VictorJuiz/thesis huggingface dataset:
Anoxia-Mediated Electrical Suppression in the Cerebral Cortex of the Western Painted Turtle (Chrysemys picta bellii): Role of the Mitochondrion

The vertebrate brain is one of the most oxygen-demanding organs of the body. In animals that are intolerant to severe hypoxia or anoxia, the brain undergoes irreparable harm within minutes of insufficient oxygen supply. The western painted turtle (Chrysemys picta bellii) has evolved the ability to survive winter months without access to air and does not experience any apparent neurological damage. It is able to achieve this by reducing energetically-demanding cellular processes and the overall electrical activity of the brain to match the reduction in energy availability, effectively balancing energetic supply and demand during anoxic periods. The aim of my research was to understand how the signal of lowered oxygen tension is translated to a reduction in electrical activity with specific focus on the involvement of mitochondria, which are oxygen-consuming organelles that provide the cell with energy in the form of adenosine triphosphate (ATP). Since mitochondria are functionally associated with oxygen availability, I hypothesized that mitochondria serve as oxygen sensors in the anoxia-tolerant brain and initiate signaling cascades that ultimately reduce energy consumption. In the following body of work, I demonstrated that: 1) anoxia leads to depolarization of the mitochondrial membrane potential, which is required for mitochondrial calcium release and glutamatergic channel arrest, and occurs via ATP-sensitive potassium channel opening balanced by proton efflux via the ATP synthase; 2) the mitochondrial depolarization event occurs independently of the enzyme protein kinase C epsilon; and 3) the anoxia-mediated reduction in mitochondrially-derived reactive oxygen species results in increased activity in fast-spiking GABAergic interneurons and elevated extracellular [GABA]. Together, this research contributes to our understanding of neuroprotective mechanisms in anoxia-tolerant organisms and demonstrates the importance of mitochondrial function during the early phases of the anoxic response.

Keywords: Anoxia tolerance
Channel arrest
Mitochondria
Spike arrest
Stellate neurons
Western painted turtle
Advisor: Buck, Leslie T
Human Umbilical Cord Blood is a Functionally and Developmentally Relevant Source of Macrophages with Therapeutic Potential

Recently, two major themes have emerged in the field of macrophage biology: developmental origin and self-renewal potential. While the overlap between these two themes remains elusive, recent mouse data demonstrate distinct functions between macrophages generated via primitive hematopoiesis versus definitive hematopoiesis. As for self-renewal potential, terminally differentiated mouse macrophages proliferate via a self-renewal gene regulatory network. Yet, how these observations are associated with each other, and how they extend to human macrophages remain poorly understood. Herein, we hypothesize that human umbilical cord blood (hUCB) is an alternative source of macrophages distinct from human peripheral blood mononuclear cell-derived macrophages (hPBMC MΦ). First, we demonstrate that macrophage-specific functions, such as phagocytosis, reactive oxygen species (ROS) production, and cytokine secretion are comparable between hPBMC MΦ and hUCB MΦ. In contrast, hUCB MΦ are distinct from hPBMC MΦ with respect to primitive hematopoiesis and self-renewal-associated genes. We highlight significantly stronger correlations between these genes in hUCB MΦ, by disrupting their gene regulatory network using siRNA. These data support the use of hUCB as a distinct source of macrophages, and suggest that the developmental origin of human macrophages may influence their gene regulatory network and consequent cellular responses. Second, noting that cardiac resident macrophages are closely associated with regenerative potential, we explore the use of this new source of human macrophages, and engineer a cardiac tissue to develop a model of cardiac disease. Specifically, we develop an engineered heart tissue (EHT) model based on human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) as an experimental platform where hUCB MΦ activities can be introduced. This reductionist approach allows the exploration of functional outputs of hPSC-CMs mimicking myocardial infarction in vitro. Our work demonstrates that human mimetic EHT can be developed and engineered to provide an experimental platform to investigate and harness immune modulation of ontologically relevant macrophages, presenting highly translatable therapeutic potential of hUCB MΦ. Overall, this thesis provides an in-depth functional characterization of hUCB MΦ and introduces a new model technology for exploring therapeutic utility of this cell source.

