Work
Welcome to HARVEST, the repository for research, scholarship, and artistic work created by the University of Saskatchewan community. Browse our collections below or find out more and submit your work.

Communities in HARVEST
Select a community to browse its collections.
Recent Submissions
Sub-zero soil CO2 respiration in biostimulated hydrocarbon-contaminated cold-climate soil can be linked to the soil-freezing characteristic curve
(Environmental Science and Pollution Research, 2025-01) Nayeema, Tasnim; Lee, Aslan Hwanhwi; Richter, Amy; Ng, Kelvin Tsun Wai; Chang, Wonjae
Extending unfrozen water availability is critical for stress-tolerant bioremediation of contaminated soils in cold climates. This study employs the soil-freezing characteristic curves (SFCCs) of biostimulated, hydrocarbon-contaminated cold-climate soils to efficiently address the coupled effects of unfrozen water retention and freezing soil temperature on sub-zero soil respiration activity. Freezing-induced soil respiration experiments were conducted under the site-relevant freezing regime, programmed from 4 to − 10 °C at a seasonal soil-freezing rate of − 1 °C/day. The effects of unfrozen water retention on extending soil respiration activity emerged at the onset of soil-freezing. The unfrozen water effect became significant below 0 °C (correlation r = 0.83–0.94) and comparable to the temperature effect (correlation r = 0.82–0.90), successfully demonstrating the coupled effects on sub-zero respiration activity. Soil CO2 respiration modelling based on the temperature dependency only (Arrhenius and Q10 models) did not accurately describe sub-zero respiration activity associated with increased unfrozen water retention in treated contaminated soils. The shifted SFCCs of the treated soils, expressed as a function of soil temperature (T) and unfrozen water content (θ), served as a key framework for efficiently developing the sub-zero respiration model (SFCC-RESP). The developed SFCC-RESP model closely approximated the changes in soil respiration rates influenced by T and θ in the treated soils (R2 = 0.94–0.98) and described the abrupt decrease and subsequent stabilization in CO2 production during the transition to the deeply frozen soil phase. The SFCC-RESP model integrated with soil thermal models (TEMP/W) can be used to produce spatial distributions of T, θ, and CO2 production in the treated soil matrix, providing a tool to approximate the abundance of unfrozen habitable niches when developing cold-tolerant bioremediation strategies.
Internal Lagrangians and spatial-gauge symmetries
(International Press of Boston, 2024) Druzhkov, Kostya
A direct reformulation of the Hamiltonian formalism in terms of the intrinsic geometry of infinitely prolonged differential equations is obtained. Concepts of spatial equation and spatial-gauge symmetry of a Lagrangian system of equations are introduced. A noncovariant canonical variational principle is proposed and demonstrated using the Maxwell equations as an example. A covariant canonical variational principle is formulated. The results obtained are applicable to any variational equations, including those that do not originate in physics.
Assessing spatial distribution and quantification of native trees in Saskatchewan’s prairie landscape using remote sensing techniques
(Taylor and Francis, 2024-12-11) Shafeian, Elham; Mood, Bryan; Belcher, Kenneth; Laroque, Colin
The importance of trees in non-forest landscapes has been the focus of only a few studies. However, these trees provide many important ecosystem services. In this study, we mapped and quantified these trees using Sentinel-2 (S2) and very high-resolution (VHR) Google satellite imagery without any field campaigns. We performed a Random Forest (RF) classification to map the spatial distribution of native trees in different scenarios. The optimal model showed an overall accuracy and kappa of 0.99 and 0.98, respectively. We mapped 40,500 km2 of tree cover, including native tree cover (approximately 29,565 km2 ≈10.5%), excluding plantations, regional and provincial parks, and water bodies in the Canadian prairie region of Saskatchewan. According to our results, the highest numbers of native trees were found in the eastern and northwestern parts of the study area – cluster “BLK_1” and the “Black” soil zone, with total cover of 5,388 and 13,233 km2, respectively. The lowest numbers of native trees were found in the southwest side of the study area – cluster “BRN_6” and the “Brown” soil zone, with total cover of 2.38 and 979.5 km2, respectively. This research is important as detecting and quantifying native trees is an integral part of studies on carbon sequestration, economics, and effective management strategies.
