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Methane consumption by a landfill cover soil under variable soil moisture and temperature conditions
No full textMethane (CH4) is a significant greenhouse gas (GHG) that contributes to climate warming when released into the atmosphere, with over 80 times the warming potential of carbon dioxide (CO2) over a 20-year period. Landfills are one of the largest anthropogenic sources of CH4, and hot-spots of CH4 emissions in landfill cover soils represent a large proportion of emissions that are thus a target for mitigation. These hot-spots can enrich microbes that consume CH4 and produce CO2 as a less potent GHG, via CH4 oxidation. CH4 oxidation rates are modulated by multiple environmental variables including soil moisture and temperature. Therefore, it is important to investigate the interactive effects of these factors on CH4 oxidation rates, to further understand the response of CH4 oxidation activity under changing conditions whether via seasonality or climate change.
In Chapter 2, I conducted a closed-headspace batch experiment with cover soil from a hot-spot of a former landfill to measure CH4 consumption and CO2 efflux rates associated with variations in soil moisture and temperature simultaneously. Soil samples were incubated under a factorial design of 5 soil moisture contents ranging from 11 to 47% WFPS (water-filled pore space), and 6 temperatures ranging from 1 to 35°C. At each temperature and WFPS combination, CH4 was spiked into the headspace, and headspace CH4 and CO2 concentrations were measured over 2 hours to calculate CH4 consumption and CO2 efflux rates. The maximum CO2 efflux rate was observed at the maximal WFPS and temperature conditions of this experiment (91.5±10.3 nmol h-1 g DW-1 at 47% WFPS and 35°C), while the maximum CH4 consumption rate was observed at intermediate soil moisture and temperature conditions (1.86±0.05 nmol h-1 g DW-1 at 25% WFPS and 25°C). The results from this experiment showed the preliminary optimal conditions for CH4 consumption and associated CO2 efflux within this range of tested soil moisture and temperature conditions, and served as a baseline for the experimental design of Chapter 3.
In Chapter 3, I conducted a series of closed-headspace batch incubations with cover soil from the same hot-spot site to expand on the findings from Chapter 2. The incubations assessed the CH4 consumption and CO2 efflux rates under simultaneous variations of soil moisture and temperature, with modifications including a wider range of soil moistures, and higher concentrations and subsequent injections of CH4. Soil samples were incubated under a factorial design of 5 soil moisture contents ranging from 20 to 100% WFPS, and 4 temperatures ranging from 1 to 35°C. At each temperature and moisture combination, CH4 was spiked into the headspace through multiple consecutive injections, and headspace CH4 and CO2 concentrations were measured to calculate CH4 consumption and CO2 efflux rates. The maximum CH4 consumption rate was observed at the moderate soil moisture and temperature conditions (330±12.3 nmol h-1 g DW-1 at 60% WFPS and 25°C), while the maximum CO2 efflux rate was observed at the maximal WFPS and temperature conditions used in the incubations (652±85.0 nmol h-1 g DW-1 at 100% WFPS and 35°C). A diffusion-reaction model was developed to simulate and fit the observed data to represent the effects of temperature and soil moisture on the CH4 consumption and CO2 efflux rates, predicting similar optimal conditions to the observed experimental data. Temperature sensitivity analysis (Q10) also supported the CH4 consumption being via CH4 oxidation. These results provide insight into how seasonal changes in soil moisture and temperature impact CH4 oxidation rates, and therefore also net CH4 emissions, in landfill cover soils and other environments.
