VictorJuiz/thesis huggingface dataset:
Regulation of Cellular Oxygen Sensing Pathways by VHL

Erythropoiesis represents a vital physiologic process that can be adjusted to combat compromised oxygen availability, otherwise known as hypoxia. The canonical response to adapt to hypoxia is mediated by the transcription factor hypoxia-inducible factor-1 (HIF-1). When oxygen is available HIFalpha subunits are hydroxylated by prolyl hydroxylase enzymes (PHD1-3) to allow for binding to the von Hippel-Lindau (VHL) tumour suppressor protein, which serves as the substrate recognition subunit of an E3-ubiquitin ligase complex that ultimately targets proteins for proteasome-mediated degradation. The work presented in this thesis demonstrates a novel role of VHL in recruiting DCNL1 to initiate E3-ubiquitin ligase enzymatic activity which, in essence, allows for the degradation of HIFalpha to commence. In hypoxia, hydroxylation does not take place and as a result HIFalpha can promote the transactivation of a repertoire of genes that aid in adaptation to hypoxia including one which encodes the glycoprotein hormone erythropoietin (EPO). EPO binds to EPO receptor (EPOR) expressed on erythroid progenitor cells to promote their proliferation and differentiation into red blood cells. An erythroid specific oxygen sensing pathway is elucidated in this thesis wherein EPOR is hydroxylated by PHD3 to promote VHL-mediated degradation in a manner analogous to HIFalpha. Combined, these findings build upon our fundamental understanding of how cells detect and counter hypoxic stress.

Keywords: Erythropoiesis
Hypoxia
Ubiquitin
Advisor: Ohh, Michael
Neurophysiologic Studies of Human Subcallosal Cingulate Regions and its Modulation of the Dorsal Raphe in Depression

Depression is the most common of all psychiatric disorders and has a lifetime prevalence of 16% (Kessler et al., 2003). In this work I employ in vivo electrophysiological techniques to investigate key regions in a complex pathway implicated in emotional regulation. First I characterize the neurophysiology of the subcallosal cingulate (SCC) region in treatment resistant depression patients (TRD) undergoing surgery for the placement of deep brain stimulating (DBS) electrodes. In the same study, I show suppression of the locally evoked field potential in the SCC following high frequency stimulation (HFS), possibly indicating impaired plasticity in this cohort of patients. In the second part of this thesis I examine the effects of HFS in the medial prefrontal cortex (mPFC), a rodent homologue of the SCC, on the activity of neurons in the serotonin-rich dorsal raphe (DR) nucleus in the midbrain. In the same study, I also show that mPFC-HFS stimulates GABA interneurons in the DR, inhibiting cellular firing. In the last chapter of this thesis, I demonstrate unequivocal characterization of 5-HT neurons using optical stimulation in transgenic mice. I also use this optogenetic model to show that mPFC-HFS exerts a non-selective inhibitory effect on both 5-HT and non-5-HT neurons. Lastly, I use fast scan cyclic voltammetry to show that 5-HT can be evoked following short high-amplitude stimulation of the mPFC and that 5-HT reuptake is accelerated following a long mPFC-HFS train. Clinically, this strong effect of long-train HFS on the 5-HT reuptake system may explain the efficacy of SCC-DBS in patients that are refractory to SSRIs. Overall, the findings in this thesis demonstrate that HFS induces both local (mPFC/SCC) and distal (DR) effects on the serotonergic projections in the human and animal brain.

