VictorJuiz/thesis huggingface dataset:
Neurostructural, Neurofunctional, and Neurocognitive Phenotypes of Self-harm among Youth with Bipolar Disorder

Youth with bipolar disorder (BD) are at greatly elevated risk for suicide. Self-harm, regardless of suicidal intent, is a leading risk factor for suicide. Given the paucity of research to date, we examined neurostructural, neurofunctional, and neurocognitive phenotypes in relation to self-harm among youth with BD. It was hypothesized that youth with a history of self-harm would have altered brain structure, functional connectivity, and poorer decision-making performance. Each of the three projects in this thesis included the following groups of participants, ages 13-20 years old: BD youth with history of self-harm (BDSH+), BD youth without history of self-harm (BDSH-), and healthy controls (HC). Neurostructural analyses examined 3T MRI measures of cortical thickness, surface area (SA), and volume, combining region-of-interest and vertex-wise approaches. Resting-state functional connectivity analyses used a seed-to-voxel approach. Neurocognition analyses focused on reward-related decision-making and risk-taking performance on an automated computerized test battery. In neurostructural vertex-wise analyses, BDSH+ had lower SA in the precentral and inferior temporal gyri, and lower caudal middle frontal gyrus volume compared to BDSH- and HC youth. In functional connectivity analyses, BDSH- had increased positive connectivity between the amygdala and occipital cortex, and between the dorsolateral prefrontal cortex and frontal pole, compared to BDSH+ and HC; and BDSH+ had increased positive connectivity between orbitofrontal cortex and precuneus compared to BDSH- and HC. In neurocognitive analyses, there was a difference in the overall proportion of points bet, such that BDSH- performed better than both BDSH+ and HC youth. Mean latency was also significant with BDSH- deliberating longer than HC youth. Risk-taking was different between groups, with BDSH- showing greater self-control compared to both BDSH+ and HC youth. Self-harm in youth with BD is associated with smaller neurostructural measures and altered connectivity in reward-related regions. In addition, youth with BD and no history of self-harm had greater self-control and lower risk-taking. We speculate this may be reflective of a compensatory process among BDSH- serving a protective role in suicide risk. These findings provide evidence of neurobiological phenotypes associated with self-harm among youth with BD, which may help refine suicide prediction and inform clinical trial designs.

Keywords: Bipolar disorder
Neurocognition
Neuroimaging
Self-harm
Suicide
Youth
Advisor: Goldstein, Benjamin I
Metallurgical Processes for Production of Critical Metal Compounds of Lithium, Cobalt, Nickel, and Rare Earth Elements Using Chemical Precipitation Method

The compounds of lithium, nickel, cobalt, and rare earth elements (REEs) are critical materials for a broad range of applications. Among the hydrometallurgical techniques, chemical precipitation is one of the most effective methods for the crystallization, separation, and purification of metal products. This PhD work is focused on developing efficient and sustainable processes for producing critical metal compounds of lithium, nickel, cobalt, and REEs using chemical precipitation method. Lithium carbonate (Li2CO3), lithium hydroxide monohydrate (LiOH.H2O), nickel and cobalt sulfate (NiSO4, CoSO4), nickel cobalt manganese carbonate coprecipitate (NixCoyMnzCO3) are common precursors for lithium-ion battery cathode material synthesis. Similarly, the REE sulfates serve as precursors for production of many strategic materials. The challenges for their production are listed below and corresponding approaches proposed in this work can be implemented: (i) There is no previous study to refine the current Li2CO3 production method. Comprehensive research is performed to improve the conventional Li2CO3 precipitation process in terms of lithium recovery and product purity; (ii) The conventional production methods for LiOH.H2O cannot achieve both high product yield and purity. An innovative process is developed to produce battery grade LiOH.H2O with high yield using barium hydroxide precipitant; (iii) The mineral ores containing nickel and cobalt usually contains magnesium impurity. A novel selective precipitation process using ethylenediaminetetraacetic acid (EDTA) chelating agent is developed to remove the magnesium from nickel and cobalt feed solution; (iv) The conventional method for preparing the carbonate precursor is lengthy and the product quality needs improvement. A novel supercritical carbonation process is developed to efficiently produce high quality NixCoyMnzCO3 precursor; (v) The low-value yttrium present in the minerals consumes significant amount of solvent during extraction process. A novel process is developed to pre-concentrate the REE leachate by partially removing yttrium using double sulfate precipitation method. In all the studies, experiments are systematically performed, and the reaction mechanisms are elucidated through comprehensive characterizations and theoretical calculations. It is expected that the results of this PhD work will help researchers in academia and industry gain a better understanding of chemical precipitation method, enable the development of efficient processes to produce critical metal compounds.