Advisor: Zandstra, Peter W
Investigation of Ferrocenoyl Histidine Conjugates and Their Interactions with Metal Ions

This thesis focuses on the use of bis peptide substituted 1, n’-ferrocene (Fc) derivatives in an attempt to provide structural models for some Zn(II) enzymes. This approach eliminates problems associated with oligomerization of peptides around the metal center and formation of intractable polymers and enabled the isolation of a series of discrete metal complexes. Both symmetric and asymmetric Fc–peptide conjugates Fc[CO-Cys(Bzl)-His-OMe]2 (2.6a), Fc[CO-Cys(Trt)-His-OMe]2 (2.6b), Fc[CO-His(Trt)-OMe]2 (2.7a), Fc[CO-His-OMe]2 (2.7b), Fc[CO-His(Trt)-Asp(OMe)-OMe]2 (3.4), Fc[CO-His(Trt)-Glu(OMe)-OMe]2 (3.5) Fc[CO-His(Trt)-His(Trt)-OMe][CO-His(Trt)-OMe] (4.3), and Fc[CO-His(Trt)-Gly-His(Trt)-OMe][CO-Gly-His(Trt)-OMe] (4.4) were synthesized and characterized spectroscopically. In all cases, the Fc group is critical for providing the framework for the peptide substituents such that the entire Fc-peptide conjugate adopts a rigid P-helical Herrick conformation allowing the metal ions to coordinate without polymerization. A strong focus was put on exploring the coordination of Fc-conjugates with Zn(II). Nevertheless, investigations with other divalent metals were conducted. Metal coordination was followed spectroscopically and caused an interesting switching behaviour in the case of 2.6a, 2.6b, 3.4, 3.5, 4.3, and 4.4, where metal coordination to the imidazole of the His resulted in a change in the axial chirality of the central Fc group from P-helical to M-helical. Metal coordination to the Fc-peptide derivatives caused changes in the electrochemical properties, and shifted the oxidation potential anodically. The ferrocene-histidine conjugates described here form discrete metal complexes. The tight interstrand hydrogen bonding between the two peptide strands offers a preassembled binding site to which metal ions can bind.

Advisor: Kraatz, Heinz-Bernhard
Trunk Function and Ischial Tissue Health in Spinal Cord Injury

Pressure injuries are a common secondary complication following spinal cord injury (SCI). Since individuals with SCI have sensorimotor impairments, they neither can feel pain associated with tissue damage due to prolonged unrelieved pressure nor are able to prevent pressure injuries due to mobility impairments. Deep tissue injury is a form of pressure injuries that occurs in the muscle and subcutaneous tissue before tissue breakdown appears at the skin surface. This thesis attempted to address four research questions pertinent to deep tissue injury and offloading in individuals with SCI. First, we proposed a quantitative ultrasound imaging approach to characterize the integrity of the tissues overlying the ischial tuberosity. We demonstrated that the thickness and gray scale measures of the skin, subcutaneous tissue and muscle has potential to be used as a tissue health monitoring approach. The second study investigated our ability to assess trunk strength and function using the multidirectional reach test. This study demonstrated that monitoring changes in trunk strength and reach distance could be used to assess trunk function in individuals with SCI. The third prospective cross-sectional study aimed at determining if there is a relationship between trunk function and offloading of the ischial tuberosities in individuals with SCI. We discovered that trunk strength was significantly higher in people who were able to Reach compared to Non-Reachers, and that offloading times over the ischial tuberosities were lower in Non-Reachers vs. Reachers. Regardless of an individual’s ability to engage in a reaching task, participants with SCI spent more time offloading the left ischial tuberosity compared to the right ischial tuberosity. The fourth exploratory prospective cross-sectional study compared thickness and texture measures of tissue overlying the ischial region in able-bodied vs. SCI participants. We discovered that the area occupied by muscle was significantly greater in the SCI participants when compared with the able-bodied cohort. Individuals who did not engage in offloading had more homogenous skin, subcutaneous tissue and muscle. These studies represent the first step towards better understanding the relationships between offloading, trunk function and health of tissue overlying the ischial tuberosity in SCI population.

Keywords: Pressure Injuries
Reaching
Sitting
Spinal Cord Injury
Trunk function
Ultrasound imaging
Advisor: Verrier, Mary C
Popovic, Milos R
Characterization and clinical applications of textile-based sensors in rehabilitation

The focus of much previous research and development in electronic textiles has been on remote sensing and monitoring, while opportunities for textile-mediated feedback to the wearer remained unexplored. Additionally, feasibility with clinical populations had not been reliably demonstrated. This thesis explores validation and clinical testing of fabric- and thread-based mechanical and electrical sensors. While conductive thread-based stretch sensors have been previously described in terms of their overall correlation with existing measurement modalities, the ability of such sensors to predict linear elongation had yet to be investigated. In a characterisation study, we developed an algorithm to predict linear elongation, given sensor resistance. Sensors based on the 5-thread coverstitch predicted linear elongation to within 5% of sensor range. Given the possibility of applying stitched sensors non-destructively to existing garments, further study of these sensors remains worthwhile. In a study combining sensor characterisation and clinical testing, we designed and tested a wearable speech generating device (SGD) incorporating resistive textile-based switches for a nonverbal pediatric participant with vision impairment. In mechanical tests, the best performing textile switch consisted of two layers of woven conductive fabrics and one layer of insulating felt. In testing the SGD with a pediatric participant, communicative interactions were found to be higher with the fabric-based SGD, particularly at school. Tactile differentiability of keys, device wearability, and aesthetic and functional personalization may be promising advantages of fabric-based SGDs for pediatric users. While electrooculography (EOG) is a promising technology for access for individuals with communication disabilities, traditional sensors can be uncomfortable and obtrusive. We therefore explored the use of fabric-based electrodes for measuring EOG in two participants with neuromuscular disabilities. We developed a peak detection algorithm which differentiated blinks based on relevant peak characteristics (peak height, prominence, and width) with minimal training. Results were promising in both participants, with 83–87% precision and 85–86% recall for online sessions. While thread- and fabric-based sensors have demonstrated efficacy for unobtrusive monitoring in healthcare and rehabilitation applications, additional uses in interaction and communication are promising and warrant further exploration.

