VictorJuiz/thesis huggingface dataset:
Understanding Sources of Perfluorinated Acids to Biological Systems
Keywords: perfluorinated acids
biotransformation
atmospheric oxidation
temporal and spatial trends

The overall aim of this thesis was to investigate the fate of perfluorinated alkyl compounds (PFCs) in biological systems. During the past several years, it has been shown that wildlife are ubiquitously contaminated with two classes of PFCs, the perfluoroalkyl carboxylates (CxF2x+1C(O)OH, PFCAs) and sulfonates (CxF2x+1SO3H, PFSAs). However, there is still considerable uncertainty regarding how wildlife are accumulating these PFCs, particularly in remote areas such as the Canadian arctic. The potential for fluorotelomer acrylate monomers (CxF2x+1CH2CH2OC(O)CH=CH2, FTAcs) to act as precursors to PFCAs through atmospheric oxidation was investigated using smog chamber experiments. FTAc atmospheric fate is determined by OH radical reaction with a lifetime of approximately 1 day. The sole primary product of this reaction was the 4:2 fluorotelomer glyoxylate which is expected to undergo further atmospheric oxidation or photolysis to ultimately yield PFCAs. Temporal and spatial trends of PFCs in arctic ringed seals and seabirds were investigated to assist in understanding PFC transport mechanisms to remote regions. In ringed seals, perfluorooctane sulfonate (PFOS) levels decreased rapidly, coinciding with the phase out by the major manufacturer. These findings are consistent with volatile precursors as the dominant source of PFCs to arctic wildlife. The bioaccumulation and biotransformation of the 8:2 FTAc was investigated in two complimentary studies with rainbow trout. During the in vivo dietary exposure study, fish rapidly accumulated and biotransformed the 8:2 FTAc, with intermediate metabolites observed within 1 hour of dosing. Perfluorooctanoate (PFOA), perfluorononanoate (PFNA) and perfluoroheptanoate (PFHpA) were formed and accumulated in low yields. The carboxylesterase activity in the trout liver and stomach was investigated using in vivo sub-cellular (S9) incubations. Very high esterase activities were shown with approximately equal efficiency in the stomach and liver. The metabolic pathway of the 8:2 fluorotelomer alcohol (8:2 FTOH) was investigated by separately dosing whole rainbow trout with three intermediate metabolites that represented important branching points. The 7:3 fluorotelomer saturated carboxylate (FTCA) did not form PFOA, but formed PFHpA and the 7:3 fluorotelomer unsaturated carboxylate (FTUCA). The 8:2 FTCA and 8:2 FTUCA did form PFOA, confirming a “beta-like-oxidation” mechanism.
The Ontario Crohn’s and Colitis Cohort: Incidence and Outcomes of Childhood-onset Inflammatory Bowel Disease in Ontario, Canada
Keywords: inflammatory bowel disease
paediatrics
epidemiology
health services research
health administrative data
socioeconomic stats
incidence
prevalence
socioeconomic status
outcomes

Inflammatory bowel disease (IBD), characterized by chronic gastrointestinal inflammation, represents a significant childhood chronic disease. In this thesis, a case ascertainment definition of paediatric-onset IBD was validated using administrative data and developed the Ontario Crohn’s and Colitis Cohort (OCCC). The epidemiology of paediatric IBD in Ontario was described, demonstrating that Ontario has one of the highest worldwide incidence rates. Statistically significant increases in incidence were noted in 0-4 year olds (5.0%/year, p=0.03) and 5-9 year olds (7.6%/year, p<0.0001), but not in other age groups. Lower income children were more likely to be hospitalized at least once (hazard ratio (HR) 1.17, 95% confidence intervals (CI) 1.05-1.30) or visit the ED (HR 1.21, 95% CI 1.09-1.35) and had more IBD-related physician visits (odds ratio (OR) 3.73, 95% CI 1.05-13.27). Lower income children with Crohn's disease (CD) (not ulcerative colitis [UC]) were more likely to undergo intra-abdominal surgery within 3 years of diagnosis (OR 1.22, 95% CI 1.01-1.49), especially if diagnosed after 2000 (OR 1.79, 95% CI 1.27-2.53). Finally, changes in health services utilization and surgical rates were described, as were changes in specialist care provision and immunomodulator use in children with IBD between 1994-2007. The changes to care included increased outpatient care provided by paediatric gastroenterologists, and increased immunomodulator use. Children diagnosed with CD, but not UC, in recent years had lower surgical rates. In CD patients, intra-abdominal surgical rates within three years of diagnosis decreased from 18.8% in children diagnosed in 1994-1997 to 13.6% in those diagnosed in 2001-2004 (P = 0.035). When stratified by age at diagnosis, this decrease was significant in children diagnosed ≥10 years old (OR 0.67, 95% CI 0.48-0.93). The OCCC will continue to be used to investigate the epidemiology and burden of paediatric IBD and to improve the care received by children with IBD in Ontario.
Hospitalizations for Ambulatory Care Sensitive Conditions among Persons with an Intellectual Disability, Manitoba, 1999-2003
Keywords: intellectual disability
hospitalization
primary care