Advisor: Azimi, Gisele
Leveraging High-Throughput Proteomics to Elucidate the Complex Pathogenic Program of Legionella pneumophila

The bacterial species Legionella pneumophila exists within microbially diverse communities in freshwater environments. Many protozoan species phagocytose L. pneumophila for nutrients, and consequently, L. pneumophila has acquired the largest collection of type IV secretion system translocated substrates, called ‘effectors’, which collectively facilitate intracellular replication within these hosts. This predator-prey relationship has spawned an evolutionary arms race that has occurred for millions of years. Effectors target diverse, conserved eukaryotic processes to facilitate the formation of a replicative vacuole within the host. Most effectors remain uncharacterized, their study obfuscated by genetic redundancy and uniqueness to the Legionella genus. Intracellular pathogens like L. pneumophila must carefully modulate their effectors to maximize replication, without rupturing the host cell prematurely. Differential transcription and translocation of effectors are two mechanisms of pathogenic regulation that have been described. Additionally, some effectors have direct inter-effector regulatory relationships with each other that can be both antagonistic and cooperative. The prevalence of direct inter-effector relationships within the arsenal of more than 300 effectors is unknown, but more than 10 direct regulatory relationships between effectors have already been identified. Here, I have developed and applied a high-throughput proteomic technology called inducible barcode fusion genetic-yeast two-hybrid to systematically query the prevalence of inter-effector interactions, identifying dozens of novel examples in the process. Leveraging this proteomic dataset, I have also mechanistically linked an uncharacterized effector called PieF to a novel, highly conserved eukaryotic host target, CCR4-NOT. PieF represents the first L. pneumophila effector described to intersect the CCR4-NOT complex and molecularly resembles the CCR4-NOT-associated BTG/TOB proteins to influence mRNA stability and expression within cells. As a critical regulator of eukaryotic gene expression, targeting CCR4-NOT may have broad implications on the eukaryotic cell and bacterial pathogenesis. PieF has an inter-effector interaction with LegK2, that was identified during iBFG-Y2H. Furthermore, the modulation of CCR4-NOT by PieF is suppressed by LegK2, in a putative metaeffector relationship.

Keywords: CCR4-NOT
effectors
inter-effector interactions
Legionella pneumophila
metaeffectors
proteomics
Advisor: Ensminger, Alexander W
Knowledge Theft at Work: A Victim's Perspective

As today’s organizational economy is increasingly defined by knowledge-based work, employees value credit in exchange for their contributions as the currency of success. Credit is conceptualized as a perceptual recognition made by others that one is responsible for a contribution or work-related outcome. Existing research documents the value of credit, revealing that accruing credit can lead to realized career success via financial rewards, promotions, and/or other forms of upward mobility within and across organizations. Although literature on credit points to a multitude of benefits associated with receiving it, little is known about the impact of having one’s credit stolen by others. I name this phenomenon knowledge theft. Across one qualitative and two quantitative studies, this dissertation explores knowledge theft from the victim’s perspective. In Study 1, I used an inductive, exploratory approach where I interviewed 30 individuals who had been a target of knowledge theft at work. I drew from literature on credit to guide my analysis. The results from this study suggested loss to career success was a defining feature of knowledge theft for victims. This loss was the catalyst for a series of behavioural outcomes that involved coping with the negative event and protecting oneself from knowledge theft in the future. In studies 2 and 3, I took a quantitative approach to replicate subsets of the relationships identified in Study 1. I drew from literature on territoriality theory and employee victimization and used a survey methodology in Study 2 and a vignette methodology in Study 3 to test the research hypotheses. Across both studies, I found further support for the role that loss to career success plays as a mechanism explaining the relationship between knowledge theft and behavioural outcomes. In Study 3, I also looked at the role power played in influencing victims’ responses. The evidence suggests that when the victims is of equal relative power to the perpetrator, victims are most likely to engage in behaviours that restore ownership over their work (i.e., active coping) and protect their knowledge in the future. I close by outlining theoretical and practical implications of my findings for individuals and organizations.