Keywords: assistive technology (AT)
augmentative and alternative communication (AAC)
e-textiles
rehabilitation
Advisor: Chau, Tom
“Great Powers yet Unsuspected in Them”: The Insurrection of Things in Victorian Fiction

This dissertation explores how Victorian concepts of subject formation resulted in the concomitant creation of “things” as a separate entity from objects: entities that, unlike objects, with their socially-encoded transparency, exhibit a radical alterity that resists systems of containment and cognition. A pervasive cultural fear of insurrectionary things is evident in the era’s most popular literary form, the novel—a genre closely tied to its notions of identity construction. Characters’ unease around ostensibly inert objects arises from the culture’s fantasy of a material world populated with matter that can be acquired, arranged, and manipulated to maintain “traces” of its owner. But if personality can inflict itself upon objects, what prevents objects from permeating personality? Historically contextualizing my close readings with guidebooks, magazines, travelogues, and home décor manuals, in this project I demonstrate that the era’s discourse of thinghood arises from an ontologically imperialistic and intensely fragile concept of a “territorialized” identity, both personal and national. My introduction describes the cultural conditions under which Victorian human-object relations developed and explains how the novel both established and problematized the fusion of person and thing. My first chapter examines Dickens’s brief hope that the newly formed Detective Police could sort out the ontological chaos of London, shedding light on the peculiar activities of Inspector Bucket in Bleak House. The next two chapters focus on the domestic interior as the problematic seat of Victorian identity: Charlotte Brontë’s Jane Eyre and Charlotte Perkins Gilman’s “The Yellow Wall-paper” use conventionally gothic motifs to expose how home design restrained women’s ability to construct autonomous selves, while Joris-Karl Huysmans’s À rebours and Oscar Wilde’s Picture of Dorian Gray display queer forms of identity formation based on a permeable relationality with the world. The final chapter examines depictions of African statues, both factual and fictional, to uncover a late-imperial “rhetoric of thinghood” used to mark and reject objects whose social histories conflict with Eurocentric ideas of human development. This dissertation relies on “thing theory” throughout to unpack the psychological and phenomenological triggers underpinning the era’s oppositional human-object interactions, which infused “things” with much of their assertive metaphysical presence.

Keywords: domestic interior
identity formation
imperialism
novels
thing theory
Victorian
Advisor: Jaffe, Audrey
Transcranial Acoustic Imaging for Guiding Cavitation-Mediated Ultrasonic Brain Therapy

The ability to treat brain cancers and other disorders of the central nervous system is inherently limited by the presence of the blood-brain barrier (BBB), a specialized structure that regulates molecular passage from the circulatory system into the brain. Ultrasound in combination with circulating microbubbles has been shown capable of transiently increasing BBB permeability in a localized and noninvasive manner, providing a window for the targeted delivery of therapeutics into the brain. Focused ultrasound (FUS)-induced BBB opening is an increasingly researched field, and the approach recently entered into clinical testing. However, sources of variability exist in the current procedures that motivate the need for real-time monitoring and control techniques to improve treatment safety and efficacy. In this thesis, hemispherical passive acoustic sensor arrays and established beamforming algorithms are employed to generate three-dimensional maps of microbubble activity within the brain during FUS-induced BBB opening; methods for mitigating trans-skull image distortion are explored and the use of imaging-based feedback to guide the procedures is investigated. An initial simulation study was carried out to establish the feasibility of transcranial passive acoustic imaging with sparse hemispherical receiver arrays. The effects of various parameters on the image quality obtained from conventional beamforming approaches, modified to incorporate patient-specific aberration corrections based on computed tomography (CT) skull morphology, were assessed in silico. Based on this study, a sparse receiver array was designed and integrated within an existing prototype hemispherical therapy array. The dual-mode system was characterized acoustically via in-vitro and in-vivo experiments with ex-vivo human skull specimens. The use of CT-based aberration corrections for trans-skull acoustic imaging was validated through comparisons with a gold standard, invasive source-based technique. Analytical and numerical models for simulating the receiver element corrections based on CT scans of the head were contrasted. Finally, the utility of passive microbubble imaging in calibrating exposure levels for FUS-induced BBB opening was evaluated using a next-generation clinical prototype system. Results of these studies are presented and their implications are discussed. The acoustic imaging-based guidance strategies developed over the course of this thesis are expected to play a major role in future cavitation-mediated ultrasonic brain treatments.