Keywords: Cellular firing
Deep brain stimulation
Dorsal raphe
Evoked field potentials
Medial prefrontal cortex
Serotonin
Advisor: Hutchison, William D
Application of Ultra-short Peptides as Building Blocks for the Rational Design of Stimuli-responsive Ferrocene-peptide Gels

The considerable attention given to understanding and utilizing gel based materials in recent years, coupled to the great potential of peptide chemistry for the design and development of stimuli-responsive materials using a bottom-up approach, has led to an ever increasing interest in the fabrication of peptide based functional materials. Considering the fact that serendipity is the usual path to the discovery of molecules capable of gelling water and organic solvents, the rational design of stimuli-responsive gels using a bottom-up approach can be a formidable task. The body of work presented herein strives to tackle the rational design of stimuli-responsive ferrocene-peptide conjugates using a bottom-up approach and relies on the stepwise modification and fine-tuning of the designs to allow the incorporation of molecular features that allow the gel materials to respond to different stimuli, including: temperature, sound, mechanical stress, redox and light. Based on this stepwise approach the ultra-short peptide Boc-L-Phe-L-Lys(Z)-OMe was selected as the peptide unit responsible for driving the gel formation. This ultra-short peptide was found through serendipitous discovery to undergo gelation in a variety of solvents in response to sonication and change in temperature. Moreover, the gels of Boc-L-Phe-L-Lys(Z)-OMe formed in aromatic solvents demonstrated mechano-responsive properties and thermal chiroptical switching. These key stimuli-responsive features rendered Boc-L-Phe-L-Lys(Z)-OMe as an attractive structural unit for installing smart and responsive behaviour in other molecules. Consequently, the dipeptide sequences Phe‐Lys(Z) and Lys(Z)‐Phe were incorporated into the structure of a variety of stimuli-responsive molecules, including: ferrocene, azobenzene and pyrene. While the designed derivatives of azobenzene and pyrene retained their inherent light and fluorescence switching behavior, the redox modulated gel to sol transition of the ferrocene containing organogels was limited by the insolubility of the oxidized gelator and oxidizing agent in toluene. The limitation of the designed stimuli-responsive systems that only allowed gelation in aromatic solvents inspired us to expand the gelation property of the ferrocene derivatives to other organic solvents. By modifying the design, the responsive property of the ferrocene based organogels of Phe‐Lys(Z) and Lys(Z)‐Phe was later expanded to other solvents to allow the reversible redox induced gel to sol phase transition in acetone. Aiming to diversify the stimuli-responsive property of the designed ferrocene gels, a photoresponsive discrete metallogelator was later developed by carefully designing a molecule that retained the photoresponsive and redox active properties of the azobenzene and ferrocene units. The multi-stimuli responsive property of this molecule allowed us to examine this gel system for studying basic logic-gate operations by using different oxidizing agents as input.

Keywords: Gels
Self-assembly
Stimuli-responsive
Advisor: Woolley, G. Andrew
Optical Coherence Tomography for Quantitative Assessment of Microstructural and Microvascular Alterations in Late Oral Radiation Toxicity

More than half of head-and-neck cancer patients undergo radiotherapy at some point during their treatment. Even though the use of conformed therapeutic beams has increased radiation dose localization to the tumor, resulting in more normal tissue sparing, still, in many head-and-neck cancer patients, the healthy tissue of the oral cavity still receives a sizeable amount of radiation. This causes acute and / or late complications in these patients. The latter occur as late as several months or even years after the completion of treatment and are typically associated with severe symptoms. Currently, the clinical method for diagnosing these complications is visual examination of the oral tissue surface. However, it has been well established that such complications originate in subsurface oral tissue layers including its microvasculature. Therefore, to better understand the mechanism of these complications and to be able to diagnose them earlier, there exists a need for subsurface monitoring of the irradiated oral tissue. Histology has been used as such a tool for research purposes; however, its use in clinical diagnosis is limited due to its invasive and hazardous nature. Therefore, in this thesis, I propose to use optical coherence tomography (OCT) as a subsurface, micron-scale resolution optical imaging tool that can provide images of oral tissue subsurface layers down to a depth of 1-2 mm (structural OCT), as well as images demonstrating vessel morphology (speckle variance OCT) and blood flow information (Doppler OCT). This thesis explains the development of an OCT setup and an oral probe to acquire images in-vivo. Moreover, it introduces a software-based quantification platform for extracting specific biologically-meaningful metrics from the structural and vascular OCT images. It then describes the application of the developed imaging and quantification platform in a feasibility clinical study that was performed on 15 late oral radiation toxicity patients and 5 age-matched healthy volunteers. The results of this clinical study show that: 1) the value of the developed metrics (such as epithelium to lamina propria thickness, vessel diameter, and blood velocity) is significantly different between the two cohorts; 2) radiation-induced abnormalities in structural OCT images are primarily observed in the regions where the total radiation dose exceeded ~50 Gy. The results of this study demonstrate the promising ability of the developed OCT imaging and quantification platform to highlight biologically meaningful differences between late oral radiation toxicity patients and healthy volunteers in the structural and vascular images. This methodology may also be used in prognostic studies to monitor the efficacy of the medication prescribed to late oral radiation toxicity patients.

