82837 research outputs found
Sort by
Segmentation of fetus from 3D ultrasound images
Get PDFIn obstetric care, ultrasound imaging provides real-time insight into the development of the fetus. The manual interpretation of these images by clinicians can be time-consuming and variable, making it necessary for automated segmentation solutions that accurately delineate fetal structures. Focusing on both traditional and state-of-the-art architectures, this thesis explores the application of advanced deep learning models for segmenting fetuses from 3D ultrasound images. We evaluated several models, including UNet-based approaches, transformer integrated models (UNETR), and diffusion-based architectures, to assess how well each model handles the challenges presented by ultrasound data, such as noise and low contrast. In spite of these complexities, nnUNet v2 demonstrated exceptional performance through its self-configuring framework, which dynamically optimizes parameters and architecture according to the data it is given. nnUNet v2 performed better than other models in medical imaging segmentation, proving its robustness and adaptability.Furthermore, this study introduces a novel module that integrates the nnUNet v2 model with 3D Slicer, making it possible to visualize fetal segments efficiently. As an additional innovation, we used the Looking Glass Factory's 3D holographic display to enhance clinicians' ability to view fetal structures in three dimensions. As a result of this integration, ultrasound data can be more readily accessed and interpreted in clinical settings.In addition to contributing to the growing body of research in medical image segmentation, this thesis emphasizes the importance of adaptable segmentation pipelines in improving prenatal diagnosis. It is expected that future research will focus on improving noise resilience, expanding datasets for improved generalization, and exploring real-time segmentation for clinical applications. We aim to support clinicians in providing accurate and timely prenatal care through automation of fetal ultrasound analysis
Enhancement of Total Shoot Lipid Content of Alfalfa and Sainfoin Using Chemical Mutagenesis and CRISPR-Cas9-Mediated Genome Editing
No full textMethane (CH4) emissions from cattle, resulting from inefficient fermentation processes in ruminants, are one of the major contributors to anthropogenic greenhouse gas emissions. One strategy to reduce CH4 emissions from ruminants is to increase the energy density of their feed through lipid supplementation. However, this approach is often costly and sometimes impractical. In the present day, available cultivars of forage crops such as alfalfa (Medicago sativa L.), a notable legume forage in terms of ruminant rations and export value, and sainfoin (Onobrychis viciifolia Scop.), a bloat-free forage, contain only ~1-3% lipid on a dry matter (DM) basis. As such, the overall aim of this study is to improve the total shoot lipid content (TSLC) of these crops using random and targeted mutation.
The first objective of this study is to generate the first generation of chemically mutagenized alfalfa and sainfoin populations with increased TSLC. M1 populations, including approximately 500 plants from each of the alfalfa (cv. AC Blue J) and sainfoin (cv. AAC Mountainview), respectively, were established in the greenhouse following treatment with 0.5-1% ethylmethane sulfonate (EMS). TSLC of samples from these M1 populations were analyzed using near-infrared spectroscopy (NIRS) and validated through Gas Chromatography-Mass Spectrometry (GC-MS). After a series of selections, approximately 16 -18 mutants with high (a relative increase of 12.3 – 12.8% lipid on a DM basis compared to control) or low (a relative decrease of 10.6 – 11.5% on a DM basis compared to control) lipid contents were selected to form M2 populations. The M2 populations were used for morphological studies and crossed together for the advancement to M3 generations (Chapter 2).
Subsequently, RNA sequencing was performed on two selected M2 genotypes from each category (low-lipid, control, high-lipid) to identify genes associated with lipid biosynthesis in leaf and stem tissues (Chapter 3). The analysis revealed 512 differentially expressed genes (DEGs) in the high-lipid vs. control, 210 DEGs in the low-lipid vs. control, and 362 DEGs in the high vs. low lipid comparison of the leaf tissue. Stem tissue exhibited a greater number of DEGs, with 657 DEGs in high-lipid vs. control, 166 DEGs in low-lipid vs. control, and 518 DEGs in high vs. low comparisons. The MapMan analysis revealed four lipid-related genes in the high-lipid mutants (high-lipid mutants vs. both control and low-lipid mutants), that included biotin carboxyl carrier protein (BCCP), beta-ketoacyl-acyl carrier protein synthase III (KAS III), CER2 protein, and lipase-like protein. In contrast, three lipid-related genes were identified in the low-lipid mutants (low-lipid vs. control), including At2g26170 (cytochrome P450, family 711, subfamily A, polypeptide 1), lipase-like protein, and BCCP. The lipid-related DEGs identified in this study provide valuable targets for genomic breeding aimed at enhancing lipid content in the vegetative tissues of forages.
