VictorJuiz/thesis huggingface dataset:
Deciphering the Pro-apoptotic Mechanism of PUMA and its Role in Neuronal Cell Death and Axon Degeneration
Keywords: Apoptosis
Axon degeneration
BAX
Neuron
PUMA

The regulation of programmed cell death (apoptosis) coordinates organismal development, while its dysregulation in the adult drives the pathology of disease. At the level of the individual cell, the functional interactions among pro- and anti-apoptotic BCL-2 family proteins regulates the committing step for a cell to die. The abnormal overexpression of anti-apoptotic proteins drives cancer progression by preventing tumour cell death, while in contrast, atypical activation of pro-apoptotic proteins can drive neurodegeneration with the premature death of post-mitotic neurons. PUMA is just one member of the BCL-2 family of proteins, with a known importance in the death and degeneration of mouse neurons, but unknown role in human neuron destruction. Moreover, newly developed small-molecule inhibitors designed to displace pro-apoptotic proteins and kill tumour cells fail to displace PUMA. As a result, a better understanding of PUMA’s pro-apoptotic mechanism is needed to better kill tumour cells, while conversely preventing neuronal cell death and degeneration. Here, the measurement of interaction between PUMA and anti-apoptotic proteins reveals a novel binding site on the carboxyl-terminal sequence of PUMA. This site prevents small-molecule displacement of PUMA by promoting a high affinity protein interaction with globular anti-apoptotic proteins, independent of its known membrane binding function. This novel binding site is also important for the interaction and activation of the pore-forming protein BAX. PUMA knockout human neurons, derived from CRISPR-modified induced pluripotent stem cells, are resistant to a plethora of apoptotic stimuli. Low expression of PUMA results in little BAX activation and axon degeneration, but does result in apoptosis. As a result, neurons require PUMA to die, but can control its expression to regulate apoptosis versus axon degeneration based on the rheostat activation of BAX.
Where Do All The Adjectives Go and What Do They Mean? Adjective Distribution and Interpretation in L1 Spanish
Keywords: language acquisition
semantics
Spanish
syntax

This dissertation investigates what Spanish speaking adults and children know about the distribution and interpretation of DP-internal adjectives in their language. The distribution of DP-internal adjectives in Spanish depends on their lexical subclass. Adults near categorically prefer pre-nominal ordinals (la segunda esquina ‘the second block’) and post-nominal relational adjectives (los animales marinos ‘the marine animals’). Despite more variability in ordering, superlatives (las riquisimas empanadas ‘the delicious empanadas’) and lexical shifts on their non-subsective (los pobres elefantes ‘the poor elephants’) and non-intersective (los buenos amigos ‘the good friends’) readings are also preferred pre-nominally [the former more so than the later]. Finally, epithets (el calido sol / el sol calido Lit. ‘the warm sun / sun warm’) and discourse contextual adjectives (los pequenos arreglos / los arreglos pequenos Lit. ‘the small repairs / repairs small’) occur in both pre- and post-nominal position. The position of the later further depends on restrictivity; pre-nominal discourse contextual adjectives are more acceptable in non-restrictive contexts, whereas post-nominal adjectives are not sensitive to context. There is little evidence for the distribution of Spanish adjectives in child directed speech. A corpus study of María (López Ornat, 1997) and Juan (Linaza, 1981) identifies few pre-nominal adjectives and finds the pre-nominal position is not productive in child speech. However, pre-nominal adjectives in the input share several semantic characteristics that could guide the learner. The results of a preference task and an acceptability judgement task support grammatical conservatism (Snyder, 2007). Children are not using the pre-nominal position in spontaneous speech because they haven’t figured out the lexical distribution of adjectives in their language. This does not result in a categorical preference for post-nominal position based on token frequency in the input, rather guessing performance is followed by the protracted emergence of ordering preferences beginning with ordinals, relational adjectives, and the high frequency lexical item pobre ‘poor’. As expected for children still figuring out the lexical distribution of adjectives in their language, even the oldest children in our sample lack awareness of the effect of restrictivity on discourse contextual adjectives. However, the acceptability of these adjectives in pre-nominal position grows with age.
Suffering Time: Nietzsche and the Generativity of Suffering
Keywords: Ascetic ideal
Eternal return
Meaninglessness
Nietzsche
Overcoming
Suffering