This thesis examines hospitalizations for ambulatory care sensitive conditions among persons with an intellectual disability living in Manitoba from 1999 to 2003. Hospitalizations for ambulatory care sensitive conditions are considered an indicator of access to, and the quality of, primary care. Intellectual disability can be defined as a disability originating before age 18 characterized by significant limitations both in intellectual functioning and in adaptive behaviour as expressed in conceptual, social, and practical adaptive skills. Between 1 and 3% of the population has an intellectual disability. This thesis addressed three objectives: 1) To identify ambulatory care sensitive conditions that are applicable to persons with an intellectual disability; 2) To compare hospitalization rates for ambulatory care sensitive conditions between persons with and without an intellectual disability in Manitoba; 3) To identify factors associated with hospitalizations for ambulatory care sensitive conditions among adults with an intellectual disability living in Manitoba. An online survey of primary care providers with experience working with persons with an intellectual disability found consensus on fifteen ambulatory care sensitive conditions applicable to persons with an intellectual disability. Large discrepancies in hospitalization rates for these conditions were found between persons with and without an intellectual disability. Controlling for age, year, sex, and region, persons with an intellectual disability were 6 times more likely to be hospitalized for an ambulatory care sensitive condition. Future research should investigate reasons for the large discrepancy in rates between persons with and without an intellectual disability. Among adults with an intellectual disability, living in a rural area (odds ratio 1.3; 95% CI=1.0, 1.8), living in an area with a high proportion of First Nations people (odds ratio 2.3; 95% CI=1.3, 4.1), and experiencing higher levels of comorbidity (odds ratio 25.2; 95% CI=11.9, 53.0) were all associated with a higher likelihood of being hospitalized for an ambulatory care sensitive condition. Dwelling in higher income areas had a protective effect (odds ratio 0.56; CI=0.37, 0.85). The results suggest that addressing the socioeconomic problems of poorer areas and specifically areas densely populated by First Nations people would likely have an impact on hospitalizations for ACS conditions for persons with an intellectual disability.
The Identification and Characterization of New Small Molecule Probes of Cell Expansion and Cytokinesis
Keywords: cell biology
chemical biology
Arabidopsis

Plant form and structure is remarkably diverse encompassing a myriad of shapes and sizes, and is a result of coordinated instances of cell growth and division. This varied form and structure represents adaptive strategies enabling plants to exploit and endure their environment maximizing fitness. Common to both cell growth and division processes, is the requirement of growth material and effectors via the secretory system. The secretory system is a dynamic pathway of organelles connected via vesicular traffic, responsible for protein modification and delivery. Challenges in studying secretion are related to its' dynamic flow between organelles, and the prevalence of redundancy and lethality, which cause difficulties in interpretation and genetic modulation. To further our understanding of the secretory process, we employed a chemical genetic approach to identify small molecule probes of secretion by first screening for inhibitors of cell expansion, followed by a microscopy based screen of GFP marker lines for perturbagens of subcellular structures. Small molecules offer the advantages of temporal and spatial application, have been shown to overcome redundancy and can be varied in concentration to control the severity of effects. We identified twenty-five small molecule probes of secretion and pursued two chemicals with striking properties, polarazine and eroonazole. Polarazine was identified as a cell division inhibitor, affecting phragmoplast structure and function, while eroonazole remodels the endoplasmic reticulum into small vesicles and is implicated in auxin signaling. This approach shows the utility of small molecule probes in furthering our understanding of secretory processes.
Mechanisms of Platinum Group Metal Catalysis Investigated by Experimental and Theoretical Methods
Keywords: Homogeneous Hydrogenation
DFT
allylic amination
kinetic isotope effect
mechanisms