Keywords: Fibrosis
Late radiation toxicity
Optical coherence tomography
Quantitative image analysis
Radiation late effects
Vascular imaging
Advisor: Vitkin, I. Alex
Virtual Holonomic Constraints for Euler-Lagrange Control Systems

In this thesis we investigate virtual holonomic constraints (VHCs) for mechanical control systems. A VHC is a relation among the configuration variables of a mechanical system that does not physically exist, but can be emulated via feedback in a precise sense that is defined within this thesis. An example of VHC is the requirement that the end effector of a robot should only move along a plane. Over the past decade, VHCs have raised to prominence in robotics as they have been successfully employed to induce stable walking motions in biped robots. There is a growing body of evidence that, for complex motion control problems, the VHC paradigm might be more appropriate than the traditional reference tracking approach. Motivated by the hope to establish a new paradigm for complex motion control problems in robotics, this thesis makes contributions in two main directions. First, the thesis presents a complete theory employing VHCs for the stabilization of repetitive â behaviorsâ in underactuated mechanical control systems with degree of underactuation one. The theory in question has a number of components, the development of which takes us along a journey that includes, among other things, the solution of an inverse Lagrangian problem, the development of an algorithm to implicitize parametric constraints, and the stabilization of closed orbits by means of VHCs parametrized by states of dynamic compensators. The second direction of this thesis is the exploration of the hypothesis that the design of controllers enforcing VHCs might represent a viable paradigm for complex motion control problems. To this end, we solve a challenging open problem in snake robotics: make a planar snake approach and follow a path with desired speed.

Keywords: Euler-Lagrange Control Systems
Inverse Problem of Lagrangian Mechanics
Snake Robotics
Underactuated Mechanical Systems
Virtual Holonomic Constraints
Advisor: Maggiore, Manfredi
Biochemical Characterization of FIKK Kinase from Cryptosporidium parvum and Discovery of Potent Inhibitors.

Cryptosporidium parasites cause serious human and animal diseases and affect millions of children worldwide. Drug discovery attempts against the parasites are insufficient and new drug targets are necessary. C. parvum harbors some unique protein kinases including one called FIKK kinase. FIKKs are parasite-specific protein kinases with distinctive sequence motifs and restricted to phylum Apicomplexa. The biochemistry and biology of the evolutionarily conserved members of the FIKK family have not been elucidated before this project. I explored the biochemical nature of the most conserved FIKK members in C. parvum and malaria causing P. falciparum, known as CpFIKK and PfFIKK8, respectively. I have identified the soluble domain boundary of the proteins and their substrate preferences, and characterized their activity in vitro. FIKKs need a ~40 residue extension to the predicted kinase domain to be soluble. They prefer Ser as phosphoacceptor residue flanked by Arg at the -3 and +3 positions in the substrate. Because their biological roles have not been completely elucidated, potent, selective and cell permeable inhibitors would be useful to understand the biological roles of FIKKs in parasites. Here, I report the first Cryptosporidium FIKK (CpFIKK) inhibitor and its selectivity profile. I systematically explored the structure activity relationship for CpFIKK inhibition and for selectivity against CpCDPK1. I identified 4b as a potent (IC50 = 0.2 nM) inhibitor of CpFIKK catalytic activity, and confirmed CpFIKK binding using a thermal melt assay. Minor variations of inhibitor structure led to significant change in selectivity profiles against CpCDPK1 and identified CpCDPK1 selective as well as dually acting C. parvum FIKK-CDPK1 inhibitors from the same structural class of compounds. I evaluated these CpFIKK inhibitors for inhibition of parasite growth in vitro. The observed effect in parasite growth did not correlate with CpFIKK inhibition.

