VictorJuiz/thesis huggingface dataset:
Towards Legal Interoperability in International Health Research
Keywords: Data Sharing
Intellectual Property
Interoperability
Licensing
Privacy
Research Ethics

Interoperability is the ability to exchange meaningful data across complex systems. Connectivity is essential for international health research, but can be hindered by incompatible laws and legal tools. First, this paper considers compatibility between intellectual property law regimes and research data licenses. Second, it reviews data privacy law regimes and how treaties, codes of conduct, and standard safeguards can maintain interoperability across borders. Third, it reviews health research regulation, seeking to reconcile the tension between openness and participant/community control over research data. This paper concludes with a critique of two generic strategies for promoting legal interoperability. The first is access governance, where policies and due diligence processes interface between different legal and organizational contexts. The second is algorithmic access, where researchers submit algorithms to run on secure datasets. Ultimately, interoperability is an essential consideration when designing norms and legal tools to support international health research.
“Mr. Big” Confessions, R v Hart, and a Proposal for a New Right of Appeal based upon Fundamental Post-conviction Changes to the Law
Keywords: appeal
Fundamental change to law
Mr. Big
Post-conviction relief
R v Hart
R v Mack

In a 2014 decision, R v Hart, the Supreme Court of Canada (SCC) held that confessions obtained from undercover “Mr. Big” sting operations would henceforth by presumptively inadmissible as evidence in criminal trials. The new exclusionary rule was motivated by concerns about wrongful convictions arising from this type of confession, which is often unreliable and highly prejudicial to the accused. The advent of this new rule, however, casts doubt upon the reliability of past criminal convictions based upon “Mr. Big” confession evidence. Presently, there are only very limited avenues for post-conviction review based on subsequent fundamental changes to the law. Accordingly, a new statutory right of appeal is proposed to allow for reopening past cases when merited by fundamental post-conviction changes to the law.
Characterizing the Role of Spegless, a Novel Inner Nuclear Membrane Protein required for spermatogenesis and oogenesis in Drosophila melanogaster
Keywords: Fat
Germ cells
Nuclear membrane
Oogenesis
Spermatogenesis

Fat is a large cadherin that plays a role in both tissue growth and planar cell polarity (PCP). How Fat regulates these cellular processes is not fully understood. A yeast two-hybrid screen previously identified proteins that can bind the cytoplasmic domain of Fat. Using genome-wide RNAi libraries of transgenic flies, I knocked down the function of each gene identified through the screen in the Drosophila eye. Through analysis of adult eye size and photoreceptor organization, several genes were identified as having possible roles in PCP or tissue growth. One gene, which I analyzed further, was a previously uncharacterized gene, CG9723, which I have named spegless (speg). When disrupted, speg had overgrowth phenotypes similar to Hpo pathway mutations in the eye. Speg is a multi-pass transmembrane protein with a conserved domain of unknown function that I have confirmed is an inner nuclear membrane protein. I generated a null allele of speg and subsequent in depth analysis of speg null mutants revealed that Speg is essential for the development of the testes and ovaries. In Drosophila, testes development is a complex process regulated by the interplay between germline stem cells and somatic (cyst) stem cells. Sperm develop in units called cysts and flies lacking speg had small testes that lacked proper cyst structure and cyst cell membrane markers. Speg is important in the cyst cells as cyst cell expression of Speg could largely rescue speg mutant phenotypes. speg mutant testes had fewer differentiated sperm cells and rarely produced late stage sperm. Speg mutants did not disrupt overall nuclear membrane structure. Also, speg mutant ovaries contained no germ cells. Thus, Speg is a novel, conserved, inner nuclear membrane protein with an essential role in the development of Drosophila testes and ovaries.
“The Life of a Reserve”: How Might We Improve the Structure, Content, Accessibility, Length Timeliness of Judicial Decisions?
Keywords: Empirical legal research
Human-centered design
Judicial decision-making

This thesis explains how judicial decisions may impact access to justice and how might we make decisions a better source of data while also making them more timely, concise, accessible, and consistent. It examines the historical and theoretical underpinnings of Canadian decisions and the relationship of decision-writing to decision-making. It then discusses the results of an original empirical study of the evolution of British Columbia trial decisions over the last forty years and a survey of Canadian courts. It argues that the current process for writing and issuing Canadian judicial decisions likely does not further the goals of access to justice and may even hinder them. To improve access to justice, it suggests that governments, academics, and judiciaries should rely on human-centered design to design standardized structures and templates for decisions, and it provides a design plan for such reforms and examines the ways judicial independence may impact such reforms.
Structural Characterization of Amyloid Assemblies and Amyloid Protein-lipid Interactions
Keywords: Amyloid Fibrils
Lipid Membrane
Nuclear Magnetic Resonance
Peptide
Structural Biology