Keywords: Credit-taking
Knowledge theft
Territoriality in organizations
Victimization
Workplace mistreatment
Advisor: Zweig, David
Material Interfaces for Cell-free Operated Genetic Circuits

Recent innovations in the field of synthetic biology have led to development of bio-safe, rapid, and low-cost molecular sensors suitable for point-of-care diagnostics. One key technology enabling such molecular sensors is bacterial cell-free systems, which can carry out in-vitro protein expression. Initial demonstrations of cell-free systems for diagnostic purposes have used in silico engineered toehold riboswitches to detect viral genetic fingerprints addressing epidemics, such as Ebola and Zika. Through multiple collaborations, I have designed and developed three main material interfaces (electrochemical, gold nanoparticles, and quantum dots) for cell-free molecular sensors that enhance multiplexed and decentralized detection. I utilized restriction enzymes as genetic circuit reporter outputs in cell-free to interact with electrodes in Chapter 3, actuating electrochemical signals, and nanoparticles in Chapter 4, triggering optical signal outputs. The developed electrochemical interface actuates up to four simultaneous signals, while the nanoparticle-based optical output mediates three-way multiplex signal detection. The nanoparticle-based optical reporters allow for rapid and visible detectable signals, eliminating costly instrumentation.

Keywords: Cell-Free Systems
Genetic Circuits
Point of Care Diagnostics
Synthetic Biology
Advisor: Pardee, Keith K.I.P
Kelley, Shana S.O.K
Synthesis of Substituted Cyclopropylamines via Metal Homoenolate Chemistry and Ni Catalysis

This thesis describes new methods for the synthesis of substituted cyclopropylamines in the contexts of metal homoenolate chemistry and nickel catalysis. These strategies represent new approaches to current synthetic obstacles and may be of interest to chemists interested in these areas. Chapter 1 introduces the properties and synthetic routes towards substituted cyclopropylamines, historical and modern developments in metal homoenolate chemistry, and an overview of nickel catalysis and reductive cross-couplings. Chapter 2 describes a new method for the synthesis of trans-2-substituted cyclopropylamines in high diastereoselectivity from readily available a-chloroaldehydes, as well as the observed cyclopropylamine cis/trans-isomerization which occurs in the presence of zinc halide salts. Chapter 3 describes a new method for the synthesis of 1- and 1,2-substituted cyclopropylamines from the corresponding cyclopropanol via intermolecular electrophilic trapping of mixed zinc/copper ketone homoenolate with amines. Chapter 4 describes a new Ni-catalyzed reductive cross-coupling of aminocyclopropane NHP esters and (hetero)aryl halides to yield 1-arylcyclopropylamines via the formation of an aminocyclopropyl radical intermediate. Chapter 5 summarizes the previous work and outlines potential future research projects with some preliminary results.

Keywords: catalysis
cyclopropylamine
homoenolate
nickel
synthesis
Advisor: Rousseaux, Sophie
Neurostructural and Neurovascular Correlates of Retinal Vascular Caliber in Adolescents with Bipolar Disorder