The results of kinetic isotope determination and computational studies on Noyori-type catalytic systems for the hydrogenation of ketones are presented. The catalysts examined include RuH2(NHCMe2CMe2NH2)(R-binap) and RuH(NHCMe2CMe2NH2)(PPh3)2. These complexes are active catalysts for ketone hydrogenation in benzene without addition of an external base. The kinetic isotope effect (KIE) for catalysis by RuH2(NHCMe2CMe2NH2)(R-binap) was determined to be 2.0 ± (0.1). The calculated KIE for the model system RuH(NHCH2CH2NH2)(PH3)2 was 1.3, which is smaller than the experimentally observed value but does not include tunneling effects. The complex OsH(NHCMe2CMe2NH2)(PPh3)2 is known to display autocatalytic behaviour when it catalyzes the hydrogenation of acetophenone in benzene. Pseudo first-order reaction conditions are obtained via addition of the product alcohol at the beginning of each kinetic experiment. The KIE determined using various combinations of deuterium-labeled gas, alcohol and ketone was found to be 1.1 ± (0.2). DFT calculations were used to explore the effect of the alcohol and the KIE. An induction period is observed at the start of the hydrogenation that is attributed to the formation of an alkoxide complex. A novel, diamine-orchestrated hydrogen-bonding network is proposed based on DFT calculations to explain how the alkoxide is converted back to the active catalyst. The tetradentate complexes trans-RuHCl[PPh2(ortho-C6H4)CH2NHCH2)]2 and RuHCl[PPh2(ortho-C6H4)CH2NHCMe2)]2 are known to be catalysts for the hydrogenation of acetophenone and benzonitrile in toluene when activated by KOtBu/KH. DFT studies were performed and a mechanism is proposed. The calculated rate limiting step for acetone hydrogenation was found to be heterolytic splitting of dihydrogen, which agrees well with experiment. The novel outer-sphere sequential hydrogenation of a CN triple bond and then a C=N double bond is proposed. A mechanism is proposed, which is supported by DFT studies, to explain the selectivity observed in the nucleophilic attack of amines or aziridines on palladium -prenyl phosphines complexes. Calculations on based on a palladium complex with two phosphorus donor ligands indicated that the observed selectivity would not be produced. Using two new model intermediates with either THF or aziridine substituted for a phosphine ligand trans to the unhindered side of the prenyl ligand did predict the experimentally observed selectivity.
Implicit and Explicit Consequences of Distraction for Aging and Memory
Keywords: memory
aging

This investigation explored implicit and explicit memory consequences of age differences in susceptibility to distraction when previous distraction occurs as target information in a later memory task. Younger and older adults were presented with either implicit (Study 1) or explicit (Studies 2 and 3) memory tasks that included previously distracting and new words. Study 1 explored whether prior exposure to distraction would transfer to improve memory when previously distracting words were included in list to be studied for a recall task. Older adults recalled more previously distracting than new words whereas younger adults recalled the same amount of previously distracting and new words. This initial study was implicit in its use of previously distracting information in that participants were neither informed nor aware of their prior exposure to words in the recall task. Here, only older adults’ memory was influenced by prior exposure to distraction and their recall actually increased to the level of younger adults with implicit use of distraction to improve performance. Subsequent studies investigated explicit influences of prior exposure to distraction on later memory. In Study 2, both younger and older adults showed reliable memory for previously distracting words in an explicit recognition task. These results suggest that although younger adults encode distraction, they do not transfer this information when previous distraction occurs as target stimuli in an implicit memory task. Study 3 investigated whether participants would transfer previous distraction to improve recall if the task was explicit in its use of previous distraction. When cueing instructions were given before the memory task informing participants of the connection between tasks, older adults once again recalled more previously distracting than new words. In contrast to the results of Study 1, younger adults also recalled more previously distracting than new words. Taken together, the results indicate that younger adults do encode distraction, but they require explicit instructions to transfer their knowledge of distraction to later tasks. In contrast, older adults apply their knowledge of distraction in both implicit and explicit memory tasks. Implications are discussed in terms of inhibitory control theory and age differences in strategies engaged in memory tasks.
Hydrogen Bond-directed Stereospecific Interactions in (A) General Synthesis of Chiral Vicinal Diamines and (B) Generation of Helical Chirality with Amino Acids
Keywords: diamine
rearrangement
amino acid
helical chirality

