VictorJuiz/thesis huggingface dataset:
Biomass to ethanol pathways: Evaluation of lignocellulosic ethanol production technologies

Ethanol derived from lignocellulose (biomass) is a promising alternative to petroleum-based fuels for light-duty vehicle transportation; in particular, because it represents a near-term liquid fuel that is renewable, domestically produced, requires moderate infrastructure changes, and has the potential to significantly reduce greenhouse gas emissions. This thesis investigates environmental and energy impacts of a set of emerging lignocellulosic ethanol technologies using life cycle assessment and statistical methods to characterize the potential performance and development of those technologies. A set of emerging pretreatment methods are investigated in combination with near-term saccharification and co-fermentation and mature consolidated bioprocessing technologies for producing ethanol from lignocellulose. Results from the research show that relative to gasoline vehicles, lignocelulose-based ethanol fuelled vehicles in blends with 15% reformulated gasoline (by volume) can reduce greenhouse gas emissions by between 25% and 130% per kilometre driven depending upon the feedstock and conversion technology selected. Furthermore, the analysis shows the potential for displacing between 9% and 40% of U.S. annual gasoline demand, and more than 100% of Canadian annual gasoline demand over the next 20 years. A major finding is the impact of co-product allocation: when electricity co-product credits are incorporated into model designs, technologies with low ethanol yield and high electricity yield are preferred from an emissions and energy perspective. However, this finding depends strongly on whether the electricity co-product is displacing mostly coal-based existing electricity facilities, and it is likely that producing larger amounts of ethanol fuels to displace gasoline will help reduce fossil and petroleum energy, and greenhouse gas emissions from light-duty vehicle transportation, as well as contribute to energy security goals for the sector. This thesis demonstrates how systems-based analytical models that measure the full set of environmental tradeoffs associated with emerging fuel technologies are essential inputs to guide decision making and policies for the next generation of transportation energy infrastructure.
Development of magnetically oriented bicelles as a medium for lateral diffusion studies of amphiphiles in bilayer membranes

Magnetically oriented bicelles, in conjunction with stimulated echo (STE) pulsed field gradient (PFG) NMR techniques, were used to investigate the lateral diffusion of polymer-grafted amphiphiles in bilayer membranes. In these experiments, I established the conditions necessary for STE-PFG NMR experiments in bicelles and found that the diffusion coefficient obtained through this method is comparable to that from FRAP. In addition, through such diffusion studies, I investigated the various factors that influence lateral diffusion in bilayer membrane such as obstructions and membrane surface viscosity. Lastly, the results from water diffusion measurements were shown to support the "perforated lamellae" mixed-bicelle morphology of bicelles and provide insights into the complex bicelle architecture.

Keywords: Biochemistry
Chemistry, Physical and theoretical
Physics
Inhibition of return without the inhibition

Inhibition has been used as an explanation for many cognitive phenomena in the past. Recently other non-inhibitory views have been proposed that actually do a better job of accounting for these phenomena, thereby questioning the need for the inhibitory views. In line with this, the present thesis questions the use of inhibition as an explanation of the phenomenon known as inhibition of return. This is accomplished over a series of ten experiments. The first three illustrate the inability of inhibitory theories to account for the data when different configurations of possible target locations are used. An alternative explanation known as attentional momentum is then described and tested with two further experiments. A link is then made between the attentional phenomenon of inhibition of return, and the memory phenomenon of representational momentum, by way of showing that a left-to-right bias is present in both phenomena. This link suggests that a common mechanism might be responsible for both phenomena. Finally, two experiments are conducted that show that both the inhibition of return and the left-to-right bias that is present in the experiments are not due to controlled processes, but are instead the result of low-level automatic processes. Therefore, despite the fact that inhibition is used in the name of the phenomenon, inhibition of return appears to be yet another cognitive phenomenon that has been inappropriately explained as resulting from inhibitory processes.
The differential effects of social and ethnocultural factors on depression and anxiety in Laotian older adults