Overall, the results from Chapters 2 and 3 together emphasize that the dominant controls on the optimal soil moisture for CH4 consumption are the interactive effects of moisture limitation of microbial activity and of gas (CH4 and O2) diffusion, whereas for the CO2 effluxes, the dominant controls are the interactive effects of moisture limitation of gas (O2) diffusion and solute mobility. The difference in optimal conditions for CH4 consumption and CO2 efflux rates also highlight the presence of different microbial groups underlying the various soil processes. These findings can be expanded on for further understanding of CH4 oxidation activity at hot-spots and for the development of tools for mitigation of CH4 emissions from landfills
Exploring Social Citizenship in the Context of Leisure in Residential Care Settings
No full textDominant stigmatizing narratives of dementia emphasize tragedy, the loss of self, and portray people living with dementia (PLwD) as ‘unagentic’ and ‘failed’ aging subjects. Due to this stigma and the medicalized structure of long-term care (LTC) settings, recreation and leisure are often focused on therapeutic goals or managing “difficult behaviours,” rather than recognizing residents’ desires and aspirations. A social citizenship framework challenges these deficit-based views by recognizing PLwD as active agents with rights, histories, and competencies, while relational citizenship highlights the role of relationships in shaping agency. Although leisure has the potential to either support or undermine social and relational citizenship, existing research has focused almost exclusively on community-based settings, leaving LTC contexts largely unexplored. This study addresses this gap by using an ethnographic approach to narrative inquiry and narrative citizenship to support PLwD in telling their own stories, an opportunity they are often denied in research due to stigma and assumptions about capacity. More specifically it explored how leisure practices in LTC shape social and relational citizenship for PLwD living in these settings. Through fieldwork in a LTC institution in Southern Ontario, I conducted participant observation of leisure programs and research conversations with both PLwD and recreation staff. Four stories reflect the experiences of PLwD and the staff who support them in this LTC setting: Holding onto Selfhood, The Right to Choose, Beyond Isolation, and Negotiating Freedom and Care. This study provides insights into how LTC environments can be reimagined through a relational model of care that intentionally supports the social and relational citizenship of residents by prioritizing interdependence, shared agency, and reciprocal relationships over individualized, person-centred approaches
Boredom as a Motivator of Pain Infliction in Psychopathy
No full textMaladaptive behaviours have been associated with both psychopathy and boredom proneness—however, there remains limited evidence of how they interact to influence these behaviours. Given that psychopathy has been linked to boredom susceptibility, it is possible that boredom contributes to harmful behaviours in psychopathy. This thesis addressed this gap by investigating the interplay between boredom proneness, psychopathy, and the inclination to inflict pain on others. Chapter 1 described the current literature on how boredom and psychopathy influence maladaptive behaviours and highlighted limitations in the extant literature. The following chapters were comprised of four studies: the first study (Chapter 2) explored how individuals with different levels of psychopathy and boredom represented emotions in their bodies, to determine whether the traits of boredom proneness and psychopathy were associated with distinct embodied representations of affect. This was deemed important given the role both state and trait boredom would play in subsequent experimental chapters. Results showed that the embodied experience of boredom did not substantially differ as a function of psychopathy or boredom proneness. The second study (Chapter 3) examined whether boredom (both trait and state) and psychopathy traits exacerbated the tendency to inflict physical pain through an online game scenario. Results showed that state boredom diminished aggression strength in those with higher levels of psychopathy, particularly primary psychopathy. The final two studies (Chapter 4) investigated the likelihood of inflicting social pain using novel scenarios in which participants could choose to inflict social pain on a fictional person. In both Study 4A and 4B, trait boredom proneness did not emerge as a significant moderator between psychopathy and choosing socially painful options. However, when forced to consider the likelihood of choosing each option, boredom proneness did act as a significant positive moderator between psychopathy (and primary psychopathy) and social pain infliction. Chapter 5 concluded with a summary of the research findings and explored possible explanations for the discrepancies observed in the results, addressed the limitations of the current studies, and suggested avenues for future research
Justice is the Real Medicine: The Tensions & In(tensions) of Radical Thinking in Liberal Institutions Across the Medical Industrial Complex