Bipolar disorder (BD) is recognized by the American Heart Association as a condition that predisposes youth to early-onset cardiovascular disease. The magnitude of this prematurity cannot be attributed to lifestyle or traditional cardiovascular risk factors alone. Early evidence suggests that microvascular structure and function may be impaired early in the course of BD. The extent to which vascular measures are related to brain structure and function in BD is not well-understood, despite the potential benefits of focusing on the vascular-brain interface in BD. This thesis examines the association of retinal vascular caliber, a proxy cerebrovascular measure, with brain structure, cerebral blood flow (CBF), and white matter integrity in adolescents with BD. We hypothesized that better retinal vascular caliber (i.e., higher arteriovenous ratio) would be associated with more positive neuroimaging phenotypes in adolescents with BD.All participants completed retinal fundus imaging, from which the central retinal arteriolar equivalent (CRAE) and the central retinal venular equivalent (CRVE) were measured. Arteriovenous ratio (AVR), a proxy measure of cardiovascular risk, was computed as a ratio of the two. All participants underwent 3D T1-weighted structural, arterial-spin labelling, and diffusion weighted magnetic resonance imaging (MRI). For each objective, retinal arteriolar caliber was higher in adolescents with BD relative to controls after adjusting for age, sex, and tobacco smoking. In the overall sample, arteriolar caliber was negatively associated with anterior cingulate cortex (ACC) volume and surface area, and with corpus callosum and forceps minor fractional anisotropy (FA). In the BD group, higher AVR was associated with greater ACC CBF, although this trend was not observed in controls. Finally, there were several diagnosis-by-retinal interaction effects on brain structure and FA, such that higher AVR was more negatively associated with regional brain structure and higher venular caliber was more positively associated with FA, in BD relative to controls. Findings from this thesis are proof-of-concept, insofar as microvascular readouts are relevant to brain health in youth. The clinical implications of these findings are likely accentuated in adolescents with BD. Overall, these results suggest that optimizing cardiovascular health may offer unique benefits from both a heart and a brain perspective.

Keywords: adolescence
bipolar disorder
brain structure
cerebral blood flow
retinal microvessels
white matter integrity
Advisor: Goldstein, Benjamin I
Characterizing the Hypothalamic Functions of Irx3 and Irx5 in Energy Balance Regulation

Obesity and overweight have become growing epidemics around the globe. The homeodomain transcription factors IRX3 and IRX5 are important risk factors of human obesity and key regulators of energy balance, acting in connection with the intronic variants of FTO. Irx3 and Irx5 are expressed in the arcuate nucleus and median eminence (ARC-ME), a hypothalamic site known to control energy homeostasis via distinct cell types, yet the identities of Irx3- and Irx5-expressing hypothalamic cells and their roles in regulating energy balance remain poorly characterized. In addition, although accumulating evidence has suggested that postnatal neurogenesis in ARC contributes to energy balance regulation and obesity, little is known about the genetic factors that are involved in this process. Using marker gene staining, lineage tracing and single-cell RNA sequencing analyses, I demonstrate that Irx3 and Irx5 are predominantly expressed in a previously unreported population of radial glia-like cells (RGL) in postnatal mouse hypothalamus, which could be targeted by Ins2-Cre. These RGLs harbor a gene signature highly reminiscent to neural stem cells (NSC) and hold the potential to give rise to other neural cells in postnatal ARC-ME. Through bioinformatics analyses and in vivo labeling experiments, I show that reduced dosage of Irx3 and Irx5 promotes postnatal hypothalamic neurogenesis, leading to elevated numbers of leptin-sensing neurons in postnatal and adult ARC. Next, I investigated the specific functions of Irx3 and Irx5 in Ins2-Cre+ cells by generating mutant mice with conditional deletion of Irx3 or both Irx3 and Irx5 in the Ins2-Cre lineage. These mutants exhibit improved hypothalamic leptin response associated with increased postnatal neurogenesis and higher numbers of leptin-sensing ARC neurons, contributing to their reduced food intake and lean phenotype. Altogether, my thesis work illustrates important roles for Irx3 and Irx5 in the hypothalamic control of energy balance and remodeling of leptin-sensing ARC neurons through postnatal neurogenesis.

Keywords: Hypothalamus
Iroquois homeobox genes
Leptin
Obesity
Postnatal neurogenesis
Radial glia-like cells
Advisor: Hui, Chi-Chung
CRISPR-mediated Modelling and Treatment of Tandem Duplications in Rare Inherited Disorders