The objectives of the study was to explore the differential effects of social and ethnocultural factors (independent variables) on depression and anxiety (dependent variables) never before studied specific refugee cohort. Participants were 58 females and 41 males with a Laotian background living in Southwestern Ontario area. Their median age was 67 years with a range from 55 to 94 years. A Hierarchical Multiple Linear Regression technique was used to test the explanatory power of social versus ethnocultural determinants of depression and anxiety (after controlling for life events). Results indicated that the social variables used in the stress-process model derived from research of mainstream communities applied to depression but not to anxiety. One third of the variance in depression (controlling for life events) was explained by income and social support. Variance in anxiety was not explained by income and social support explained only 9% of variance in anxiety. However, ethnic identity, family allocentrism, and ingroup activities, contributed an additional 11% to the variance in anxiety. Ethnocultural specific variables appeared to be more relevant to the understanding of individual differences in the experience of anxiety.
Thermo-mechanical behaviour of plasma sprayed yttria stabilized zirconia thermal barrier coatings

Thermally sprayed ceramic coatings deposited from agglomerated feedstock powder have often demonstrated improved properties relative to coatings produced from conventional powders. These types of coatings have been reported to exhibit better wear resistance and higher adhesion strength compared to conventional deposits. In order to apply these types of coatings on turbine blades and diesel engine combustion chambers, the thermo-mechanical properties of plasma sprayed yttria stabilized zirconia coating were investigated. Creep strains and creep rates were measured using free standing thick coatings (3 mm) loaded in the four-point bend configuration at a range of temperatures (from 800 to 1200°C in air) and loads (27 to 49 N). Creep exponents and activation energy of the coatings were measured and the results were compared. Under the same test conditions the coating produced from agglomerated feedstock showed a lower creep strain than that produced from conventional powders. The creep strain of deposits was correlated to the microstructure of the coating. A model was developed to predict creep behaviour of coatings based on the thickness of splats. The results showed that the creep resistance is directly proportional to the splat thickness; the thicker the splat the higher is the creep resistance. The effect of splat interface on physical and mechanical properties of zirconia, such as thermal conductivity and elastic modulus of coatings, was investigated, too. It was shown that the high density of splat interfaces results in a lower thermal conductivity and elastic modulus.
Characterization of structural and catalytic domains of the Neurospora VS ribozyme

The Neurospora VS ribozyme is a small catalytic RNA that performs site-specific endonucleolytic and ligation reactions and requires counterions for folding and activity. It has a substrate domain that consists of a stably folded hairpin with an internal loop that contains the cleavage site, and a ribozyme domain that can act in either cis or trans on the substrate. I have analyzed the contribution of the sugar-phosphate backbone of the ribozyme to site-specific self-cleavage activity using nucleotide analogues to probe the role of pro-Rp phosphate oxygen and 2′-hydroxyl functional groups. Using nucleotide analogue interference mapping I have identified a large number of backbone functional groups that are important for cleavage. The location of these important phosphates and 2′-hydroxyls in the context of a recently developed helical orientation model of the ribozyme provides insight into the nature of local and long-range tertiary interactions. These interactions help determine the native three-dimensional structure, and provide a large number of functional constraints with which to evaluate future structural models of the ribozyme. Metal ion specificity switch experiments provide the first evidence of localized cation binding sites in the VS ribozyme, the locations of which suggest specific roles in folding and catalysis by the ribozyme. Based on the results of the interference mapping, I proposed the existence of a uridine turn in one of the two three-helix junctions of the ribozyme domain. Using site-directed mutagenesis, kinetic and chemical modification experiments, I provided evidence for the existence of this uridine turn, determined its role in the formation of stable native structure, and showed that it could be functionally substituted with a hairpin. This demonstrates that functionally equivalent three-dimensional RNA structures can be constructed from different secondary structure elements. I proposed a role in catalysis for a functionally important metal ion binding loop in an internal loop in helix VI of the ribozyme domain. Using deletion analysis, I localized the catalytic domain to a subdomain of the ribozyme which contains the candidate active site loop. Using site-directed mutagenesis, kinetic and chemical modification experiments, I demonstrated that this loop is essential for site-specific cleavage activity. Substitution of the candidate active site loop with a variety of sequences revealed an unprecedented flexibility in the requirements for the ribozyme active site.
Rape: an act of genocide or a crime against gender?