No full textThis dissertation navigates the tensions that arise when radical, political, approaches intersect with the liberal frameworks of health institutions and organizations. Grounded in the interdisciplinary methodology of research-creation, this study interrogates how systems of care, equity, and justice are negotiated, disrupted, and re-imagined within institutional boundaries. Drawing from critical social theories and concepts, the research utilizes pragmatic methods including the plugging-in technique, critical friend collaborations, radical workshops, emergence, affirmative refusal, and skill-sharing, to mobilize knowledge and foster collective insights. The study reveals how liberal, health spaces such as hospitals and long-term care homes often constrain radical political praxis, requiring actors to navigate a delicate balance between complicity and resistance. Through research-creation, it emphasizes the transformative potential of collaborative, creative, and reflexive practices in making visible the affective and structural forces that sustain complicity to white institutionalization. By employing affirmative refusal and emergence as methodological strategies, this research highlights the generative possibilities of refusing predetermined pathways while remaining attuned to the unforeseen. Moreover, radical workshops served as spaces of collective learning and experimentation, fostering community-based knowledge production and challenging state-sanctioned, institutional norms. This work contributes to scholarship on radical politics, health justice, and research-creation by offering practical and theoretical tools to disrupt and reimagine the boundaries of care and well-being within liberal organizations. Ultimately, it argues for the necessity of holding tension as a productive site for transformation, where institutional critique and creative praxis coalesce to envision more just futures
Reassembling Moments in Aldershot Quarry, Burlington: A Narrative Outside of Time
No full textJust as stardust reassembles into life, Earth’s materials are continuously broken down, transported, and reshaped, whether by natural forces or human intervention. Quarrying represents a moment of acceleration in this process, where human activity directs the pace and scale of material redistribution. However, this also brings disputes between industry, environmental conservation, and local communities about environmental degradation, community impact, and resource over-extraction. The thesis reads the quarry from the perspective of material movements, understanding extraction sites as dynamic landscapes where geological, biological, and human-driven forces intersect. Treating site rehabilitation as a media to reveal the material movements. This thesis asks, “What are the design principles for revealing the assembly moments and integrating human activities into natural processes on a post-extraction landscape?”
Aldershot Quarry is selected as the site because it contains ecologically sensitive areas and water systems, is close to transportation, and is part of a growing urban area. The site is a Queenstone shale quarry, which includes two active sites and an undeveloped one. The thesis focuses on the West Quarry and the existing Meridian Brick plant as the basis for the design proposal.
This thesis explores three design principles: “Expose”, “Encounter”, and “Unfinish”. Expose identifies key elements in the Aldershot Quarry. Encounter defines spaces where visitors can read and experience material reassembly moments, integrating public interaction with the site evolving. Unfinish challenges conventional rehabilitation by leaving natural and social forces to shape the site beyond the designer’s control. These principles guide the thesis structure as well, transitioning from the research of material movements in a quarry to the site analysis of Aldershot Quarry, developing a design proposal that applies these principles to a quarry rehabilitation project.
The design proposal engages with the existing extraction and rehabilitation process, integrating site-specific interventions to reappear reassembly moments by revealing material movements and ecological succession. Factory as the symbol of site memory, and the core elements push the materials movements, are regenerated as a community centre to invite the public to build connections with the site. Water strategies expand former quarry ponds into wetlands, reinforcing the local hydrological connectivity and improving water quality. Quarry landforms are preserved and reassembled into walking and cycling trails, making the naked geological surface an interactive experience. Some areas are left intentionally unfinished, fostering passive ecological succession and allowing plant and habitat regeneration. Inspired by the Memorial Park of IBC and Don Valley Brickworks Park, this approach balances natural adaptation with human intervention.
By defining quarries as dynamic landscapes, this thesis challenges the traditional dichotomy between industrial extraction and natural restoration. The design proposal locates Aldershot Quarry as a site where material movements, ecological processes, and public engagement are gathered. Instead of treating quarries as land scars that need to be erased, the research identifies their potential as evolving spaces that bridge industrial heritage, ecological renewal, and material reassembly
Engineering Aerotolerance and Quorum Sensing into Clostridium for Use as a Live Biotherapeutic Product against Solid Tumors
No full textTumor targeting remains a significant challenge in cancer therapy, particularly for solid tumors, which constitute approximately 80% of all cancer types. Hypoxia, a hallmark of solid tumors, plays a crucial role in tumor progression and metastasis. However, hypoxia also serves as a distinguishing feature of tumor cells compared to healthy tissue, presenting an opportunity for targeted therapeutic strategies. One such approach involves the use of anaerobic bacteria, particularly clostridia, which have been known for over 60 years to selectively colonize the hypoxic and necrotic regions of tumors. Studies have demonstrated that infection with wild-type clostridia strains can induce tumor lysis and regression. However, despite their ability to degrade hypoxic tumor regions, tumor regrowth from the viable outer rim often leads to incomplete tumor elimination, limiting the efficacy of clostridia-based tumor therapy.
