VictorJuiz/thesis huggingface dataset:
A Novel Antibody Detection Technique Using the Agglutination of Surface Displaying Yeasts

Blood screening for disease in the developing world remains an enormous challenge despite significant advances in modern biotechnology. Simple, affordable, and easily deployed tools for antibody detection in blood and other fluids are still desperately needed. A simple yeast-based agglutination assay that requires no electricity, no sophisticated equipment, and minimal training is described here, using established methods for displaying stable fusion proteins on the surface of S cerevisiae. Strains displaying peptides with known binding regions for generic human immunoglobulin G antibodies, and for specific human antibodies against T. cruzi (the causative agent for Chagas’ disease) and dengue virus were created and grown. The cells displaying disease epitopes were mixed with the samples positive for the disease antibodies, and have been shown to capture the specific antibodies to their surfaces. After washing, the coated cells were mixed with cells displaying the Z domain derived from S. aureus, which binds to the Fc region of the captured antibodies, linking the cell types together. The links formed between the cell types cause the cells to agglutinate, resulting in positive and negative signals that are easily distinguishable to the naked eye. Factors affecting the agglutination, including ionic strength, cell mass, the geometry of the well, and proper growth conditions were studied to produce a working protocol for the assay. The key strengths of the assay: simplicity, stability, modularity, low cost, low technical requirement, and broad familiarity with similar tests, give it promising potential to be a new alternative to current industry methods.

Keywords: agglutination
antibody
Chagas
dengue
diagnostic
yeast
Advisor: McMillen, David R
Chaucer's French Sources — Literary and Codicological Play and the Author's Persona

This dissertation studies the ways that Chaucer and his French contemporaries, Guillaume de Machaut, Jean Froissart, Oton de Graunson, and Eustache Deschamps, craft poetic authority. They do so in relation to the books that convey their writing and literary reputations to their audiences. Chaucer, translating the work of these French poets, reacts to the constructions of authority he finds in medieval sources, in manuscripts, and in a scribal culture in which the transmission of texts can be unpredictable. I argue that Chaucer adapts Machaut's pseudo-autobiographical narrative voice in his own poetry. He responds to a contrast evident in manuscript culture between the single-author codex — for example, surviving books of Froissart's poetry, Paris, BNF f.fr. 830 and 831 — and the ubiquitous miscellany, a contrast that seems to operate along gendered and poetic as well as codicological lines. Chaucer adapts the poetic form of Graunson's "Cinq Ballades" to ensure that his "Complaint of Venus" circulates as a single piece, unlike some copies of his source text. Finally, I argue that Deschamps invites Chaucer to participate in a cross-Channel exchange of invective, one that is part of a bookish and literary tradition. The main argument of my dissertation is that Chaucer puts ideas about books into play in his poetry. He imagines manuscripts as forms for literature and as forms for authority, like the way the disordered aesthetic of the Canterbury Tales creates — ironically — a work of literature resembling a single-author manuscript: a collection of works by one author that circulates intact. Chaucer's investigation of bookish forms is playful, but it also has high poetic stakes: for Chaucer, as for his French contemporaries, play locates the poet in an authoritative literary tradition and secures his future renown.

Keywords: Authorship
Chaucer
Fourteenth-century French poetry
Manuscripts
Narrative persona
Advisor: Gillespie, Alexandra
Kullmann, Dorothea
Identification and characterization of a pathological TDP-43 variant in amyotrophic lateral sclerosis and frontotemporal lobar degeneration