Is wartime rape a crime against gender or a genocidal act that implicates both gender and ethnicity? Rape-as-a-crime-against-gender is the very distortion of women's identities and experience that its proponents resist. It implies a one-dimensional victim, whose identity lies substantially in her sex. Its proponents style ethnicity, race, religion or nationality as secondary, if not irrelevant, identities. Rape is reduced to a closed exchange as between man and woman, in which the vulnerabilities to intersecting identities are not merely distorted, but denied. Rape-as-genocide accurately describes a systemic campaign of sexual assault without sacrificing the subjective experience of the victim. Though it acknowledges the community-wide implications to rape, this acknowledgement is peripheral to its real exercise, in which women are conceptualized as beings vested with identities beyond their anatomies, and sex as more than an erotic exchange between its immediate actors.
Dopamine D1 and D2 receptor heterooligomerization: Generation of a novel signaling complex with distinct functions

The neurotransmitter dopamine mediates its function through dopamine receptors, which are members of the G protein coupled receptor superfamily. Dopamine receptors have been demonstrated to functionally synergize in a variety of experimental paradigms. This synergism may be mediated by a mechanism involving the co-localized D1-like and D2-like receptors, which has been observed in native neurons. The aim of this study was to explore the functional interactions between Dl and D2 receptors within cells. Using specific D1 and D2 receptor antibodies, we demonstrated co-localization of D1 and D2 receptors in individual neurons of human and rat brains. By biochemical and biophysical methods, Dl and D2 receptors were observed to form Dl-D2 heterooligomers in vitro and in vivo. The co-activation of D1 and D2 receptors within these heterooligomers resulted in the generation of a calcium signal, which was not observed for Dl and D2 homooligomers. This calcium signal, which was dependent upon the activation of Gq/1 I proteins and intracellular calcium release, was observed to increase CAMKIIalpha levels and its phosphorylation in rat brain. Agonist-mediated desensitization of the calcium signal was demonstrated and this process was dependent on the activity of specific G protein coupled receptor kinases. In addition to this novel signaling property, the D1-D2 heterooligomer also displayed unique cellular trafficking and internalization properties distinct from Dl and D2 homooligomers, resulting in enhanced D2 receptor expression at the cell surface, decreased D1 receptor cell surface expression and agonist-induced D1 and D2 receptor co-internalization. Calcium signaling properties of the DI-D2 heterooligomer were distinct compared to those of the D5 homooligomers and D5-D2 heterooligomers. Overall, the discovery of D1-D2 heterooligomers is important in dopamine receptor research since novel signaling and trafficking properties were demonstrated for dopamine receptor heterooligomers that were not observed for the constituent dopamine receptor homooligomers. These new properties may be important in dopamine-mediated neurotransmission and function in brain.
Performance enhancement and content adaptation in pervasive networking systems

Pervasive computing implies that information permeates through networks to seamlessly reach a user with the highest degree of embeddedness, performance, and reliability. In this thesis, the networks with an end-device are considered as a virtual machine. An associated active pervasive network infrastructure (APNI) framework is proposed to deploy programmable agents at the periphery of the networks to virtualize the interactions between end-users and programmable network elements. Specifically, this work develops: (1) content adaptation for expedited deliveries and cognitive preferences in different user environments, and (2) network-layer reliability to offer adaptations over different network conditions, availability of resources, reliability criteria and user preferences. Data and program slicings are designed to enable concurrent deliveries and computations in APNI. The throughput and delay performances are demonstrated to improve consequently. A prototype has been built and the design framework has been validated through experiments from the user perspective of adaptiveness, reliability, and performance.
The role of carbonic anhydrase in the CO2-concentrating mechanism of cyanobacteria