Hydrogen bonding interactions have been applied to the synthesis of chiral vicinal diamines and the generation of helical chirality. A stereospecific synthesis of vicinal diamines was developed by using the diaza-Cope rearrangement reaction driven by resonance-assisted hydrogen bonds (RAHBs). This process for making a wide variety of chiral diamines requires only a single starting chiral diamine, 1,2-bis(2-hydroxyphenyl)-1,2-diaminoethane (HPEN) and aldehydes. Experimental and computational studies reveal that this process provides one of the simplest and most versatile approaches to preparing chiral vicinal diamines including not only C2 symmetric diaryl and dialkyl diamines but also unsymmetrical alkyl-aryl and aryl-aryl diamines with excellent yields and enantiopurities. Weak forces affecting kinetics and thermodynamics of the diaza-Cope rearrangement were systematically studied by combining experimental and computational approaches. These forces include hydrogen bonding effects, electronic effects, steric effects, and oxyanion effects. As an example of tuning diamine catalysts, a vicinal diamine-catalyzed synthesis of warfarin is described. Detailed mechanistic studies lead to a new mechanism involving diimine intermediates. Decreasing the NCCN dihedral angle by varying the diamine structure results in an increase of the enantioselectivity up to 92% ee. Hydrogen bonds have been used to generate helical chirality in a highly stereospecific manner with a single amino acid and 2,2′-dihydroxybenzophenone. DFT computational and experimental data including circular dichroism (CD), X-ray crystallography and 1H NMR data provide insight into the origin of the stereospecificity. A signalling dizao group can be attached to the receptor for general sensing of amino acid enantiopurity.
Development of Synthetic Peptide Sequences for Mitochondrial Delivery and Disruption
Keywords: mitochondria-penetrating peptides
mitochondrial delivery
mitochondrial disruption
proapoptotic peptides
MPPs

The mitochondrion is an important therapeutic target due to its roles in energy metabolism, reactive oxygen species production, and activation of cell death. The connection of these cellular processes with diabetes, obesity, neurodegenerative disorders, and cancer makes this organelle a potential control point for treatment of these diseases. The advancement of mitochondrial medicine will be accelerated by the development of organelle-specific cellular transporters as well as by strategies to enhance the activity of mitochondrially-active drugs. Here, the discovery and development of a new class of mitochondria-specific agents, mitochondria-penetrating peptides (MPPs), is described. These peptides, exemplified by the sequences (FXY)3 and (FXY)4 where FX=cyclohexylalanine and Y=basic arginine or lysine residues, display hydrophobic and cationic residues critical for access to this organelle, and appear to accumulate within cells and mitochondria through membrane potential-dependent mechanisms. Subcellular localization of the peptides was determined by the interplay of hydrophobicity and positive charge, and necessary lipophilicity “thresholds” for access to the mitochondrion. MPPs can be engineered to have minimal mitochondrial disruptive activity and cytotoxicity through minimization of hydrophobicity and length. Furthermore, MPPs appear to accumulate predominantly in the mitochondrial matrix, a feature which places them within an exclusive class of mitochondria-specific transporters and may enable delivery applications for a number of therapeutically-relevant cargoes. Information gained from MPP studies on the physiochemical parameters that drive mitochondrial localization were applied to improve the activity of the anticancer peptide d-(KLAKLAK)2, an agent that activates apoptosis through mitochondrial disruption. Residue substitutions that increased peptide hydrophobicity, regardless of changes to secondary structure, enhanced mitochondrial localization, activity, and cytotoxicity induced by the peptide. In conclusion, these studies provide important guidelines for how to drive the subcellular localization and activity of peptides, and expand the possibilities for mitochondrially-targeted therapeutics.
Metallic and Semiconductor Nanoparticles: Cellular Interactions, Applications and Toxicity
Keywords: nanotechnology
toxicology
gold nanorods
hyperthermia
cancer
nanomaterial

