VictorJuiz/thesis huggingface dataset:
Regulation of Hippo Pathway Kinases MST1/2 by DLG5 and Other Signaling Factors
Keywords: AP/MS
DLG5
Hippo pathway
MARK3
MST1
MST2

The Hippo signal transduction pathway plays critical roles in regulating development, organ size, and cancer progression, and is broadly conserved across metazoans. Mammalian Sterile 20-like Kinase 12 (MST1/2) are mammalian homologues of the Drosophila Hippo kinase, and along with downstream Large Tumor Suppressor Kinase 12 (LATS1/2), constitute the core kinases of the Hippo pathway. How MST1/2 are regulated, and in particular, what mechanisms connect them to upstream signaling components is a key question in the field. To address this, I employed affinity purification coupled to mass spectrometry to identify novel interacting proteins with important regulatory roles for MST1/2 and the Hippo pathway. I examined 25 different bait proteins related to the pathway, and identified 274 high confidence protein-protein interactions (PPI). The most intriguing PPI I identified was between MST1/2 and Discs Large Homolog 5 (DLG5), a widely conserved, large, multi-domain containing protein, which plays a role in maintenance of epithelial cell polarity. Using human, mouse, and fly model systems, fellow collaborators and I investigated the potential functional connections between DLG5, MST1/2, and other components of the Hippo pathway. We found that DLG5 acts as an inhibitor of Hippo signaling, in vivo and ex vivo. Mechanistically, I demonstrate that DLG5 binds directly to both MST1/2 and MAP/Microtubule Affinity-Regulating Kinase 3 (MARK3) and promotes their association. I found that MARK3 promotes hyperphosphorylation of MST1/2 and inhibits MST1/2 kinase activity. I propose a model wherein DLG5 recruits MARK3 to inhibit MST1/2 and the Hippo pathway. Although additional details of MARK3 regulation of MST1/2 await exploration, I have characterized DLG5 as a new and conserved component of the Hippo pathway and a negative regulator of MST1/2, providing the first example of a scaffold protein that directly links MST1/2 to other regulatory kinases and cell polarity factors.
Technical Developments of in vivo Proton Magnetic Resonance Spectroscopy
Keywords: Diffusion-weighted Spectroscopy
Magnetic Resonance Spectroscopy
Parallel Imaging
Relaxometry

Proton magnetic resonance spectroscopy (MRS) is a powerful non-invasive technique to probe the biochemistry of the brain and body. Because MRS signals are collected from metabolites in concentrations on the order of a few mM in biological tissues, (rather than from water at approximately 40 M concentration, as in magnetic resonance imaging) low signal-to-noise ratio (SNR) poses a major challenge. In the face of this challenge, there is an ongoing need for improved techniques to enhance the clinical applicability of MRS. One area of interest, for example, involves using MRS data as a biomarker for the assessment of early response in radiation therapy. This thesis focuses on the development of three MRS techniques, with the ultimate goal of this work being used in early radiation detection response protocols. First, a technique is developed to extend single voxel MRS to MRS of a small number of voxels (eg. two) without the need for spatial frequency encoding, using customized selective radiofrequency (RF) excitation and the localized sensitivity of multichannel receiver coils. The SNR efficiency of this technique is demonstrated in phantoms, healthy adult volunteers and patients with brain cancer. Second, a novel inversion and saturation recovery sequence is developed in conjunction with a spectral editing module to estimate the longitudinal relaxation time (T1) of lactate in vivo at 3 T. Lactate is of significant interest due to its role in cellular metabolism, and particularly its elevation in tumors. The resulting T1 estimate enables further optimization of MRS protocols and assists in estimating the absolute concentration of lactate from MRS data. Third, a diffusion-weighted two-dimensional spectroscopy sequence is developed, subsequently referred to as DW-JPRESS. This sequence, as well as an optimized processing pipeline, is demonstrated to provide estimates of the apparent diffusion coefficient (ADC) of brain metabolites beyond those typically accessible at 3 T, namely glutamate, myo-inositol and scyllo-inositol. The DW-JPRESS data provide unique information concerning the local diffusion environment of each measured metabolite, with the potential to characterize microstructural changes from different brain pathologies including cancer. Collectively, the technical development undertaken in this thesis promises to enhance future clinical applications of MRS, such as its use in distinguishing between neoplastic and nonneoplastic lesions, or for assessing tumor recurrence.
Translation and Development of Molecular Imaging Probes for Detecting Response of Breast Cancer to Trastuzumab
Keywords: breast cancer
HER2
molecular imaging
monoclonal antibodies
nuclear medicine
translational research