This study aims to address the challenge of tumor regrowth by developing an aerotolerant strain of Clostridium sporogenes that cannot grow in healthy tissue but can proliferate in the viable outer rim of tumors. As a part of this effort, the water-forming NADH oxidase gene (noxA) from Clostridium aminovalericum was cloned downstream of the thl promoter from Clostridium acetobutylicum and introduced into C. sporogenes. Experimental analysis confirmed that the heterologous expression of noxA conferred aerotolerance, allowing C. sporogenes to grow in the presence of oxygen.
To couple aerotolerance with tumor colonization, the expression of this gene should be regulated. We chose to employ a quorum sensing (QS) promoter. In parallel, a QS regulatory system was designed to enable density-dependent control of gene expression in C. sporogenes. The well-characterized agr operon from Staphylococcus aureus, a Gram-positive bacterium, was introduced into C. sporogenes. Growth and fluorescence assays were conducted to characterize the behavior of the QS system, demonstrating its potential to function as a switch-like regulatory mechanism in C. sporogenes. Additionally, a mathematical model based on kinetic principles was developed and calibrated using experimental data to describe the dynamic of this synthetic QS. While the final integration of noxA under QS control was not completed within the scope of this study, the successful development of both aerotolerance and a functional QS circuit establishes a strong foundation for future assembly and implementation of a regulated-aerotolerant strain of C. sporogenes
Development of Ecohydrological Processes on a Partially Removed Well Pad Undergoing Restoration to a Peatland on the Western Boreal Plain, Alberta, Canada
No full textPeatlands on the Western Boreal Plain have been disturbed at a landscape scale by industrial developments including those associated with the oil and gas industry. Among these disturbances are in-situ well pads, which are constructed to provide a stable base for oil and gas drilling and extraction infrastructure. In the province of Alberta, Canada, well pads must legally be returned to a state of ‘equivalent land capability’ after decommissioning. For well pads constructed in peatlands, equivalent land capability has recently been defined as including the reestablishment of a self-sustaining and peat accumulating vegetation community. One method proposed to reintroduce peatland vegetation (including peatland mosses) onto decommissioned well pads involves the partial removal of the mineral fill used to construct a well pad. Termed the ‘Partial Removal Technique,’ this approach aligns the reprofiled surface elevation of a pad with that of the water table in the surrounding peatland. Peatland vegetation propagules are then introduced onto the residual mineral substrate using a modified version of the established Moss Layer Transfer Technique. However, considerable uncertainty has remained surrounding the efficacy of the technique as a form of peatland restoration, as it had not yet been applied at the scale of a full-size well pad.
Accordingly, a five-year ecohydrological study was undertaken following the first full-scale implementation of the Partial Removal Technique on a well pad. The subject well pad was located in a fen complex on the Western Boreal Plain near the town of Slave Lake, Alberta, Canada. A series of field studies were undertaken to assess the extent to which the residual mineral substrate would support environmental conditions requisite for the initiation and establishment of a peatland vegetation community. Specific objectives addressed included characterization of the hydrophysical properties of the residual mineral fill and their effect on hydrological connectivity with an adjacent fen, and assessment of whether hydrological connectivity was sufficient to maintain a near-surface water table and optimal moisture availability to mosses across the entire site. The role of additional water balance terms in supporting near-surface water tables and water availability was also assessed, including quantification of snowmelt, vertical groundwater exchange, and evapotranspiration. Additionally, monitoring of the development of biogeochemical processes in the first five years post-partial removal was undertaken, including quantification of the rates of nutrient cycling and supply. The effects of microtopography and application of straw mulch and rock phosphate fertilizer on moisture and nutrient dynamics were also assessed.