The objectives of this thesis were to optimize the synthesis and surface coating of metallic and semiconductor nanoparticles, to understand how these materials interact with cells and physiological systems and to investigate how they can be used to deliver thermal therapy for medical applications. Reproducible high-yield synthesis of gold nanorods and surface coating with a variety of polymers and silica was optimized. Using gold nanorods as a model system, the relationship between particle surface chemistry, surface charge and cellular uptake was studied, as well as the toxicity of nanoparticles of different surface chemistry. Low toxicity in vitro was encouraging and was confirmed in vivo by intravenously injecting Sprague-Dawley rats with semiconductor quantum dots of various surface coatings. Low toxicity was found during biochemical, haematological and pathological assessment, and these results indicate that applications of nanoparticles should be further investigated. One such application is the use of near infrared absorbing gold nanorods in remotely activated hyperthermia. It was shown that gold nanorods act synergistically with the chemotherapeutic cisplatin to improve cytotoxicity, and reduce the required cytotoxic drug dose to 33% of the unheated amount. Due to the success of hyperthermia treatment in vitro, continuing and future work involves the use of gold nanorods ex vivo on excised human corneas in a novel application to weld corneal tissue for improved wound closure following cataract surgery.
The Role of Innate Immunity in the Pathogenesis and Treatment of Experimental Pulmonary Hypertension
Keywords: pulmonary hypertension
immunity
natural killer cells
hyaluronan

In this thesis, the monocrotaline (MCT)-induced rat model of pulmonary arterial hypertension (PAH) was used to investigate the role of innate immunity in the pathogenesis of PAH and the mode of action of experimental therapies. The first section of this thesis is an investigation of the therapeutic mechanism of human, early and late-outgrowth endothelial progenitor cells (EPCs) in the MCT-induced, nude rat model of PAH. While late-outgrowth EPCs provided no therapeutic benefit in this model, early EPCs (E-EPCs) prevented the elevation of right ventricular systolic pressure (RVSP, P<0.001) and right ventricular (RV) hypertrophy (P<0.01). Ablation of natural killer (NK) and natural killer T cells with anti-asialo GM-1 antiserum (ASGM-1) enhanced human cell retention in the lung but abrogated the therapeutic capacity of E-EPCs. In vitro studies demonstrated that E-EPCs are similar to monocyte-derived regulatory dendritic cells (DCs) and possess the capacity to stimulate both autologous and rat NK cells in co-culture. Imatinib mesylate has been reported to reverse established PAH both clinically and in the MCT model. Imatinib can also induce NK activation through inhibition of c-kit signaling in DCs, suggesting that imatinib and the DC-like E-EPCs may prevent PAH through a similar, NK-mediated mechanism. In the second section of this thesis, imatinib prevented MCT-induced increases in RVSP (P<0.001) and RV hypertrophy (P<0.01) in immunocompetent Fisher 344 rats, but not in nude rats or Fisher rats following ablation of NK cells and T lymphocytes with ASGM-1. These data suggest that the stimulation of NK activity by imatinib is insufficient to prevent disease in the absence of T lymphocytes. Hyaluronan (HA) fragments are a potent inflammatory stimulus, capable of inducing macrophage activation and DC maturation. In the third section of this thesis, HA synthesis and degradation were investigated in the MCT model of PAH. While the early stages of disease were characterized by enhanced hyaluronidase-1 activity and a loss of high molecular weight (HMW) HA, severe disease was associated with HMW HA synthesis and HA accumulation in the lungs. The early degradation of HMW HA may drive inflammation and stimulate pathological vascular remodeling in PAH.