The human epidermal growth factor receptor 2 (HER2) is overexpressed in up to 20% of breast cancers (BC) and confers an aggressive phenotype and a poor prognosis. Trastuzumab (Herceptin®) is a humanized anti-HER2 monoclonal antibody approved for immunotherapy of HER2-positive BC, however, many eligible patients do not derive benefit and better predictors of response are needed. SPECT/CT imaging with 111In-labeled pertuzumab has previously been shown to sensitively detect trastuzumab-mediated HER2 downregulation as a marker of response to trastuzumab therapy in HER2-overexpressing mouse xenografts. To advance this agent to the clinic, a kit for the preparation of 111In-BzDTPA-pertuzumab injection was developed under good manufacturing practices and tested against and consistently met quality specifications, including labeling efficiency, purity, sterility and endotoxins. Biodistribution, pharmacokinetic and radiation dosimetry studies of 111In-labeled pertuzumab in non-tumour bearing mice revealed no abnormal uptake in organs, slow elimination from the blood (t½β=228.2 h), and a projected total body radiation absorbed dose of 0.05 mSv/MBq. In an acute toxicity study of normal mice administered 23-times the planned clinical radioactivity dose (scaled), blood analyses revealed only slight changes in hemoglobin and serum creatinine levels; no differences in body weight between control and radiotracer injected groups, and no histopathological abnormalities of tissues were noted. A Phase I clinical trial was approved by Health Canada and initiated. A PET probe, 64Cu-NOTA-pertuzumab F(ab')2 was constructed to similarly detect HER2 changes in response to trastuzumab and was expected to have a lower radiation absorbed dose due to the faster elimination of F(ab')2 fragments and shorter half-life of 64Cu. The total body radiation absorbed dose projected for 64Cu-NOTA-pertuzumab F(ab')2 in humans was 0.015 mSv/MBq, a 3.3-fold reduction compared to 111In-BzDTPA-pertuzumab. PET/CT showed specific accumulation of 64Cu-NOTA-pertuzumab F(ab')2 in SK-OV-3 xenografted mice. Image analysis of mice treated with trastuzumab showed 2-fold reduced uptake of radioactivity in BT-474 xenografts injected with 64Cu-NOTA-pertuzumab F(ab')2 after 1 week of trastuzumab normalized to baseline, and 1.9-fold increased uptake in SK-OV-3 xenografts after 3 weeks of trastuzumab, consistent with tumour response and resistance, respectively. These results demonstrate that radiolabeled pertuzumab-based imaging probes are able to detect response to trastuzumab therapy.
Flow Fields and Particle Trajectories in Abrasive Slurry-jet Micro-machining of Sintered Ceramics and Metallic-layered Structures
Keywords: abrasive
computational fluid dynamics
erosion
jet
micro-machining
slurry

The extreme hardness of sintered ceramics makes it difficult to machine them economically. Abrasive slurry-jet micro-machining (ASJM), in which a target is eroded by the impingement of a micro-jet of water containing fine abrasive particles, is a low-cost alternative for micro-machining of sintered ceramic materials without tool wear and thermal damage, and without the use of patterned masks. The experimental phase of the present research utilized several model systems that have industrial relevance while incorporating sufficient generality to illustrate generic characteristics of ASJM of ceramics and metallic-layered structures. Experiments were complemented by extensive computational slurry-flow modeling to understand the effects of the ASJM process parameters on the particle trajectories and the resulting erosion. In this study for the first time, computational fluid dynamic (CFD) modeling was used to derive a generalized relation between channel geometry and erosive flow, which was used in an existing numerical-empirical model to predict the cross-sectional profiles of ASJM micro-channels in sintered ceramics. The predictions agreed with experimental measurements to within about 8%. It was found that cavitation played a significant role in the slurry erosion of curved features such as the edges of holes and channels. Features with sharper edges, flat bottoms, and relatively steep sidewalls could be machined by minimizing cavitation through the use of liquids with low vapor pressure and relatively high viscosity. The use of ASJM to polish channels was investigated experimentally and with CFD. Post-blasting channels after their initial machining under typical process conditions reduced the Rrms roughness to about 23 nm in brittle and ductile targets. Flat micro-pockets in sintered ceramic substrates containing copper-filled through-holes were machined using a hybrid AJM (abrasive jet machining)-ASJM methodology, in which AJM was used to selectively erode the brittle ceramic without etching the ductile copper, followed by levelling of the protruding copper pillars to the depth of the ceramic using ASJM. It was demonstrated that electrodeposited copper and nickel-phosphorous layers could be selectively removed without eroding the underlying ceramic or metallic substrate using over-lapping ASJM channels. A CFD-aided process design methodology was developed to predict the ASJM parameters to remove a given coating thickness.
Statistics of class groups and related topics
Keywords: Arithmetic statistics
Class groups
Cohen-Lenstra heuristics
Number fields
Number theory