Results indicate that hydrological connectivity between the residual well pad and the adjacent fen was limited by the low hydraulic conductivity of the mineral fill and the compacted peat underlying it. Combined with rapid drainage from the mineral fill into the underlying peat following rainfall, this resulted in the water table being poorly regulated across just over half of the pad’s surface area. The deeper water tables observed in those areas were associated with non-optimal moisture availability to mosses (i.e., exceedance of literature desiccation thresholds), particularly in the late growing season when rainfall inputs were infrequent. Combined with high rates of water loss through evapotranspiration, it appears that much of the pad’s surface area is likely to be favourable for the establishment of only those mosses with a high desiccation tolerance. The establishment of a vegetation community characteristic of swamps may thus occur over the long term in areas that are hydrologically disconnected from the fen. Nonetheless, hydrological connectivity with the adjacent fen was sufficient to maintain a water table within 6 cm of the surface in areas located within approximately 20 to 30 metres of the upgradient pad edges. This water table depth was associated with optimal water supply at the surface for moss survival and growth. As such, the establishment of a peatland true moss community is likely to be supported across just under half of the pad’s surface area. Snowmelt may also have provided a large source of water in the early season, although additional study is required to determine the extent to which snowmelt may be lost from the pad as overland flow. Surface runoff from an upland feature constructed out of the excess mineral fill produced during the partial removal process did not constitute an appreciable source of water to the pad.
Nutrient cycling and availability demonstrated limited spatial variability across the residual well pad. Owing to the high cation content of the calcareous residual mineral fill, cation supply rates were sufficiently high to further increase the likelihood of peatland true moss establishment in areas with optimal substrate moisture availability. However, low rates of nitrogen production and a low ratio of nitrogen to phosphorus supply rates indicate that productivity of the vegetation community on the residual pad may be nitrogen limited. This may change over time, as a layer of organic litter was observed to accumulate on the surface of the residual well pad during the study. This is likely to result in increased rates of decomposition, and thus also of nutrient mineralization over time.
Combined, the results of this thesis indicate that there is a need to increase horizontal hydrological connectivity with adjacent peatlands in future implementations of the Partial Removal Technique. This may improve the availability of moisture across a greater proportion of the surface area of residual well pads, while also ensuring the long-term development of anaerobic biogeochemical processes. Additional work is also required to reduce water losses in the form of both vertical drainage from residual mineral substrates and evapotranspiration from the surfaces of residual well pads. Overall, the Partial Removal Technique appears to have promise as a strategy to create favourable environmental conditions for the initiation and establishment of peatland mosses on decommissioned well pads
Characterizing the effects of temperature variation on metabolic capacity in darter fish (Etheostoma spp.)
No full textWith progressive increases in global temperatures from climate change, aquatic ectotherms are particularly at risk, considering they are incapable of maintaining their internal body temperatures. As environmental temperatures increase, metabolic rate rises in ectothermic poikilotherms, with thermal extremes presenting potentially lethal implications. By gaining an understanding of the metabolic functioning of local species, we can draw conclusions on the implications of thermal stress on biochemical responses. Here, we focused on understanding the effect of increased temperatures on enzyme activity in the brain, heart, and muscle tissues of three closely related darter species found in the Grand River of Southern Ontario: Johnny (Etheostoma nigrum: JD), Fantail (Etheostoma flabellare: FTD) and Rainbow darter fish (Etheostoma caeruleum: RBD) to determine whether energetic enzymes are a potential limiting factor in thermal tolerance. Analysis of enzymatic activity of four key metabolic enzymes including lactate dehydrogenase (LDH), pyruvate kinase (PK), malate dehydrogenase (MDH) and citrate synthase (CS) were conducted via enzyme assays through a temperature profile, ranging from 20C to 34C, just past the predetermined critical thermal maximum (CTmax), or upper thermal tolerance, at 30.7C ± 0.9, 31.9C ± 0.6 and 33.3C ± 0.8 for RBD, JD and FTD, respectively (Weber & Craig, 2025). Through modelling enzymatic activity in a segmented regression, breakpoint estimates were found for brain at 22.0C ± 0.8, heart at 22.0C ± 5.0 and muscle at 26.0C ± 4.7 indicating decreases in enzymatic activity at higher temperatures. These results indicate that enzymatic activity in brain and heart tissue is most impacted by increased temperatures as evident by the lower trending breakpoints, suggesting that these tissues may be implicated in defining thermal tolerance limits. Muscle tissue enzymatic activity also decreased at higher temperatures but had a higher trending breakpoint, suggesting compensatory mechanisms. Moreover, breakpoints also occurred far before previously determined CTmax values for these fish, indicating that biochemical processes decline in performance prior to ecological death. Overall, these findings enhance our understanding of the biochemical processes that limit thermal tolerance in these local species, with potential implications for conservational efforts in defining temperatures of concern