This dissertation explicates and extends Friedrich Wilhelm Nietzsche’s idea that “the ascetic ideal” provides meaning for suffering. I argue that responding to meaningless suffering is the singularly most important feature in the generation of religious, political, and moral narratives that identify, define, and enclose suffering within frameworks that dynamically seek to hold the reality of suffering as meaningful. I take it as given that meaningless suffering is cognitively and morally intolerable and essentially requires a response. The problem of suffering, as I understand it in this dissertation, is a problem of how to understand the dynamic relationship that narratives hold with suffering. Narratives shift and redefine the meaning of suffering as the terrain of suffering itself shifts. This constant movement discloses to us that cultivating better responses to suffering is a practice of critique of inherited ideas about suffering, as well as an ongoing and never-ending practice of relating oneself to the terrible novelty that meaningless suffering brings with it. I argue that interpretations of suffering tell us about the vision of life to which these interpretations belong, and interpretations of suffering are themselves generative of religious, political, and social realities that, in turn, condition the vision of life from which they emerge. Ultimately, the problem of suffering is not a problem that can be solved, but only a problem that can be lived through. Further, I extend Nietzsche’s critique of pessimism and suicidal nihilism to argue that how narratives understand suffering points toward ideas about the value of life itself. A truly “life affirmative” stance is one that can affirm the eternal repetition of our identical lives. Time, as our currency on earth, is limited and the suffering that comes with this recognition is an ever-present feature within Nietzsche’s analysis of the concept of suffering. I argue that in addition to providing a key way of understanding the generation of narratives of existential import, suffering is inherently temporal: both because it is temporary, but also because suffering occurs in time.
Training Efficiency and Robustness in Deep Learning
Keywords: Adversarial Robustness
Applied sciences
Deep Learning
Machine Learning
Multimodal Representation Learning
Stochastic Optimization

Deep Learning has revolutionized machine learning and artificial intelligence, achieving superhuman performance in several standard benchmarks. It is well-known that deep learning models are inefficient to train; they learn by processing millions of training data multiple times and require powerful computational resources to process large batches of data in parallel at the same time rather than sequentially. Deep learning models also have unexpected failure modes; they can be fooled into misbehaviour, producing unexpectedly incorrect predictions. In this thesis, we study approaches to improve the training efficiency and robustness of deep learning models. In the context of learning visual-semantic embeddings, we find that prioritizing learning on more informative training data increases convergence speed and improves generalization performance on test data. We formalize a simple trick called hard negative mining as a modification to the learning objective function with no computational overhead. Next, we seek improvements to optimization speed in general-purpose optimization methods in deep learning. We show that a redundancy-aware modification to the sampling of training data improves the training speed and develops an efficient method for detecting the diversity of training signal, namely, gradient clustering. Finally, we study adversarial robustness in deep learning and approaches to achieve maximal adversarial robustness without training with additional data. For linear models, we prove guaranteed maximal robustness achieved only by appropriate choice of the optimizer, regularization, or architecture.
Systematic Characterization of Transcriptional Regulators by Site-specific Protein Recruitment
Keywords: CRISPR
dCas9
pooled screens
Transcription factors