The second objective of the study is to enhance TSLC in alfalfa by downregulating PEROXISOMAL ABC TRANSPORTER 1 (PXA1) and SUGAR DEPENDENT 1 (SDP1) genes, which are involved in lipid breakdown, using the Clustered Regularly Interspaced Palindromic Repeat (CRISPR) and CRISPR Associated Protein 9 (Cas9) genome editing tool (Chapter 4). Gene editing frequency droplet digital PCR (GEF-ddPCR) assays and Sanger sequencing were employed to confirm the presence of mutations at the target sites. Eight unique PXA1-edited and 11 unique SDP1-edited genotypes were identified, with gene editing frequencies ranging from 25% to 75%. Lipid content analysis revealed that some edited genotypes of PXA1 and SDP1 exhibited significant disruptions in lipid accumulation and fatty acid composition as indicated by the increase in either leaf or stem lipid content or both. However, there were no consistent morphological variations in either the PXA1 or SDP1 mutants, with the exception of poor morphological traits observed in SDP1-gRNA3 mutants and consistent delayed flowering in all SDP1 mutants.
In conclusion, this study explores the use of EMS-mediated mutagenesis and CRISPR-Cas9 editing to improve TSLC in forage legumes like alfalfa and sainfoin.
The research highlights the potential to reduce CH₄ emissions, improve animal performance, and enhance the quality of ruminant feed. Key genes involved in lipid metabolism were identified, and further work is needed to optimize genetic modifications. The resulting germplasms will provide high-quality feed and benefit both producers and consumers
Environmental and Crystal Chemical Controls on the Products and Efficiency of Carbon Mineralization Reactions
No full textNegative global consequences associated with the climate crisis are expected to become more extreme and continually worsen as Earth’s mean global temperature approaches, or exceeds, a 2 °C rise from pre-industrial revolution temperatures. To combat this, countries have pledged to transition to sustainable energy systems to limit emissions, primarily as CO2; however, this is a slow process. In order to minimize environmental and societal damage related to anthropogenic climate change, rapid implementation of large-scale carbon dioxide removal (CDR) technologies is necessary to mediate historic and current emissions. While many strategies for CDR are being explored, CO2 storage in geologic environments or as benign carbonate minerals presents a safe, long-term repository for anthropogenic emission. In my thesis, I examine how environmental conditions and biogeochemical processes influence CO2 storage in carbonate minerals to help advance carbon mineralization and enhanced rock weathering (ERW) technologies. Furthermore, this research examines how cation substitution in the Mg–Ca–Fe(II) –H2O–CO2 system affects the long-term stability of secondary carbonate minerals targeted for CDR. This was achieved by integrating data from four research projects (Chapters 2–5):
Chapter 2 describes detailed temporal mineral transformation and recrystallization pathways for Ca, Mg, and Ca Mg-carbonates in simulated saline/diagenetic conditions, between 40 and 80 °C, while concomitantly tracking metal partitioning (Sr and Li) and stable oxygen isotope fractionation. Multi-phase assemblages of carbonate minerals formed in a laboratory experiment following the transformation of amorphous Ca-Mg-carbonate. Mineralogical and chemical compositions varied depending on reaction temperature. These results have implications for predicting the evolution of carbonate precipitation reactions and their long-term stability, as well as associated metal release, during CO2 sequestration in saline environments.
Chapter 3 examines how Fe(II)-substitution in brucite [Mg(OH)2] and prevailing environmental conditions — reduction-oxidation (redox) state and background anions — affects the long-term stability of secondary Mg–Fe carbonates and the overall carbonation efficiency. These results highlight the importance of considering metal substitution when estimating the CO2 sequestration potential of both mine wastes in surficial environments and serpentinite deposits in subsurface conditions. Long-term carbon sequestration potential in Fe bearing phases is typically limited to siderite (FeCO3) and pyroaurite [Mg6FeIII2CO3(OH)16∙4H2O]. But, as a consequence of the redox sensitive tendencies of Fe bearing phases, captured CO2 can be released from Fe bearing phases during redox fluctuations and environmental changes.
Chapter 4 elucidates the influence of dissolved silica and Fe(II) on Mg-carbonate precipitation and transformation pathways, along with co-evolving (low-temperature) silicate formation. This research shows that dissolved silica can accelerate Mg-carbonate nucleation; however, the amount of Mg-carbonate formed depended on the initial silica concentration as amorphous silicates scavenge Mg cations. In Mg-only experiments, the rate of dypingite formation increased as the initial silica concentration increased and, interestingly, nesquehonite did not form as an intermediary phase in experiments containing 100 mM Si but rather dypingite was the sole phase. Carbonate (re)crystallization in solutions containing a mixture of Mg and Fe(II) is controlled by redox conditions and, to a lesser extent, Si concentration. This work demonstrates the importance of considering relationships between carbonate and silicate precipitation reactions and, therefore, these results support our current understanding of silicate–carbonate cycling (i.e., enhanced rock weathering) in alkaline systems.