TAR DNA-binding protein 43 (TDP-43) proteinopathy is a key pathological feature of a majority of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) cases. One key feature of pathological TDP-43 is the presence of lower molecular weight (MW) C-terminal species of 25 and 35 kDa, the origins of which were unclear. In investigating the mechanism(s) which generate such species, we identified an abnormal TDP-43 splice variant, TDP-43 r.[106_196del], that was upregulated in ALS. TDP-43 r.[106_196del] contains a 91 base pair splicing deletion in exon 2, leading to translation from a downstream methionine and the production of a N-terminally truncated protein of 35 kDa. This protein isoform, herein referred to as TDP-35, resembles the pathological 35 kDa C-terminal species seen in disease. Expression of TDP-35 in cultured cells and primary motor neurons showed that TDP-35 has reduced solubility, cytoplasmic distribution, increased tendency to form aggregates, and the capacity to induce motor neuron death. Generation of a neo-epitope TDP-35 antibody immunolabeled the pathological 35 kDa TDP-43 species in ALS and FTLD tissues as well as pathological inclusions in ALS spinal cords, providing evidence that the 35 kDa TDP-43 species in ALS and FTLD can be generated by aberrant alternative splicing leading to the use of a downstream start codon, Met85. Expressing TDP-35 in transgenic mice led to the development of regionally selective neuropathology that included downregulation of endogenous mouse TDP-43, age-dependent neurodegeneration, and associated neuroinflammation. Furthermore, TDP-35 transgenic mice developed age-dependent non-spatial memory deficits and were impaired in emotional processing, but retained an intact spatial memory, all of which closely resemble the selective cognitive deficits observed in clinical frontotemporal dementia (FTD). To elucidate the underlying disease mechanism, our interactome study that identified TDP-35-interacting proteins pinpointed the mitochondria-associated ER membrane (MAM) as an affected cellular pathway in TDP-35-mediated pathogenicity. More specifically, TDP-35, but not endogenous TDP-43, redistributes to the MAM and this was associated with an increased mitochondrial-ER association and abnormal morphologies of the ER and mitochondria. In summary, the work encompassed by this thesis has uncovered a novel and exciting cellular mechanism underlying TDP-43-mediated pathogenesis in ALS and FTLD.

Keywords: Amyotrophic lateral sclerosis
Frontotemporal dementia
Frontotemporal lobar degeneration
Mitochondria-associated ER membrane
Neurodegeneration
Transgenic mouse model
Advisor: Robertson, Janice
Improving the Thermal Performance and Durability of Historic Masonry Buildings

Historic buildings are less energy efficient than modern structures due to the nature of their construction. Although envelope improvements can reduce operating energy, such retrofits can potentially accelerate the deterioration of the historic facade. Consequently, the challenge is to improve the energy performance while maintaining a durable facade. This research proposes a retrofit approach for historic buildings that addresses both energy consumption and durability of the masonry facade. To improve energy performance, an 1879 historic solid masonry home was retrofitted using an innovative Nested Thermal Envelope Design (NTED). An envelope controlling heat, moisture and air movement was constructed around Core and Perimeter zones that were independently operated. Conditioning the entire house provided 36% space heating energy savings below the Ontario Building Code 2012, while turning off the heat to the Perimeter areas increased savings to 68%. To address durability concerns arising from insulating the masonry walls, the use of a vented airspace installed between the masonry and the thermal insulation was explored. The vented airspace at the first field trial increased the drying potential of the historic masonry during the winter when the brick was most vulnerable to freeze-thaw damage. An estimated 1.1 kg/m2/a was removed at South and East walls. The second field trial showed drying between 4.3 kg/m2/a and 5.7 kg/m2/a at the South and 0.08 kg/m2/a wetting at the North. In situ moisture content levels of the brick varied between 10% - 15% while laboratory testing of similar brick revealed a saturated moisture content of 29%. Both field trials showed that the vented airspace drying potential was influenced by facade orientation and solar radiation levels. An alternative way of constructing the airspace was then tested in the laboratory to explore the use of air permeable insulation in lieu of a clear airspace. Walls constructed with rock wool insulation and vent holes, but with no clear airspace, removed between 52% - 90% of moisture, depending on the insulation density and vent hole area. Walls featuring a clear airspace removed between 59% - 95% of moisture. These laboratory tests showed that enough air was able to move through the air permeable insulation thereby improving the drying potential of the walls.