We prove several results concerning class groups of number fields and function fields. Firstly we compute all the moments of the p-torsion in the first step of a filtration of the class group defined by Gerth for cyclic number fields of degree p, unconditionally for p = 3 and under GRH in general. We show that it satisfies a distribution which Gerth conjectured as an extension of the Cohen-Lenstra-Martinet conjectures. In the p = 3 case this gives the distribution of the 3-torsion of the class group modulo the Galois invariant part. We follow the strategy used by Fouvry and Kluners in their proof of the distribution of the 4-torsion in quadratic fields. Secondly, we compute all the moments of a normalization of the function which counts unramified H8-extensions of quadratic number fields, where H8 is the quaternion group of order 8, and show that the values of this function determine a point mass distribution. Furthermore we propose a similar modification to the non-abelian Cohen-Lenstra heuristics for unramified G-extensions of quadratic fields for several other 2-groups G, which we conjecture will give finite moments which determine a distribution. These are all cases in which the unnormalized average is known or conjectured to be infinite. Our method additionally can be used to determine the asymptotics of the unnormalized counting function, which we also do for unramified H8-extensions. This part of the thesis is joint work with Brandon Alberts. Thirdly we present several new examples of reflection principles which apply to both class groups of number fields and picard groups of curves over P1/Fp. This proves a conjecture of Lemmermeyer about equality of 2-rank in subfields of A4, up to a constant not depending on the discriminant in the number field case, and exactly in the function field case. More generally we prove similar relations for subfields of a Galois extension with group G for the cases when G is S3, S4, A4, D2l and Z/ lZ × Z/rZ. The method of proof uses sheaf cohomology on 1-dimensional schemes, which reduces to Galois module computations.
Integrated Sources of Polarization Entangled Photon Pair States via Spontaneous Four-Wave Mixing in AlGaAs Waveguides
Keywords: Four-wave mixing
Integrated optics
Nonlinear optics
Quantum entanglement
Quantum optics

Polarization-entangled photon pair states (PESs) are indispensable in several quantum protocols that should be implemented in an integrated photonic circuit for realizing a practical quantum technology. Preparing such states in integrated waveguides is in fact a challenge due to polarization mode dispersion. Unlike other conventional ways that are plagued with complications in fabrication or in state generation, in this thesis, the scheme based on parallel spontaneous four-wave mixing processes of two polarization waveguide modes is thoroughly studied in theory and experimentation for the polarization entanglement generation. The scheme in fact needs the modal dispersion, contradictory to the general perception, as revealed by a full quantum mechanical framework. The proper modal dispersion balances the effects of temporal walk-off and state factorizability. The study also shows that the popular standard platform such as a silicon-on-insulator wafer is far from suitable to implement the proposed simple generation technique. Proven by the quantum state tomography, the technique produces a highly-entangled state with a maximum concurrence of 0.97 from AlGaAs waveguides. In addition, the devices directly generated Bell states with an observed fidelity of 0.92 without any post-generation compensating steps. Novel suspended device structures, including their components, are then investigated numerically and experimentally characterized in pursuit of finding the geometry with the optimal dispersion property. The 700 nmx1100 nm suspended rectangular waveguide is identified as the best geometry with a predicted maximum concurrence of 0.976 and a generation bandwidth of 3.3 THz. The suspended waveguide fabrication procedure adds about 15 dB/cm and 10 dB/cm of propagation loss to the TE and TM mode respectively, on top of the loss in corresponding full-cladding waveguides. Bridges, which structurally support the suspended waveguides, are optimized using the particle swarm algorithm to maximize the power transmission, and they were experimentally verified. This work greatly simplifies the generation of the PES and identifies a novel device structure suitable for such the PES generation. In combination with the reported promising advances in interferometric components and single photon detectors implemented in AlGaAs, the result of this thesis represents a step toward realizing a complete integrated quantum photonic circuit empowered by polarization-based protocols.
The Pedagogical Practices of Clinical Nurse Educators
Keywords: Clinical Nurse Instructors
Grounded Theory
Nursing
Patient Safety
Pedagogy
Undegraduate Curricula