Advisor: Hynynen, Kullervo H
Investigating the Intersection of Nickel and pH in Helicobacter pylori through the HpNikR Transcription Factor

Helicobacter pylori is a pathogenic bacterium that colonizes the human stomach. To survive its acidic environment, H. pylori synthesizes large quantities of the nickel-containing urease enzyme, which hydrolyzes urea into ammonia to neutralize the local environment of the cell. The importance of nickel to the survival of H. pylori is counterbalanced by the cytotoxicity of nickel, and the nickel-responsive HpNikR transcription factor helps maintain this balance by regulating a variety of genes in H. pylori in response to elevated nickel concentrations. Previous evidence also suggested that HpNikR can also bind DNA in a pH-responsive manner, but the biological relevance of this observation was unclear. In this work, the nickel-responsive regulon of HpNikR was probed, and two novel targets of nickel-dependent repression by HpNikR in vivo were identified. The pH-responsiveness of HpNikR was also explored, and cytosolic pH measurements confirm that the cytoplasm of H. pylori becomes sufficiently acidic to trigger pH-dependent DNA binding by HpNikR when the bacteria are exposed to pH 2 conditions. This drop in cytosolic pH allows HpNikR to regulate several genes in the acid adaptation pathway in a pH-dependent manner, including ureA and amiE. Biochemical characterization of an isogenic H. pylori ΔnikR strain revealed that HpNikR is important for the survival of H. pylori undergoing severe acidic shock, and that the loss of viability in the ΔnikR strain is not because of over-acidification of the cytoplasm. The network of gene regulation in H. pylori is very complex, and understanding the role that HpNikR plays during acidic shock is critical to elucidating how this bacterium survives the harsh environment of the human stomach. Understanding how H. pylori survives in the stomach can facilitate new treatment strategies and reveal how this pathogen has evolved to colonize its unique biological niche.

Keywords: Acid Adaptation
Helicobacter pylori
Nickel
Transcription Factor
Advisor: Zamble, Deborah B.
Isolation, Detection and Functional Characterization of Circulating Tumor Cells Using Microfluidic-based Technologies

Primary tumors shed thousands of cells into blood circulation every day. These circulating tumor cells (CTCs) play a key role in metastasis. The application of CTCs, regarded as a real-time, non-invasive and cost-effective “liquid biopsy”, has drawn much attention in the last two decades. However, their application in clinical practice has been limited due to their extreme rarity and heterogeneity. Highly specialized technologies have been developed to address these challenges. So far, the majority of technologies have focused on separating CTCs from a background of millions of blood cells with high purity and sensitivity. Despite the technological advancement in CTC enrichment, the clinical relevance of these cells is still controversial. In-depth characterization is therefore needed to elucidate their functionality in the metastatic cascade. The principal aim of this thesis is to characterize heterogeneous populations of CTCs, sorting them into subpopulations and assessing the CTCs for aggressive phenotypes. In this thesis, specialized microfluidic-based technologies are used for isolating CTCs and profiling their phenotypes according to a surface marker expression. We describe a two-dimensional separation approach that separates phenotypically-distinct subpopulations of cancer cells. Profiling CTCs based on an epithelial marker enabled us to identify CTCs that have undergone the epithelial to mesenchymal transition (EMT). The EMT-transformed cells exhibited greater invasive phenotypes, as confirmed by an in vitro collagen uptake assay. Using magnetic ranking cytometry (MagRC), a new technology designed for profiling rare cells, we successfully obtained phenotypic profiles from cancer cells and xenograft CTCs. To investigate metastatic phenotypes of CTCs, CTCs from mice bearing prostate cancer xenografts with different levels of aggressiveness were analysed by MagRC. Real-time monitoring of dynamic changes in CTC phenotypes during cancer progression and a course of chemotherapy gave us insights into tumor evolution and treatment efficiency. Metastatic xenografts showed a heterogeneous population of CTCs with epithelial-mesenchymal plasticity. A decrease in heterogeneity followed by a reduction in metastasis incidence was observed after a course of chemotherapy administered to highly metastatic xenografts. Phenotypic profiling of CTCs can potentially be used for cancer prognostic profiling and therapeutic selection.

Advisor: Kelley, Shana O