Simulation study to evaluate when Plasmode simulation is superior to parametric simulation in comparing classification methods on high-dimensional data
No full text© 2025 Stolte et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Simulation studies, especially neutral comparison studies, are crucial for evaluating and comparing statistical methods as they investigate whether methods work as intended and can guide an appropriate method choice. Typically, the term simulation refers to parametric simulation, i.e. computer experiments using pseudo-random numbers. For these, the full data-generating process (DGP) and outcome-generating model (OGM) are known within the simulation. However, the specification of realistic DGPs might be difficult in practice leading to oversimplified assumptions. The problem is more severe for higher-dimensional data as the number of parameters to specify typically increases with the number of variables in the data. Plasmode simulation, which is a combination of resampling covariates from a real-life dataset from the DGP of interest together with a specified OGM is often claimed to solve this problem since no explicit specification of the DGP is necessary. However, this claim is not well supported by empirical results. Here, parametric and Plasmode simulations are compared in the context of a method comparison study for binary classification methods. We focus on studies conducted with some specific data type or application in mind whose true, unknown data-generating mechanism is mimicked. The performance of Plasmode and parametric comparison studies for estimating classifier performance is compared as well as their ability to reproduce the true method ranking. The influence of misspecifications of the DGP on the results of parametric simulation and of misspecifications of the OGM on the results of parametric and Plasmode simulation are investigated. Moreover, different resampling strategies are compared for Plasmode comparison studies. The study finds that misspecifications of the DGP and OGM negatively influence the ability of the comparison studies to estimate the classification performances and method rankings. The best choice of the resampling strategy in Plasmode simulation depends on the concrete scenario.Research Training Group "Biostatistical Methods for High-Dimensional Data in Toxicology", RTG 2624 Project P1 || Deutsche Forschungsgemeinschaft (DFG), German Research Foundation - 427806116
Advanced AI for Histopathological Whole Slide Image Classification and Captioning
No full textMicroscopic assessment of histopathology images is vital for accurate cancer diagnosis and treatment. Classification and captioning Whole Slide Images (WSIs) for pathological analysis is an essential but not extensively explored aspect of computer-aided pathological diagnosis. Challenges arise from insufficient datasets and the effectiveness of model training. Generating automatic caption reports for various gastric adenocarcinoma images is another challenge. Moreover, microscopic WSIs face challenges such as redundant patches and unknown patch positions due to subjective pathologist captures.
The thesis is divided into two folds. At first, a hybrid method referred to as TransUAAE-CapGen is introduced to generate histopathological captions from WSI patches. The TransUAAE-CapGen architecture consists of a hybrid UNet-based Advereasrial Autoencoder (AAE) for feature extraction and a transformer for caption generation. The hybrid UNet-based AAE extracted complex tissue properties from histopathological patches, transforming them into low-dimensional embeddings. The embeddings are then fed into the transformer to generate concise captions.
The second fold focuses on how to reduce redundant patches and handle the unknown patch positions due to subjective pathologist captures. To address these challenges, a novel GNN-ViTCap framework is introduced for classification and caption generation from histopathological microscopic images. A visual feature extractor is used to extract feature embeddings. The redundant patches are removed by using deep embedded clustering to dynamically cluster the images and extracting representative images through a scalar dot attention mechanism. The graph is formed by constructing edges from similarity matrix, ensuring that each node is connected to its closest neighbors. Therefore, graph neural network is utilized to extract and represent contextual information from both local and global areas. The aggregated image embeddings are then projected into the language model’s input space using a linear layer and combined with input caption tokens to fine-tune the large language models for caption generation.
Our proposed methods are validated using the BreakHis and PatchGastric microscopic datasets. Several ablation studies have been performed to validate our methods. Experimental analysis demonstrates that the proposed TransUAAE-CapGen and GNN-ViTCap architectures outperform state-of-the-art approaches. Our approaches can be integrated into clinical workflows to facilitate early diagnosis and treatment planning, ultimately enhancing patient care using whole slide images