Clinical practica forms an important component in undergraduate nursing education, which directly involves clinical nurse educators who are primarily involved in teaching student nurses. The purpose of this study was twofold: to theorize the pedagogical practices of clinical nurse educators and to explore the challenges that they encountered while teaching in the clinical arena. These participants taught in undergraduate nursing programs in a large metropolitan city in Ontario, Canada. Grounded theory methodology forwarded by Charmaz (2010) was used in this study design, and semi-structured interviews were conducted with twelve clinical nurse educator participants. Coding strategies forwarded by Corbin and Strauss (2008, 2015) and Charmaz (2010, 2011), such as constant comparison and theoretical sampling, were used to analyze the data. Study results were further analyzed using a constructivist approach to learning and a critical pedagogical approach to education. Initially, five main concepts emerged from the data and these concepts were further conceptualized to form the central theory that underpins this study. The substantive theory in this study is: The pedagogical practices of clinical nurse educators and the navigation of constraints in complex educational institutions. This central theory encompasses the main concepts and includes, the forms of knowledge that participants portrayed in their teaching, the ethics in teaching that underpin their practice, varied approaches to teaching that emerged from the data, and the context which describes the teaching milieu. The results from this study provide a deeper and broader understanding of teaching in the clinical arena. The results also reveal a traditional and progressive approach to teaching in nursing education and how each approach effects curricula development, pedagogy, and the building of teacher-student partnerships. The results from this study led to two important recommendations: the first, an education program for all nurse educators so as to improve their knowledge and understanding in developing curricula and pedagogy in nursing education; and the second provides a re-conceptualist approach to developing undergraduate nursing curricula and re-conceptualizing of patient safety concepts in the development, design and implementation of nursing curricula in undergraduate nursing programs.
Development of Point-of-Care Nanoparticle Based Diagnostic Platforms
Keywords: Gold nanoparticles
MNAzyme
Point-of-Care diagnostics
Quantum Dot Barcodes
Quantum Dots
Recombinase Polymerase Amplification

Despite the substantial improvement of diagnostic technologies over the last few decades, the most advanced diagnostic tests are centralized, require expensive facilities and expertise, and are therefore inaccessible to many patients and healthcare professionals in resource-limited areas. Point-of-Care (POC) diagnostics, which emphasize the idea that medical tests are conducted near the patients and subsequently lead to rapid clinical decisions, aim to overcome these limitations by decentralizing simple and cost-effective diagnostic approaches. Advances in nanotechnology have also shown the potential to improve POC diagnostics by offering tunable optical, electrical and magnetic properties that can transduce signals or simplify diagnostic procedures. Nonetheless, many nanoparticle-based molecular assays have been limited to the investigation of synthetic targets due to low analytical sensitivity, and clinical validation of nanodiagnostics has not been thoroughly explored yet. The work presented herein explores the development of ultrasensitive nanoparticle-based POC diagnostic platforms. Specifically, Quantum Dot (QD) barcode and multicomponent nucleic acid enzyme-gold nanoparticle (MNAzyme-GNP) assays were incorporated with Recombinase Polymerase Amplification (RPA) to demonstrate multiplexed and colorimetric detections respectively, improve the detection limits, and present clinically relevant diagnosis of infectious diseases. Overall, the combined advantages of nanotechnology and isothermal nucleic acid amplification strategy provided highly sensitive and specific detection platforms that are promising for diagnosis of infectious diseases in resource-limited settings.
Fostering Students' Mathematics Communication in Measurement: A Grade 3 Teacher's Perceptions and Practices
Keywords: area
elementary mathematics education
mathematics communication
perimeter