Keywords: durability
energy efficiency
historic buildings
masonry
Advisor: Pressnail, Kim D
Novel Single Cell Methods to Identify the Genetic Composition at a Single Nuclear Structure

Reported here are two novel techniques that allow for the identification of DNA obtained from a nanoscale region of a single cell nucleus based on either direct DNA dissection with high-precision nano-tools operated inside a scanning electron microscope, or the ligation of oligo probes to subnuclear sites of double stranded breaks induced by 2-photon irradiation. It is demonstrated that these techniques afford the ability to identify loci occupying a shared site at a single nuclear substructure, and are thus uniquely suited for identifying specific sets of loci that converge non-randomly at a shared nuclear body (NB; the "gene hub" model of nuclear organization). The techniques are applied towards determining DNA in the vicinity of single PML nuclear bodies and yield novel loci that show significant frequency of association with PML bodies in a population of cells. As the "gene hub" model may be a general feature of nuclear organization, these techniques, applied to other NBs, may reveal specific sets of convergent loci that reflect novel gene co-regulatory relationships.

Keywords: microscopy
nanodissection
optical dissection
single cell
single molecule pcr
Advisor: Bazett-Jones, David
Expression, Regulation and Functional Roles of the Intermediate Conductance Ca2+-dependent K+ channel, KCa3.1 (KCNN4/IK/SK4) in the MLS-9 Microglial Cell Line and Primary Rat Alternatively Activated by Interleukin IL-4

`Alternative' activation of microglia by interleukin (IL)-4 up-regulates anti-inflammatory molecules and aids with repair processes. Blockers of the Ca2+-activated K+ channel, KCa3.1 (KCNN4/IK1/SK4) improve the outcome in several rodent models of CNS damage but nothing was known about this channel and its roles in the alternative activated state. Therefore, I first characterized the KCa3.1 current in primary rat microglia (unstimulated and IL-4 treated), and in the MLS-9 rat microglial cell line. KCa3.1 current expression was low in untreated microglia; fewer than 30% displayed a small-amplitude current, and it required a positive gating modulator, riluzole or NS309. In contrast, KCa3.1 current was reliably activated in every MLS-9 cell tested, making this cell line useful for studying channel activation and regulation. In MLS-9 cells, I discovered a selective coupling of KCa3.1 to UTP-mediated P2Y2 receptor activation. Following P2Y2-mediated Ca2+ store depletion, KCa3.1 was activated by Ca2+ entry through Orai1/CRAC channels, and it then promoted Ca2+ influx and refilling of Ca2+ stores; however, the Ca2+ required for channel activation was surprisingly high. In alternative-activated primary microglia (IL-4 treated), I discovered that both KCNN4 mRNA and KCa3.1 current were greatly up-regulated, and it then contributed to several functional outcomes. The signaling pathway involved binding of IL-4 to the Type I receptor, activation of the Ras/MEK/ERK pathway, and AP-1 mediated induction of the KCNN4 gene. I discovered that, once KCa3.1 current was induced in alternative activated microglia, UTP activated it, and both the UTP-mediated Ca2+ influx and migration required KCa3.1 current. Next, I found that KCa3.1 is post-translationally regulated by cGMP protein kinase and by PI3K via a signaling cascade involving intracellular ROS, which activates CaMKII and increases the KCa3.1 current. A similar process was seen in MLS-9 cells. Subsequently, KCa3.1 was involved in a positive feedback loop that potentiated ROS production. Overall, these discoveries demonstrate that KCa3.1 is up-regulated in alternative activated rat microglia, and then contributes to several fundamental processes. This work will contribute to our understanding of microglia after CNS damage or disease and to the potential for targeting KCa3.1 to improve the outcomes.

Advisor: Schlichter, Lyanne C
The Cloning and Characterization of MADD-4, A Novel Guidance Cue in C. elegans