Analyzing water uptake of apple trees using isotopic techniques in the Shandong Peninsula, China
(Elsevier, 2025-01-03) Pang, Tianze; Zhao, Ying; Poca, Maria; Wang, Jianjun; Li, Hongchen; Liu, Jinzhao
Study region
The hilly area of Shandong Peninsula is a pivotal apple-producing region in China. However, the precise water sources utilized by the apple trees for transpiration remain poorly understood in this region.
Study focus
Here we quantify the water sources used by apple trees in this area using stable isotopic tracing methods. Through on-field studies in a representative apple orchard and subsequent isotopic assessments, the primary water sources tapped by the apple trees were identified in three plots with contrasting soil characteristics and through 5 days of sub daily sampling.
New hydrological insights for the region
Our results show that apple trees have a marked preference for soil water centered at the 60 cm depth, with more deep water use at plots without weathered layers. Notably, the isotopic compositions of the xylem water leaned more towards signatures of soil water, rather than immediate irrigation water or groundwater. Given the irrigation water used to be the dominant water source recharging into soil, the weak contribution of irrigation water to plant would be attributed to the high soil evaporation rates during the growth phase, which strongly alter the isotopic composition of irrigation water in shallow soil layers. These insights boosted our comprehension of water sourcing mechanisms in the sloped orchard ecosystems in the Shandong Peninsula and lay the groundwork for deeper exploration into the irrigation ratio to rainwater utilized by apple trees in comparable regions.
Health Sciences and Beyond: An Investigation into Canadian Librarian Participation in Systematic Reviews Across Disciplines
(Association of College & Research Libraries, 2025-01) Boden, Catherine; Bolton, Susan; Gerrard, Angie
The aim of this survey was to describe academic librarian roles in systematic reviews (SR) in any discipline, as a follow-up to a previous survey of Canadian academic health sciences librarians. A convenience sample of librarians at Canadian universities who support SRs were invited to complete a survey. Respondents were asked about their roles, training, knowledge, and barriers to providing SR services. Ninety-four librarians responded to the survey. The most common roles were in the literature search; time and training were the most frequently reported barriers. Librarians are supporting reviews in multiple, diverse disciplines, primarily as expert searchers.
Temporomandibular joint assessment in MRI images using artificial intelligence tools: where are we now? A systematic review
(Dentomaxillofacial Radiology, 2025-01) Manek, Mitul; Filipe Bezerra Silva, Diego; de Melo, Daniela Pita; Major, Paul W; Jaremko, Jacob L; T Almeida, Fabiana
Abstract
Objectives
To summarize the current evidence on the performance of artificial intelligence (AI) algorithms for the temporomandibular joint (TMJ) disc assessment and TMJ internal derangement diagnosis in magnetic resonance imaging (MRI) images.
Methods
Studies were gathered by searching 5 electronic databases and partial grey literature up to May 27, 2024. Studies in humans using AI algorithms to detect or diagnose internal derangements in MRI images were included. The methodological quality of the studies was evaluated using the Quality Assessment Tool for Diagnostic of Accuracy Studies-2 (QUADAS-2) and a proposed checklist for dental AI studies.
Results
Thirteen studies were included in this systematic review. Most of the studies assessed disc position. One study assessed disc perforation. A high heterogeneity related to the patient selection domain was found between the studies. The studies used a variety of AI approaches and performance metrics with CNN-based models being the most used. A high performance of AI models compared to humans was reported with accuracy ranging from 70% to 99%.
Conclusions
The integration of AI, particularly deep learning, in TMJ MRI, shows promising results as a diagnostic-assistance tool to segment TMJ structures and classify disc position. Further studies exploring more diverse and multicentre data will improve the validity and generalizability of the models before being implemented in clinical practice.