Tandem duplication mutations are increasingly found to be the direct cause of many rare inheritable diseases, including Duchenne muscular dystrophy (DMD) and MeCP2 duplication syndrome (MDS). Unfortunately, animal models recapitulating such mutations are scarce, limiting our ability to study them and develop therapeutic options for the affected patients. In my thesis, I explored the potential of the CRISPR/Cas9 system to model and correct tandem duplication mutations at large. First, a novel DMD duplication mouse model (Dup18-30), harbouring a patient multi-exonic duplication in the Dmd gene, was generated and characterized. The Dup18-30 mouse model faithfully recapitulates DMD disease phenotypes, developing early-onset motor and cardiac complications. I then implemented an in vivo single-guide RNA CRISPR/Cas9 approach to correct the disease-causing tandem duplication. This approach precisely removed the duplication mutation, restored full-length dystrophin expression, and resulted in marked improvements in both histopathological and clinical phenotypes. In an effort to broaden the applicability of these strategies, I further translated them in the context of MDS, a rare neurodevelopmental disease. A CRISPR/Cas9 fusion proximity-based approach was developed to improve the efficiency of tandem duplication generation, and it was utilized to generate an Irak1-Mecp2 tandem duplication mouse model (Mecp2 Dup) that recapitulates an MDS patient mutation. The Mecp2 Dup model displays neurological phenotypes and an abnormal immune response in keeping with MDS disease manifestations. The Mecp2 Dup mouse line thus provides an innovative tool to investigate disease mechanisms and advance therapeutic development. Ultimately, the results derived from my PhD project highlight the tremendous potential of CRISPR/Cas9 in both modeling and treating tandem duplication mutations, opening new horizons in research for patients affected by duplication disorders.

Keywords: disease modelling
genome editing
muscular dystrophy
neurodevelopmental disease
tandem duplication
Advisor: Cohn, Ronald D
Novel Ex-Vivo Strategies to Predict and Prevent Reactivation of Latent Human Cytomegalovirus in Lung Transplant Patients

Cytomegalovirus (HCMV) transmission from a latently infected donor lung with subsequent viral reactivation after transplantation is common and has impact on quality of life and survival in lung transplant patients. Therefore, efforts to decrease the transmission of donor virus by targeting its latent reservoir would be the ideal strategy for these patients. Recently, a highly specific immunotoxin named F49A-FTP that targets US28 expressed in the membrane of HCMV-infected cells has shown efficacy in killing HCMV-latently infected cells with subsequent reduction of HCMV reactivation. Ex-vivo lung perfusion (EVLP) is an innovative platform that creates a window of opportunity for the reconditioning and treatment of donor allografts before transplantation. Moreover, EVLP is an excellent platform for drug discovery and diagnostics. In this thesis, we first explored the feasibility and efficacy of delivering F49A-FTP to human donor lungs during EVLP. Since the virus is species-specific, the use of animal models of EVLP followed by LTx was not possible here. Therefore, the first main objective was to develop an assay capable of detecting HCMV reactivation events in lung tissue specimens to use as an efficacy read-out for the EVLP phase. After I successfully developed the reactivation assay, we moved on to deliver F49A-FTP to human lungs. HCMV-seropositive donor lungs were perfused for 6 hours with F49A-FTP and resulted in much lower reactivation events when compared to control EVLP lungs that were perfused as in the clinical practice. Importantly, we didn’t observe any acute effects on the donor lungs when delivering F49A-FTP. In the last part of the thesis, we wanted to elucidate whether the higher-risk donors associated with EVLP assessment could have any impact on HCMV viremia rates after transplantation. By performing a retrospective clinical analysis of more than 1000 lung transplant recipients, we did not observe any negative impact of EVLP practice on HCMV outcomes. We then collected EVLP clinical perfusate samples from 203 HCMV-seropositive donors to measure a 15-plex panel of pro-inflammatory cytokines and associate their levels with HCMV outcomes. Interestingly, we identified that higher levels of IL-7 and IL-12 are both associated with the development of viremia and significantly fewer HCMV-free days after transplant. Both prediction of higher-risk donor lungs prone to develop HCMV after transplant and a highly efficient targeted therapeutic approach to clear the latent HCMV reservoir investigated in this thesis, are promising for clinical translation and may not only improve survival but also improve patients’ quality of life and decrease costs of managing HCMV complications post-transplantation.

Keywords: cytomegalovirus
ex-vivo lung perfusion
immunotoxin
lung transplantation
Advisor: Cypel, Marcelo