Directed cell migration is fundamental to the development of all multicellular organisms including humans. To investigate the molecular underpinnings of directed cell migration, our lab primarily exploits plasma membrane extensions called muscle arms, from the body wall muscles in the tiny nematode Caenorhabditis elegans. Through genetic screens for genes required for muscle arm extension, we found that the UNC-40/DCC netrin guidance receptor directs muscle arm extension to the midlines. Surprisingly, neither the UNC-6/netrin cue (the canonical ligand for UNC-40) nor other well-characterized guidance cues such as the slits, ephrins and semaphorins were found to be the primary cue for muscle arm extension. This suggested that muscle arms were likely responding to a novel guidance cue. In this thesis, I describe the cloning and characterization of MADD-4, a novel secreted cue that diffuses and attracts muscle arms and sensory axons along the dorsoventral axis in C. elegans. MADD-4 is a member of the non-enzymatic ADAMTSL family of proteins and is well conserved among animals. Very little is known about the biological role of any of MADD-4's orthologs. Together with Kevin Chan, I found that MADD-4's guidance function is dependent on an EVA-1-UNC-40 co-receptor complex. We found that MADD-4 interacts with both EVA-1 and UNC-40. Similarly, we found that EVA-1 and UNC-40 likely physically interact and this interaction is critical for the MADD-4 response. Furthermore, we found that the binding of EVA-1 to UNC-40 increases UNC-40's sensitivity to MADD-4. This enhanced sensitivity becomes especially meaningful within a field of other ligands capable of binding UNC-40 like UNC-6. In the absence of UNC-6, UNC-40's responsiveness to MADD-4 becomes less dependent on EVA-1. Hence, by regulating UNC-40's sensitivity to MADD-4, EVA-1 may increase the precision by which UNC-40-directed processes can reach MADD-4-expressing target cells. Collectively, the work discussed in this thesis recounts the first description of a novel guidance cue and its mechanism of action. Furthermore, since the biological role of any ADAMTSL family member outside of MADD-4 is largely unknown, it is very likely that my work on MADD-4 will broaden our understanding of the biological role of the ADAMTSL family of proteins.

Keywords: ADAMTSL
C. elegans
DCC
EVA-1
MADD-4
Netrin
Advisor: Roy, Peter J
Formulation Design for Surfactant-coated Iron Nanoparticle Suspensions

This work describes the design of surfactant formulations used to coat iron oxide nanoparticles and nanoparticles of zero-valent iron (NZVI) with the purpose of imparting colloidal stability and target delivery properties while maintaining the reactivity of NZVI. Iron oxide nanoparticles, although useful as an adsorbent for arsenic and other contaminants, were also used as a non-reactive homologue for the oxide shell structure of partially oxidized NZVI. NZVI can act as reducing agents to transform contaminants such as dense non-aqueous phase liquid (DNAPL) into hydrocarbons and chlorides. Desirable NZVI properties for DNAPL remediation include colloidal stability, mobility in porous media, preferential affinity for contaminant zones (target delivery characteristics), and sustained reactivity with the chlorinated contaminants (for NZVI).

Keywords: formulation
interaction
nanoparticles
surfactant
suspension
Advisor: Acosta, Edgar J
Nonlinear Intermittent Field Dynamics in the Early Universe

We explore nonequilibrium dynamics of inhomogeneous nonlinearly interacting scalar fields in several cosmological settings. In particular, we explore the effects of (initially small) asymmetric fluctuations around field configurations with a high degree of spatial symmetry. These symmetric configurations include planar domain wall and SO(2,1) vacuum bubble collisions, and oscillations of a homogeneous scalar field condensate after inflation. In the last of these, it is well known that linear fluctuations may experience a variety of dynamical instabilities --- a process known as preheating. By extending methods from the Floquet theory of ODEs to PDEs, we demonstrate that linear fluctuations around the planar wall and vacuum bubble collisions also experience exponential growth. This effect has been ignored in the existing literature. We use sophisticated numerical lattice techniques to study the full (3+1)-dimensional dynamics of the collisions. Once the fluctuations begin to interact nonlinearly, the original spacetime symmetries of the collision are badly broken. In each model we study, this symmetry breaking occurs through an inhomogeneous annihilation of the walls. As a result of this annihilation, a collection of oscillons is produced in the collision region. In our study of preheating, we focus on entropy generation as the field transitions from a homogeneous, coherent state to an inhomogeneous, incoherent state. We introduce a coarse-graining procedure based on maximizing the (differential) Shannon entropy subject to a collection of observational constraints. Using lattice simulations, we find a sharp spike in the entropy production rate around the onset of strong nonlinearities amongst the fluctuations. Based on an analogy with a hydrodynamic shock as randomization front, we dub this sudden increase in entropy as the ``shock-in-time''. In each of the systems considered, the new dynamics we discover suggest potential observational signatures. Perhaps the most interesting new signatures are the production of gravitational waves from individual vacuum bubble collisions and the production of nonGaussian density perturbations during preheating. A novel aspect of these signatures is that they are spatially (or temporally) intermittent. Although this thesis focusses on the underlying dynamics responsible for these signatures, it suggests interesting future work developing the necessary methods to observationally constrain them.