Amyloids are insoluble aggregates rich in β-structure that result from the self-assembly of polypeptides in a non-native structural fold. The deposition of these aggregates onto organs has been traditionally linked to many human diseases, however the discovery of functional amyloids in nature suggests there may also be beneficial roles for this self-assembly process. Pathogenic and functional amyloids both contain a cross-β backbone composed of β-sheets that run perpendicular to the fibril axis, but there lacks clear molecular details on the structural differences to explain their divergent biological behaviours. Solid-state NMR (SSNMR) has become an invaluable tool for structural determination of amyloids, as poor solubility of these assemblies make them challenging for traditional X-ray crystallography and solution NMR methods. This thesis aimed to identify key structural features between cytotoxic and non-cytotoxic amyloid fibrils using SSNMR, and to examine the effects of protein-lipid interactions on membrane disruption and amyloid formation that can reflect amyloid cytotoxicity. First, three amyloid fibrils formed from fragments of the human prion protein were examined, with the findings that a parallel β-sheet arrangement and packing of hydrophobic residues into the fibril core defined the basic structure in these assemblies. Next, these three peptide amyloids were sonicated to explore fragmentation-associated cytotoxicity of these amyloids. The results here highlighted the importance of solvent-exposed hydrophobicity on amyloid-membrane interaction, linking the increased surface hydrophobicity of fragmented fibrillar species to greater membrane disruption and cytotoxicity. Finally, SSNMR experiments were applied to characterize the structure of human apolipoprotein serum amyloid A when associated with high-density lipoprotein (HDL)-like particles and when misfolded into amyloid fibrils. The results led to a preliminary model that can explain functional differences between lipid-free and HDL-associated SAA. Together, these findings highlight the differing effects of lipid interaction on the pathogenicity of amyloid fibrils.
Investigation of Post-translational Strategies to Enhance Recombinant Human Bone Morphogenetic Protein-2 Production in Mammalian Cell Culture Systems
Keywords: Bone morphogenetic protein
Chinese hamster ovary (CHO) cells
Pro-domain
Proprotein convertase
Proteolytic cleavage
Recombinant protein

Bone morphogenetic proteins (BMPs) have been found useful in repairing craniofacial defects, treating non-union long bone fractures, and in spinal fusion procedures. However, the widespread use of recombinant human BMPs (rhBMPs) is hindered by the difficulties in obtaining large quantities of pure and biologically active rhBMPs. Standard approaches to improve recombinant protein yields such as increasing transgene expression by having strong promoters and/or utilizing gene amplification methods still result in low yields when applied to BMPs. The impact of altering the post-translational processing on recombinant BMP-2 yields in mammalian cell expression systems was investigated in this dissertation. We attempted to modify the proteolytic cleavage of BMP-2 by 1) adding a BMP cleavage inhibitor to the cell culture medium, 2) mutating a cleavage site on BMP-2 sequence, and 3) overexpressing BMP-cleaving proprotein convertases in cells producing rhBMP-2. All three methods led to significant increases in the yield of biologically active rhBMP-2. Characterizing the rhBMP-2 produced from these methods, the data revealed that proteolysis of BMP-2 could also influence the biological activity of the mature protein. Taken together, these results suggest that targeting post-translational processing is a useful and practical strategy to improve the yield of BMP-2 and possibly other difficult to express recombinant proteins in mammalian expression systems. As an increasing number of recombinant proteins become extremely valuable therapeutic options today, the findings from this study contribute to the collective understanding of enhancing recombinant protein yield in mammalian cell expression systems.
Re-Thinking Expert Evidence
Keywords: Expert Evidence
Mohan
Reliability
White Burgess

The jurisprudence surrounding expert evidence in Canadian law has evolved since the 1994 case, R. v. Mohan, but it is still replete with numerous problems. This thesis challenges the current admissibility test for expert evidence in Canadian law, and suggests a new, more focused test, which places reliability as the predominant factor in admitting expert evidence. This thesis will argue that changing the admissibility test in this direction will make the jurisprudence in this area more coherent, and lead to better admissibility outcomes.
Transrectal Diffuse Optical Tomography Monitoring of Photothermal Therapy for Localized Prostate Cancer
Keywords: photothermal therapy
prostate cancer
transrectal diffuse optical tomography