This study explores and describes the teaching perceptions and practices of a Grade 3 teacher as she attempts to foster students’ mathematics communication skills in the content strand of measurement. For this inquiry, the qualitative data collected were: 1) semi-structured teacher interviews, and 2) classroom observations. The categories of program planning, learning environment, mathematics tasks, knowledge construction, technology, manipulatives, and assessment were identified and presented. The data for this case study were first organized, analyzed, and interpreted within sub-units of lesson vignettes. Afterwards, the identified teaching perceptions and practices from the lesson vignettes were consolidated, and presented as a “whole” case. The sub-units and whole-case analysis identified five major findings related to the topic of fostering students’ mathematics communication in the classroom. Summarized, these are: 1) Teachers need to create opportunities for students to productively struggle with increasingly abstract concepts. The appropriate selection of mathematics tasks, the discussions on mathematical misconceptions, and the posing of effective questions may guide and encourage students as they express their understanding and misconceptions. 2) Teachers need to foster students' self-monitoring and self-assessment skills, as students communicate their emerging mathematical thoughts. 3) Teachers should strive to provide students with opportunities to learn to reason and justify their perspectives. Such opportunities can occur as students read, write, draw, and/or listen to recently learned mathematical concepts. 4) Teachers should intentionally define and explore various meanings and usages of subject-specific and unit-specific vocabularies. The learning of increasingly abstract ideas (e.g. area and perimeter) requires the acquisitions of new vocabularies, so that meanings can be more clearly articulated by the students. 5) When teaching and learning the topic of measurement, various education components such as program planning, learning environment, mathematics tasks, constructing knowledge, technology and manipulatives, and assessment are often intricately and purposefully linked with one another.
To ancillary and beyond: CO2 activation and redox activity of NN chelate actor ligands
Keywords: actor ligands
CO2 activation
insertion
NN chelates
paramagnetic stannylene
redox-active ligands

This thesis examines the fundamental coordination chemistry and subsequent reactivity of actor and redox-active ligands. In this context, the two NN chelate ligand classes that are explored are 4,5-diazafluorene and o-phenylenediamine. In Chapter 2, actor diazafluorenyl ligands were explored. New Ru and Zn diazafluorenyl complexes undergo C–H borylation of the diazafluorenyl ligand to form the corresponding diazafluorenylboronic ester complexes, which can insert CO2 into their C–B bonds to form boryl ester functionalities. The relevance of this new reactivity to catalytic CO2 reduction was also explored. In Chapter 3, the initial coordination chemistry of the redox-active N,N’-bis(2,6-diisopropylphenyl)-o-phenylenediamido ligand (L2-) was investigated. Li2L(THF)3 reacts with iron(II) sources in toluene to yield LFe(η6-toluene). DFT, NMR, and X-ray data indicate that L2- oxidized to L1- in this transformation. [FeL(η6-toluene)] reacts with CO to generate [FeL(CO)3], with concomitant oxidation of L- to L0. Two equivalents of Li2L react with both MoCl4(THF)2 and VCl2(tmeda)2 yielding trimetallic sandwich compounds. In Chapter 4, reactivity of Pb(II) and Sn(II) complexes of L2- was investigated. [PbL] and [SnL] react with mesityl azide in analogous C-H activations in which L2- behaves as an actor ligand. [PbL] forms a Lewis pair with ONMe3, demonstrating the behaviour of L2- as an ancillary ligand. [SnL] reacts with AgOTf to yield [SnL(OTf)], demonstrating the ligand’s redox activity as L2- is oxidized to L-. [SnL(OTf)] is a paramagnetic stannylene, a type of compound which has been previously observed in situ, but hitherto has not been isolated. In Chapter 5, the coordination of different o-phenylenediamido sources towards [TaMe3Cl2] was explored. The opda framework acted as a reducing agent, as a sponsor of heterodinuclear complexes, or as a robust ancillary ligand. The use of K2L provided access to [TaLMe3]. The reactivity of its methyl ligands was studied; notably, UV irradiation causes formal loss of methyl radical to yield dimeric [LTaMe2]2.