Keywords: Bubble Collisions
Cosmology
Inflation
Phase Transitions
Preheating
Topological Defects
Advisor: Bond, J. Richard
Poppitz, Erich
Grain, Stone, and Red Velvet: The Material Assemblages of a City on the Vistula River in Poland, c. 1555 - c. 1655

This dissertation examines Kazimierz Dolny, a city situated at the geo-political center of the vast Polish-Lithuanian Commonwealth within a time span of approximately one hundred years, 1550-1655. During this time the city became a significant mercantile port due to its location on the Vistula River - the main trade route in early modern Poland. The merchants of Kazimierz Dolny oversaw the storage of grain and its export to Gdansk, a commodity that was then shipped to other Baltic and North Sea ports. From this exchange, the merchants made significant financial gains that were channeled into the renovation of their city. Their investments included private stone-constructed granaries and ornamented residences, as well as public commissions such as churches and chapels. This thesis considers the ways in which mercantile networks and the movement of goods shaped a distinct material world where architecture functioned as a commodity.

Keywords: Building
Commodity
Granary
Materiality
Space
Urban
Advisor: Anderson, Christy
A Biologically Inspired Hierarchical Cyber-Physical Integrated Security Analysis Framework for Smart Grids

The last few years have witnessed the radical transformation in structure and functionality of electrical energy systems. Such systems were traditionally executed in the physical world and are now also cyber-enabled. This cyber-enabled energy system, called smart grid, can be envisioned as the marriage of information technology with the electricity network. While its increased dependence on cyber infrastructure aims to enable greater reliability, efficiency and capacity of power delivery, this reliance also creates a host of unfamiliar vulnerabilities. Due to the highly integrated and connected nature of smart grids, it is important to account for their salient cyber-physical coupling when making critical design decisions and identifying solutions to promote security. In this dissertation, we present a biologically-inspired cyber-physical integrated security analysis framework for maintaining smart grid stability under various forms of physical and cyber attacks. Through this security analysis framework, we demonstrate real-time cyber-physical integrated control and communication strategies using "wisely"-placed Phasor Measurement Units (PMUs) and energy storages. Our research has evolved in three stages. We first propose a cyber-physical multi-agent dynamical systems paradigm to model the cyber-physical interactions in smart grids, in which each agent is modeled as having dynamics that synergistically describe physical and information couplings with neighboring agents. Inspired by the analogy between the flocking rules and the smart grid stability requirements, we develop a flocking-based scheme to formulate the cyber-physical integrated action for each agent. In the second stage, we extend the multi-agent dynamical systems paradigm to a two-tier hierarchical framework which reduces information acquisition by leveraging physical couplings between the agents and applying cyber controls selectively on critical agents. In the context of the hierarchical framework, we propose a witness-based security protocol for identifying and mitigating information corruption on the critical agents. In the third stage, we develop an intelligent multicast routing strategy for timely synchronous data delivery in smart grids, called Goal-Seeking Obstacle and Collision Evasion (GOALiE), which is resilient to network congestion and Denial-of-Service (DoS) attacks.

Keywords: Cyber-Physical Integrated Security
Flocking-Based Dynamical Systems
Smart Grid
Advisor: Kundur, Deepa
The Imprinted Polycomb Group Gene Sfmbt2 is Required for Trophoblast Maintenance and Placenta Development

Embryos with two maternal copies of the genome and no paternal contribution (parthenogenetic embryos), die early in development due to failure to sustain a functional extraembryonic tissue of trophoblast origin. The reported phenotypes of parthenogenetic embryos have been correlated with absence of expression from an imprinted paternally expressed gene (PEG) with critical roles in maintenance of trophoblast stem (TS) cells and their derivatives. To find the genes responsible for the observed phenotypes of the murine parthenogenetic embryos, I performed a survey of known PEGs and identified the paternally expressed

Keywords: Extraembryonic Tissue
Imprinting
Placenta
Polycomb Group Protein
SFMBT2
Trophoblast Stem Cells
Advisor: Varmuza, Sue