The clinical management for localized, low- to intermediate-risk prostate cancer (PCa) has become more complex as more therapeutic options become available, while it remains very challenging as physicians try to find a treatment that offers both excellent oncological results and minimal morbidity. Photothermal therapy (PTT) is currently undergoing clinical trials and has shown potential to be one such technique. However, the clinical outcome of PTT is suboptimal, mainly due to the lack of direct monitoring of the coagulated lesion that is generated during PTT. Transrectal diffuse optical tomography (TRDOT) has been proposed to localize the photocoagulation boundary based on changes in tissue optical properties upon coagulation, particularly scattering. A baseline study of phantom experiments with corresponding numerical simulations was first conducted using an existing TRDOT system to investigate its signal sensitivity to a growing coagulating lesion. After gaining critical guidance in building an instrumentation, a clinical propotype TRDOT system, which comprises a 32-channel fiberoptic-based, MR-compatible transrectal probe, was designed and fabricated specifically for the clinical application of in vivo monitoring of PTT by localizing the boundary of the coagulated lesion. The performance of the instrument was tested and characterized. Calibration methods were developed for the system and the probe. The accuracy and reliability of calibrated TRDOT measurements were investigated and characterized in homogeneous phantoms. The in vivo feasibility of the system was tested in a canine PCa tumor model. TRDOT’s ability in monitoring PTT and accuracy in localizing the boundary of a coagulated lesion were investigated through a series studies using thermal coagulating phantoms, ex vivo canine prostates, and in vivo canine prostate models. This demonstrates TRDOT’s potential of visualization of the extent of coagulation during PTT, which will contribute improving PTT’s safety and clinical outcome.
Integrated Circuits for Quantized Analog Signal Processing
Keywords: Dynamic Range
Integrated Circuit
Linearity
Quantized Amplifier
RF Receiver
Wireless

This thesis presents the new concept of Quantized Analog Signal Processing, which is a method to expand the dynamic range of an analog system by using multiple units covering different portions of the rail-to-rail input range. This allows amplification of full-swing signals at the input, without saturating the overall output. Another benefit of the proposed system is the ability to linearize the input-output transfer characteristics of a quantized amplifier, irrespective of the linearity properties of a single unit. In the first chapter of the thesis, a theoretical formulation is developed for the thermodynamic minimum power limits of analog circuits by using prior literature. Then it is shown that the quantized analog signal processing can allow expanding this thermodynamic limit beyond what has been theoretically possible with any prior analog architecture. In Chapter 2, theoretical and behavioral simulations are performed on a quantized voltage amplifier, to support the claims of Chapter 1. Chapter 3 presents an RF receiver integrated in a 65nm CMOS, with the quantized-analog RF front-end. Experimental results show that the receiver has an unprecedented power efficiency in the analog signal path for a given dynamic range. The last chapter presents an upgraded version of the receiver, with extra added features, and on-chip delta-sigma ADCs, which is designed in 28nm CMOS.
The Regulation of Cerebellar Granule Neuron Development by Suppressor of Fused
Keywords: cerebellum development
granule cell proliferation
medulloblastoma
sonic hedgehog
spatial patterning
sufu-gli

Cerebellar granule cell (GC) development relies on precise regulation of the Sonic Hedgehog (Shh) signaling pathway. Mutations that impair the pathway cause reduced GCP proliferation and cerebellar hypoplasia, underlying multiple motor dysfunction disorders. In contrast, aberrantly activated signalling is associated with medulloblastoma, a debilitating pediatric malignant brain tumour. However, intracellular mechanisms that establish the correct level of pathway activity within GCPs have not been defined. The pathway regulator, Suppressor of Fused (Sufu) controls early cerebellar development and is mutated in human and mouse medulloblastomas. As it interacts with both Gli activator and repressor (Gli-A/R) proteins, its precise function in Shh pathway regulation is highly context-dependent and remains enigmatic. Here, Math1-Cre-mediated deletion of Sufu from GCPs demonstrates that Sufu is required to restrain postnatal GCP proliferation and promote cell cycle exit, together restricting the GCP proliferative window. This function relies on maintenance of Gli3R levels and, surprisingly, suppression of Gli2, together allowing Sufu to dynamically modulate Shh activity. Genetic overexpression of Gli3R and reduction of Gli2 not only rescued the Sufu-deficient phenotype, but revealed intriguing spatial differences in Sufu function. GCPs in the central cerebellar lobules were more deleteriously impacted by Sufu deficiency, and more strongly dependent on suppression of Gli2. RNA-Sequencing further identified novel Sufu gene targets, including Fgf8. The overproliferation of Sufu-deficient GCPs was suppressed by Fgf8 neutralising antibodies, while exogenous Fgf8 was sufficient to stimulate GCP proliferation, demonstrating a previously unknown mitogenic function of Fgf8. Finally, interrogation of non-Cre targeted cells identified non-cell autonomous effects of GC-localised Sufu on BG differentiation. Collectively, these findings implicate Sufu in the spatial and temporal modulation of Shh signalling, and in mediating cross-talk with other signalling partners, to control GCP proliferation and cerebellar development. Moreover, they provide a platform to interrogate the dysregulation of Shh signalling underlying congenital and pathogenic disorders.
Phosphoinositide metabolism and signaling during late phagosome maturation and phagolysosome resolution
Keywords: Immunity
Macrophages
Phagocytosis
Phosphoinositides
Phospholipids