Chapter 5 evaluates whether burial of sulfide minerals, derived from chemoheterotrophic microorganisms (i.e., sulfate reducing microorganisms), and organic carbon facilitates long-term storage of carbonate minerals in Mg- and Fe-rich saline environments. To achieve this, I studied a unique saline playa lake, Basque Lake #2 (near Ashcroft, British Columbia, Canada), where formation of low-temperature magnesite (MgCO3) is associated with sulfidic sediments. Field observations were integrated with laboratory microbial experiments, to determine the role of chemoheterotrophic microorganisms during carbon mineralization. Based on analysis of core samples, it was estimated that only ~1.0% of the total magnesite was generated by alkalinity derived from sulfate reduction: this finding is also supported by microcosm experiments. Additionally, results suggest that previous studies that examined the capability of sulfate reducing microorganisms to induce carbonate precipitation may have overestimated their contribution. The implications from this work extend to developing biogeochemical CDR methods in alkaline mining environments and subsurface geologic systems.
This research improves the current understanding of mineralogical, chemical, and biological controls on secondary carbonate precipitation in geologic systems. Overall, my thesis will support future development of CDR methods in geologic environments by integrating these novel findings into future practices
“Connected to the land and to each other”: Clam harvesting, Inuit community health, and wellbeing in Nunavut
No full textInuit communities in Nunavut hold deep and intricate relationships with country food, which are integral to daily life, health, and wellbeing. Country food provides nutrient rich food that supports good health, cultivates mental and spiritual wellbeing, and fosters sharing of Inuit knowledge and skills. Celebrating the importance of country food, the community-led Nunavut research program, called the Niqivut Silalu Asijjipalliajuq (NSAP): Our Food and Climate Change program engages in research focused on country food, food security, nutrition, and climate change in Nunavut. The NSAP program, led by Inuit women, aims to advance climate-food-health research by engaging country food knowledge, and supporting Inuit-led research, policy, and capacity sharing. Within the NSAP program, clams (Mya truncata) were identified as a country food species that provide important sustenance for many Inuit communities. Situated within this larger research project, this collaborative thesis research aimed to characterize and share the ways in which clams and clam harvesting practices support Inuit health and wellbeing in Nunavut using a multi-methods research approach. First, to understand the extent, scope, and nature of published research on clams across human, animal, and environmental domains, we conducted a scoping review of the literature on clams in Nunavut, Canada. Of the 24 articles included, this review revealed that most studies focused on clams described in terms of ecological histories (n = 10/24; 24.0%), physical characteristics (n = 7/24; 29.17%), and environmental indicators (n = 5/24; 20.83%). Two studies examined clams as sources of foodborne illness (n = 2/24; 8.33%), but no studies investigated the nutritional value of clams or described the role of clams in food security and community health. Finally, we found no studies that engaged Indigenous knowledge systems in the context of clams or clam harvesting. To address these research gaps, we explored the significance of clams through the holistic lens of Inuit community health and wellbeing. Using a community-led approach, we conducted in-depth conversational interviews and group discussions (n = 15), followed by reflexive thematic analysis to characterize clams and clam harvesting in the Qikiqtani region of Nunavut. Inuit knowledge holders emphasized the importance of clams for physical and nutritional health, mental and social wellbeing, and community connection and culture. Clams were described as an accessible source of nutrition that supports food sovereignty, and clam harvesting was seen as a way to share Inuit knowledge and skills, fostering a community-centered approach to food systems. Inuit knowledge holders also highlighted the impacts of changing country food systems on diet, sharing practices, and the environment. These findings have practical implications for public health, community nutrition, government policies, and future research. In collaboration with the NSAP team and other Nunavummiut, three community resources were developed: 1) an updated clam section for the Nutritional Fact Sheet Series on Inuit Traditional Foods, 2) a social media poster for the NSAP website, and 3) an Inuktitut labelled clam drawing. This thesis research describes the holistic relationship between Inuit food systems, community health and wellbeing, and the environment, highlighting not only the importance of clams for Inuit communities, but also the critical role of Inuit voices, lived experiences, and perspectives in ecosystem health and public health policy in Nunavut
FI Leave Here Tomorrow: Improving Inclusion in Canada’s French Immersion Programs
Get PDFThis paper presents a synthesis of the literature on inclusion in French immersion (FI) programs in Canada from the last 20 years. A lens of sociolinguistics for change (Davis, 2024; Roy, 2020) is used to examine policies around inclusion in FI, compare these policies to the realities of inclusion in FI, and seek approaches for making FI more inclusive. The policy landscape of inclusion in Canada is explored through key court cases. The gaps between inclusion policy and practice are described in terms of themes identified in the literature: multilingual learners, special education, and colonialism. The identified approaches to making FI more inclusive are addressing the FI teacher shortage; increasing FI research; more research-informed FI educators, leaders, and decision-makers; more diverse and inclusive learning and teaching resources in French; using plurilingual pedagogy; and using a professional learning community approach