Many transcriptional regulatory proteins and chromatin-associated factors have been identified and their DNA binding sites elucidated. The functional role of most, however, remains unclear. Furthermore, many regulators tend to be multifunctional as their roles can vary depending on the genomic context where they bind. Here I present a novel pooled approach for systematically testing the transcriptional activity of thousands of proteins. By utilizing dCas9, I have developed an ORFeome-wide tethering screen and recruited ~14,000 human proteins to the basal promoter of a reporter gene integrated into the human genome. In a pooled screen, I identified over 200 proteins capable of robustly activating the reporter. Known activators, such as mediator components, were highly enriched in the screen. Interestingly, many highly homologous transcription factors had strikingly different activation profiles, suggesting they form functionally distinct groups despite similar DNA binding specificities. Moreover, a number of novel transcriptional activators were identified. Characterization of these factors with affinity purification coupled to mass spectrometry indicated they activate transcription by interacting with distinct activator complexes. Utilizing the same platform to recruit protein fragments of known activators, I was able to identify multiple new transactivation domains in a single experiment. Finally, I profiled a number of KRAB domains for their ability to repress both a reporter and endogenous targets. This led me to identify a potent repressor that outperformed other CRISPRi platforms described to date.
Healthcare Costs and Cost-effectiveness of Epilepsy Surgery, MR-guided Laser Interstitial Thermal Therapy and Medical Therapy in Children with Drug Resistant Epilepsy
Keywords: Cost-effectiveness
Epilepsy surgery
Healthcare costs
Medical therapy
MR-guided laser interstitial thermal therapy
Pediatric epilepsy

Epilepsy can negatively impact on children’s cognition and psychosocial well-being. This dissertation aligns with the National Academy of Medicine’s call for research on healthcare costs of epilepsy and its treatment, by addressing these objectives: #1) Assess the economic burden of epilepsy in children from healthcare payer perspective; #2) Evaluate seizure outcome of pediatric resective epilepsy surgery; #3) Determine the long-term healthcare costs of surgery compared to medical therapy in children with focal drug resistant epilepsy from the healthcare payer perspective; and #4) Assess the cost-effectiveness of MR-guided laser interstitial thermal therapy (MRgLITT) compared to resective surgery and medical therapy from the healthcare payer and societal perspectives. Our cohort study leveraged health administrative databases to show that healthcare costs were higher for pre-diagnosis and initial care than ongoing care, which were driven by hospitalization costs. Costs were higher in children with epilepsy than without epilepsy across most phases-of-care, as well as for five-year cumulative costs. The results identified avenues for remediation, such as enhancing care around the time of epilepsy diagnosis, to reduce hospitalization costs. Our meta-analysis demonstrated that epilepsy surgery was more effective than medical therapy to control seizures (OR=6.49 [95%CI: 2.87, 14.70]). Seizure freedom declined over time after surgery, and varied by surgery location, pathologies and MRI abnormality. These findings will assist with pre-surgical counselling. Children treated with epilepsy surgery and medical therapy at the Hospital for Sick Children were linked to health administrative databases to assess their healthcare costs. Despite the initial high costs of surgical care, costs of intermediate- and long-term care were lower among surgical than medical patients, resulting in lower long-term healthcare costs of surgery. The long-term economic benefits of epilepsy surgery may justify the initial high costs of surgery for the stakeholders. Our microsimulation model showed that MRgLITT was cost-effective relative to surgery and medical therapy, and was the preferred strategy above cost-effectiveness threshold $30,000/ quality adjusted life years. There is also value in additional research to reduce uncertainty in the evidence on effectiveness of MRgLITT. The results will support decisions on the diffusion of MRgLITT, and further research on the effectiveness of MRgLITT.
Establishing an In-vivo Model of Low-grade Glioma
Keywords: brain cancer
cancer risk
glioma
low grade glioma
Neuro oncology
non-coding genome