Keywords: Cryptosporidium parvum
Drug discovery
Enzymatic characterization
FIKK kinase
Inhibitor screening
Structural biology
Advisor: Edwards, Aled M
Sicheri, Frank
Chronic Pain as the Embodiment of Hardship: A Narrative Study

This narrative study explored the subjective experiences of 12 individuals (eight women, four men) who had suffered from chronic pain for at least one year. Among participants, the etiology of their pain was often unknown; however, when diagnostic testing had isolated an organic cause, physicians had informed them that the degree of pain they were experiencing exceeded the level of pain expected from their injuries. A phenomenological theory of embodiment was used as a framework for this study. Guided by the belief that the body is a carrier of meaning, the researcher aimed to discover patterns in chronic pain sufferersâ narratives, which may have contributed to the onset and/or prolongation of their pain. When invited to speak about momentous life events, all participants disclosed hardships they had endured. Furthermore, respondents had a strong propensity to downplay, or even deny, the severity of their often-traumatic life events. A tendency was also noted for respondents to act as caregivers and to place other peopleâ s needs above their own. The implications of the studyâ s findings for theory and practice related to counselling psychology are discussed.

Keywords: chronic pain
hardship
narrative
qualitative
Advisor: Chen, Charles
The Powers of the United Nations Security Council under Law

In the light of concern about the growing levels of power which the United Nations Security Council has begun to exercise in recent years, this thesis aims to establish the limits of the Council’s powers under law. It does so through a study of the two main elements of the Council’s anti-terrorism programme, approached through the lens of the legal philosophy of Lon Fuller, as adapted to international law by Jutta Brunnée and Stephen Toope. The thesis sets out the two anti-terrorism programmes, “listing” and “legislation”, and analyzes the reaction to them of other actors in the international legal system. It shows that the former phenomenon, listing, still faces considerable resistance, but that Council legislation has generally been accepted over time. In terms of the traditional, positivist account of international law, these responses might suggest that listing is unlawful and that legislation is valid, and that the Council therefore has the capacity to produce new, general legal norms. However, Brunnée and Toope’s legal theory suggests otherwise: that listing has moved closer to compliance with law over time, but that both the substance of the Council’s legislative resolutions and the process by which it adopts them fail to meet the requirements of law. This thesis is structured, first, to propose the applicable theoretical framework (chapter two), and then to consider a set of cases that provided the tools for some of the challenges to the anti-terrorism measures (chapter three). The two sets of anti-terrorism measures, and the responses to them, are then explored in detail (listing in chapter four and legislation in chapter five). Chapter six, the conclusion, compares the differing histories of the two anti-terrorism measures, and considers, in particular, the prognosis that the Council might develop the capacity to legislate.

Keywords: Fuller
Interactional International Law
International Law
Security Council
Terrorism
United Nations
Advisor: BrunnĂŠe, Jutta
In situ High-Pressure Structural Changes of Diopside-Anorthite (CaMgSi2O6-CaAl2Si2O8) Glasses: A Multi-Spectroscopic Approach