Effects of External Pacing Type on the Cross-Education of Motor Skill
(Journal of Motor Behavior, 2025-01) Andrushko, Justin W; Zirk, Dakota T; Kurniawan, Aryan R; Renshaw, Doug W; Farthing, Jonathan P
Cross-education (CE) is a phenomenon whereby motor training of one limb leads to improved performance in the opposite untrained limb. External pacing of a motor task can enhance CE; however, the influence of different pacing methods is poorly understood. This study explored how motor training with auditory (AP) and visual pacing (VP) impacts CE with a visuomotor force target task. Sixty-one participants performed a unimanual motor task. Participants were randomized into a visual (n = 31) or auditory (n = 30) pacing stimuli condition. The primary outcome was cumulative error scores for each hand, before and after visuomotor training. Pacing type did not yield different magnitudes of CE. However, after adjusting for baseline differences, a significant hand (trained vs. untrained) × practice side (dominant or non-dominant) interaction (p = .013, ηp2 = .106) and a group main effect (p = .036, ηp2 = .165) were observed. Visual pacing resulted in greater improvements in task performance compared to auditory pacing regardless of hand or practice side, while training the dominant limb resulting in a greater interlimb asymmetry regardless of pacing stimulus. These findings have implications for applying pacing strategies during rehabilitation from unilateral injury or neurological impairment.
SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies
(Methods, 0001) Todd, Clarence; Jin, Lingling; McQuillan, Ian
This paper proposes a detailed process for SV calling that permits a data-driven assessment of multiple SV callers that uses both genome assemblies and long-reads. The process is implemented as a software pipeline named Structural Variant − Jaccard Index Measure, or SVJIM, using the Snakemake [20] workflow management system. Like most state-of-the-art SV callers, SV-JIM detects the presence of variations between pairs of genomes, but it streamlines the numerous SV calling stages into a single process for user convenience and evaluates the multiple SV sets produced using the Jaccard index measure to identify those with the highest consistency among the included SV callers. SV-JIM then produces aggregated SV results based on how many callers supported the reported SVs. For validation, SV-JIM was assessed through three case studies on the Homo sapiens genome and two plant genomes – Brassica nigra and Arabidopsis thaliana. Executing SV-JIM identified a significant amount of inter-caller variance which varied by tens of thousands of results on the larger Brassica nigra and Homo sapiens genomes. Further, aggregating the SV sets helped simplify better retention of the less frequently occurring SV types by requiring a level of minimum support rather than from a specific SV caller combination. Finally, these case studies identified a potential for inflated precision reporting that can occur during evaluation. SV-JIM is available publicly under MIT license at https://github.com/USask-BINFO/SV-JIM
Avulsion of the lateral origin of the gastrocnemius muscle mimicking cranial cruciate ligament deficiency in a dog
(Vet Record Case Reports, 2023-12) Zadeh, Abedin Shaban; Boston, Sarah Elizabeth
Avulsion of the lateral head of the gastrocnemius is an uncommon diagnosis. Nonetheless, it is a possible cause of lameness in dogs, and it could be misdiagnosed as a cranial cruciate ligament injury if a systematic approach to clinical case management is not followed. The treatment of choice for avulsion of the gastrocnemius is surgical stabilisation. The proximity to the peroneal nerve and scarcity of bone for purchase for stabilisation are surgical challenges. However, the stabilisation by a spiked washer and screw can yield an excellent outcome for return to function.
Dioctophyme renale (giant kidney worm) in a dog: A review of a parasitic disease requiring surgical treatment
(Vet Record Case Reports, 2025-01) Zadeh, Abedin Shaban; Carr, Anthony P; Jenkins, Emily J
Infection with the nematode Dioctophyme renale (giant kidney worm) in dogs and other mammals occurs following the ingestion of an aquatic host containing the infective larvae. This parasitic disease has no known effective pharmaceutical treatment. This case report describes a 7-month-old, entire, female Husky with a 2-month history of haematuria and intermittent vomiting. An abdominal ultrasound examination and microscopic finding of eggs of D. renale in urine sediment helped to establish the diagnosis. The affected right kidney and retroperitoneal worms were removed by exploratory celiotomy. The sonographic features of the worms and a comprehensive review of the latest literature, suggesting future research topics on early serological diagnosis, medical treatment options and the most recent nephron-sparing nephrotomy techniques (via nephroscopy or laparoscopy), are discussed.