Gliomas account for 80% of malignant central nervous system cancers and current therapies have shown limited success in treating this disease1. Characterization of the mutational landscape of these tumours has led to the identification genetic low grade glioma (LGG) subtypes within adults2 ,3,4. These are largely defined by neomorphic mutation in the genes coding for isocitrate dehydrogenase (IDH1 or IDH2), presenting in both IDH mutant astrocytoma and IDH mutant oligodendroglioma. However, these subtypes differ with respect to their mutational landscapes and clinical manifestations, with IDH mutant astrocytoma having a worse prognosis and limited therapeutic options2,3. IDH mutant oligodendroglioma harbor truncal mutations in IDH and the TERT promoter as well as co-deletion of chromosomal arms 1p and 19q. IDH mutant astrocytoma is associated with truncal mutations in IDH, TP53, and ATRX2. In addition to these canonical LGG mutations, the rs55705857 single nucleotide polymorphism (SNP) has been shown to increase the risk of IDH-mutant LGG by an odds ratio of 6 and 9 within IDH mutant astrocytoma and IDH mutant oligodendroglioma respectively1-4, however the mechanism through which this SNP confers increased LGG risk has been elusive.I have generated mouse models for IDH mutant astrocytoma using a strategy combining CRISPR gene-editing with Cre-recombinase technologies to precisely model the mutations believed to initiate LGG pathogenesis, as well as bred two rs55705857 mutant alleles into these models. Our IDH mutant astrocytoma model develops LGG-like tumours in brain tissue with a penetrance of 30% at a latency of 463 days, while the addition of mutant rs55705857 elevates tumour penetrance to ~75% while decreasing latency to 172 days. In collaboration with the Jenkins Lab at the Mayo Clinic, I have uncovered one of the mechanisms through which the rs55705857 risk allele enhances gliomagenesis. We demonstrated that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding and thus prevents OCT2/4 mediated repression of the MYC promoter, inducing increased MYC expression. Lastly, I’ve developed and executed an in-vivo CRISPR and ORF screens to identify the genes such as Notch1 and Pten that drive malignant progression of LGG into deadly glioblastoma (GBM).
Application of Bioreagents to Mitigate the Negative Effects of Anisotropic Clay Particles in Mineral Processing
Keywords: Adsorption
Biopolymers
Clay particles
Flocculation
Flotation
Mineral processing

The depletion of high-grade ore resources and ongoing demand for mineral products has led to an increase in the exploitation of low-grade complex ores, which often contain colloidal clay particles that are detrimental to flotation and dewatering operations. Non-renewable chemical reagents are commonly used as dispersants and flocculants for clay particles in wastewater treatment, papermaking, and mineral processing; however, environmentally benign reagents are highly desired due to the non-biodegradability and negative impacts of synthetic reagents on aquatic life. As part of an effort to find environmentally benign reagents, I evaluated the performance of six protein- and polysaccharide-based biopolymers for their potential as dispersants and/or flocculants for swelling and non-swelling clay particles (kaolinite, serpentine, talc, illite, and vermiculite) at various pH via a capillary suction timer, filtration, froth flotation, settling, and turbidity tests. Dewatering results were compared under the same conditions using polyacrylamide as a traditional organic polymer. Zeta potential, adsorption isotherm by total organic carbon, and quartz crystal microbalance with dissipation tests were also conducted to elucidate interactions between biopolymers and clay mineral surfaces. Cationic proteins (lysozyme and protamine) significantly improved the flocculation of clays, whereas polysaccharide-based biopolymers (pectin, alginic acid and lignin) were effective dispersants of clays such as kaolinite, talc, illite, and vermiculite at pH 7 and 10. The use of anionic pectin as a dispersant significantly improved the grade and recovery of Ni and Cu in flotation at pH 10. Pectin successfully flocculated talc and serpentine in dewatering at pH 7, showing its potential as a switchable biopolymer. Similarly, chitosan was an effective switchable biopolymer for kaolinite and illite. Thus, biopolymers could switch from being an effective dispersant at pH 10 to an efficient flocculant at pH 7. The main mechanisms of biopolymer adsorption on clay surfaces are electrostatic attraction and/or hydrogen bonding, while for dispersion, they could be electrostatic repulsion or steric stabilization. This study demonstrated that the anisotropic nature of clay mineral particles should not be overlooked when analyzing adsorption data. Surface properties of clay minerals and polymer/biopolymers characteristics such as chain length, charge, solubility, and functional groups influence interactions between clay particles and biopolymers.
Strains of Self-propagating Protein Aggregates in Human Neurodegenerative Disease
Keywords: Aβ
Neurodegeneration
Protein aggregation
Protein strains
α-synuclein