Phagocytosis, the regulated uptake of particulate matter by cells, is essential to immunity and homeostasis. Phagocytes are tasked with the immune surveillance that prevents infection by invading pathogens. Additionally, these cells clear accumulated apoptotic debris that results from the daily turnover of billions of cells. In order to fulfill these paramount functions, phagocytes recognize targets and internalize them into membrane-bound compartments termed phagosomes. Following internalization, cells degrade the phagosomal contents and dispose of them resuming the immune response. Phagocytosis is therefore divided into three stages: formation, maturation and resolution. Formation refers to the recognition and engulfment of prey. The transformation that enables degradation of the target is termed maturation. Finally, the elimination and often re-utilization of degraded contents is known as resolution. Most of the phenomena that govern each of these stages are orchestrated by acute signaling events. Specialized signaling phospholipids known as phosphoinositides mediate the recruitment of effector proteins to phagosomes. While the roles of diverse phosphoinositides during formation and the early maturation have been studied and partially elucidated, little is known about them during the late maturation and resolution stages. These late stages are essential for degradation of the phagocytic targets, processing of phagosomal contents and return to homeostasis by phagocytes in order to resume their responses. The work described in this dissertation was conducted with the aim of characterizing phosphatidylinositol 4-phosphate (PtdIns4P)—a phosphoinositide present in the plasma membrane, Golgi apparatus and late compartments—during phagocytosis. Additionally, bacterial species such as Legionella, have been shown to commandeer PtdIns4P metabolism during infection, emphasizing the potential importance of this phosphoinositide during the innate immune response. For this work, I specifically focused on elucidating the dynamics, metabolism and functions of PtdIns4P during each stage of phagocytosis. Chapter I, consists of relevant background on the cell biology of phagocytosis and the involvement of phosphoinositides during the process. The aims and hypothesis of my work are described in Chapter 2. Chapter 3 describes the methodology used throughout this work. In Chapter 4, I detail PtdIns4P dynamics and metabolic mechanisms during phagosome formation and maturation. Additionally, I define the functional implications of PtdIns4P in maturing phagosomes. In Chapter 5 I detail how the endoplasmic reticulum regulates both phagosomal PtdIns4P levels and recruitment of its effectors to the compartment. Finally, I explore the relevance of these events during resolution. This work establishes the importance of PtdIns4P during phagocytosis emphasizing the necessity of an exquisite coordination of lipid metabolism during the process.
Structural and functional characterization of dual kinase-endoribonucleases, IRE1 and RNase L
Keywords: Biochemistry
Small molecule
Structural biology

IRE1 and RNase L are a unique set of protein kinases found in the human kinome. They are unique in that both possess a protein kinase domain fused to an endoribonuclease domain. Although IRE1 and RNase L share similar structural domain architectures, they are involved in regulating different cellular pathways. IRE1 is involved in the unfolded protein response (UPR) signaling pathway while RNase L is involved in the interferon antiviral response signaling pathway. In the first data chapter, I describe purified and crystallized IRE1 bound to three hydroxy-aryl-aldehyde (HAA) small molecule analogues that inhibit IRE1’s ribonuclease activity but not its protein kinase activity. The IRE1-HAA structures revealed that the HAA analogues engaged a preformed pocket in the ribonuclease active site of IRE1. Inhibitors binding to the pocket is supported by an essential covalent yet reversible Schiff base interaction between the lysine 907 and the aldehyde moiety of the inhibitor. Further mutational studies, modeling, SAR, and enzymology characterizations were performed to validate the binding mode and mechanism of action of the HAA inhibitors. These IRE1-HAA structures provided the first view of an inhibitor engaging the ribonuclease active site of IRE1. In the second data chapter, I discovered two potent polyphenol compounds that potently and selectively inhibited RNase L’s ribonuclease activity relative to its closest relative IRE1. I performed further SAR and enzymology characterization to gain insight into the binding mode and mechanism of action of these small molecules. Additionally, in collaboration with the Silverman and Weiss labs, we performed in cell studies that demonstrated that our newly discovered inhibitors are functional against RNase L enzyme and superior to the only other RNase L inhibitor characterized to date, namely sunitinib. These polyphenol compounds represent the first small molecules to inhibit RNase L’s ribonuclease activity by binding specifically to the enzyme- RNA substrate complex.