In this thesis the structure of haplobasaltic glasses is investigated using a multi-spectroscopic approach. At ambient conditions, X-ray absorption near edge structure spectroscopy is used to determine the local environments around each element within these glasses which range in composition from diopside (CaMgSi2O6) to anorthite (CaAl2Si2O8). These results show that silicon and aluminum are tetrahedrally coordinated throughout all compositions. The mean Si-O bond length is estimated to range from 1.58 to 1.66 Ë A. The Si L2,3-edge results show low lying d orbitals which appear to respond to changes in the tetrahedral bonding environment. The direct observation of d orbitals in Si - O bonding is an unexpected result. The two alkaline earth elements, Mg and Ca, display separate behaviors. Magnesium appears to be dominantly in five-fold coordination in the diopside glass and does not appear to change coordination number until the Di60An40 composition, after which four-fold coordination is thought to be important. Calcium appears to show a linear shift in coordination from seven- to eight-fold between anorthite and diopside glass, respectively. At high pressure, Brillouin, X-ray Raman and Raman spectroscopies have been used to characterize the local to intermediate range order within haplobasaltic glasses. In situ high pressure O K -edge X-ray Raman results suggest [5]Si forms in diopside glass as low as 3 GPa. Raman spectra on diopside glass are interpreted to show a closure of the inter-tetrahedral angle of 2-3â Ś/GPa between 0 and 4 GPa, and 1â Ś/GPa thereafter. In situ Brillouin spectra of anorthite glass display no change upon compression until 5 GPa, after which the Brillouin frequency shift becomes positive. This behavior is comparable to that of magnesium metasilicate glasses and natural basaltic glasses. This may be due to changes in the tetrahedral ring structure populations or the formation of highly coordinated network formers. High pressure Raman spectroscopy shows that the bridging oxygen (BO) vibrations of intermediate haplobasaltic glass compositions display comparable evolution with pressure. The vibrations of BOs associated with more polymerized parts of the silicate network appear to diminish between 7 and 9 GPa, whereas BO vibrations associated with more depolymerized parts of the silicate network are observed up to 14 GPa. I suggest that the loss of these vibrations corresponds to the inability of the silicate network to densify by kinking of connected tetrahedra and/or by wrinkling of ring structures. These densification mechanisms may be found in a wide range of silicate melt compositions, including those of natural magmas.

Keywords: Diopside - Anorthite
Glass
Haplobasalt
High pressure
Melt
Spectroscopy
Advisor: Henderson, Grant S
Financial Reporting Quality and Dual-holding of Debt and Equity

In this dissertation, I examine the causes and consequences of investors’ simultaneous participation in a firm’s syndicated loan and equity (“dual-holding”). In the first chapter, I investigate whether the financial reporting quality of a firm is associated with investors’ dual-holding in that firm. Using hand-collected data on institutional investors’ loan and equity holdings from 2006 to 2014, I predict and find that investors are more likely to be dual-holders in firms with low financial reporting quality. Two possible explanations of this result are: (1) investors use dual-holding as a viable channel to gain access to better information in firms with low financial reporting quality and to make profitable trades in the firm’s equity based on material non-public information, thus extracting rent from other shareholders (“rent-extraction”), and (2) investors use dual-holding to mitigate the conflict of interest between shareholders and creditors that is exacerbated by the firm’s low financial reporting quality (“incentive-alignment”). Consistent with the rent-extraction hypothesis, I find that dual-holders achieve risk-adjusted abnormal annualized returns of approximately 6% in the borrower’s equity in the time period between the syndicate origination and the next quarterly earnings announcement. Contrary to the incentive-alignment hypothesis, I find that firms with dual-holders do not experience any improvements in their operating and market performance. In the second chapter, I analyze the consequences of investors’ dual-holding. I first examine how dual-holders influence the firm’s information uncertainty and disclosure environment. Using hand-collected data on lenders that simultaneously hold equity-position in the borrower, I find that dual-holders decrease the firm’s information uncertainty by causing the equity prices to adjust to firm-specific information more rapidly. Furthermore, consistent with shareholders’ increased scrutiny following dual-holder participation in a firm, I find that managers of such firms are more likely to issue earnings forecast following loan origination. Taken together, My findings have important implications for investors and policymakers and shed light on the importance of weighting the overall benefits versus the costs of informed-trading to the investors and capital market by the SEC and investors before enforcing insider trading rules and scrutiny of dual-holding institutions.

Keywords: Dual-holding
Financial reporting quality
Incentive-alignment

Informed trading
Rent-extraction
Syndicated loans
Advisor: Hope, Ole-Kristian
Lu, Hai