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are devastating, progressive disorders of the ageing brain that are currently incurable. Patients with AD and PD exhibit the hallmark feature of cerebral misfolded protein inclusions, the major proteinaceous components of which are the Aβ and α-syn proteins, respectively. These proteins exhibit characteristics reminiscent of the prion protein, the causative pathogenic protein in the prion diseases. Like the prion protein, Aβ and α-syn are capable of misfolding, aggregating and propagating through the brain. Prions also exist as strains, conformationally-distinct prion protein aggregates that drive disease heterogeneity. Interested in whether conformational variability among Aβ and α-syn conformers might also contribute to phenotypic diversity among their related diseases, I analysed AD and synucleinopathy patient-derived species of Aβ and α-syn aggregates. Using techniques to determine the conformational characteristics of Aβ and α-syn species in tandem with transgenic mouse transmission assays, the project outlined here established the utility of the APPNL-F transgenic mouse for transmission experiments and found that spAD cases are associated with a spectrum of Aβ conformers. Using the same investigative framework, MSA-derived α-syn aggregates were found to be conformationally distinct and aggressively induced disease in the TgM83+/- mouse model compared to α-syn aggregates associated with DLB and AD patient samples, though mutant G51D familial PD samples, despite possessing MSA-like disease features such as notable glial pathology, did not mimic the behaviour of MSA-derived α-syn fibrils. In summary, this thesis more deeply investigated the link between true prion strains and those composed of α-syn and Aβ aggregates.
The Transdiagnostic Relationship of Cumulative Lifetime Stress with Memory, the Hippocampus, and Personality Psychopathology
Keywords: Cumulative stress
Hippocampus
Memory
MRI
Personality psychopathology

Stress has a detrimental impact on memory and the hippocampus. Most research has studied the impacts of stress on specific psychiatric diagnoses, although less is known about factors that mediate the relationship between stress and personality psychopathology from a dimensional perspective. The present work investigates the transdiagnostic relationship of cumulative stress with episodic memory (via subjective reports and neurocognitive tests) and hippocampal structure and function. The role of cumulative stress as a potential mediator of the effect of personality psychopathology on these neural correlates is also examined. Cumulative lifetime stress was assessed in a sample of females recruited to vary in stress exposure and severity of personality psychopathology. This included individuals with a depressive disorder (DD), with or without comorbid borderline personality disorder (BPD), and others with neither diagnosis. Participants completed a T2-weighted high-resolution magnetic resonance imaging (MRI) scan of the medial-temporal lobe and underwent functional MRI (fMRI) while completing a learning and recognition memory task. Participants also completed a neurocognitive test battery and questionnaires assessing psychopathological symptom severity and subjective memory complaints. Cumulative stress was significantly related to greater memory complaints but not to performance on the episodic memory task or neurocognitive tests. Cumulative stress was inversely correlated with bilateral hippocampal volume and positively correlated with encoding-related hippocampal activation associated with the presentation of novel stimuli. Cumulative stress was also associated with greater activity in prefrontal, temporal, and cingulate cortices. Furthermore, cumulative stress significantly mediated the relationship between personality psychopathology and both hippocampal volume and activation. To my knowledge, this work is the first to demonstrate that cumulative lifetime stress is related to both smaller hippocampal volumes and greater novelty-induced encoding-related hippocampal activation across individuals with varying levels of personality psychopathology. Structural and functional neuroimaging-based hippocampal biomarkers observed across various psychiatric diagnoses in prior studies may share cumulative stress as a common factor, which may mediate broadly reported relationships of psychopathology with hippocampal volume and function.