Heterologous expression of other putative cyanobacterial CAs and characterization of directed cyanobacterial mutants in these proteins failed to indicate that enzymatic activity was associated with any of these putative CAs. Examination of carboxysomal polypeptides from certain marine cyanobacteria and chemolithoautotrophic bacteria resulted in the discovery of epsilon-CA, a novel fourth class of the enzyme. The expression of epsilon-CAs among several of the dominant primary producers in the world's oceans suggests that this carboxysomal CA may also be essential for autotrophic CO2 fixation and may influence the bio-geochemical cycling of carbon on a global scale. Carbonic anhydrase (CA) is a zinc metalloenzyme that catalyzes the interconversion of CO2 and HCO3-. This enzyme family is comprised of three distinct classes (alpha, beta, and gamma), is and distributed throughout all domains of life, where it is involved in many fundamental biological processes, including photosynthesis. In cyanobacteria, a CO2-concentrating mechanism (CCM) operates to elevate the CO 2 concentration around the primary carbon-fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), thereby enhancing photosynthetic performance. The operation of the CCM involves the light-dependent transport of inorganic carbon (Ci) from the medium and the generation of CO2 within the RuBisCO-containing carboxysome, both of which involve CA activity. However, the identity of the proteins involved in these activities and the specific roles they play in the CCM are largely undetermined. This study provides a detailed examination of the CA activity and its involvement in the cyanobacterial CCM. Antibodies raised against the beta-CA from the freshwater cyanobacterium, Synechocystis sp. strain PCC6803, revealed that the enzyme was localized almost exclusively to the carboxysome and was consequently re-designated CcaA (c barbelow;arboxysomal c barbelow;arbonic a barbelow;nhydrase protein A barbelow;). A fully-segregated mutant deficient in CcaA expression was generated that could not survive on air and required elevated levels of CO2 for growth. This mutant retained the ability to transport Ci and accumulate a large intracellular pool, but was incapable of efficiently utilizing the Ci for carbon fixation. This suggests that CcaA functions in the CCM by catalyzing the dehydration of intracellular HCO3 - to CO2 for fixation by the carboxysomal RuBisCO, and is consequently essential for efficient photosynthesis.
Characterization of the MoxR family of AAA+ ATPases

The MoxR family of AAA+ proteins is widespread throughout bacteria and archaea, but surprisingly little is known about their function. Here I present experimental characterization, bioinformatics analysis and an in-depth literature review of the MoxR family. My study reveals at least seven distinct MoxR lineages (subfamilies) including the MoxR Proper (MRP), TM0930, RavA, CGN, APE2220, PA2707 and YehL, and supports a role for these proteins in a variety of different systems. Despite their diversity, however, MoxR proteins appear to share a common method of action, namely an involvement in the assembly of multimeric complexes and a possible role in metal insertion. My gene neighbourhood analysis reveals a clear association between MoxR AAA+ and Von Willebrand Factor Type A (VWA) protein-encoding genes, in addition to a number of subfamily specific associations. I also present an in-depth analysis of the RavA subfamily, including a phylogenetic profiling study across a subset of RavA-containing organisms and extensive experimental characterization of a representative RavA protein from Eschcrichia coli K12 MG 1655. My experimental work includes biochemical, structural, and gene expression analysis. I demonstrate that RavA is a functional ATPase, which forms hexameric rings in the presence of nucleotide. Expression of RavA is under the control of the sigma S promoter, suggesting that it is important under stress response conditions. In addition, I provide evidence supporting an interaction between RavA and its corresponding VWA-encoding protein ViaA, suggesting the two proteins function as a system. RavA also interacts with the inducible lysine decarboxylase enzyme, Ldcl, forming a large cage-like structure which may be important in the regulation of RavA activity. The results of my profiling study and a microarray analysis using RavA/ViaA deletion and overexpression strains identify a number of candidate substrates, interaction partners and systems with which RavA and ViaA appear to be involved. My work provides invaluable information regarding the MoxR proteins and presents a useful groundwork upon which to base future studies.
Sequence skill learning and the transition to automaticity in adults who stutter

The current studies investigated whether persons who stutter (PWS) showed poor motor sequencing skill after practice and on dual tasks compared to fluent speakers (PNS). Studies 1 and 2 compared the speech and nonspeech motor sequencing performance of 9 PWS and 9 PNS over practice. Significant group differences were found in sequence reaction time after practice, and on retention and transfer tests. Study 3 was a replication of Study 2 (the speech sequencing study) with 12 PWS and 12 PNS. Data from Studies 1, 2, and 3 supported the interpretation that PWS were less able than PNS to improve sequence reaction time. PWS were slower on both finger tapping and syllable reading sequences compared to PNS, suggesting that differences were not limited to the speech system. Two follow-up studies investigated the relationship between early stage skill learning and automaticity in PWS. Study 4 investigated the transition to increased automaticity after practice by PWS on a nonspeech sequencing task using a dual-task paradigm. In this study, 12 PWS and 12 PNS completed finger tapping sequences alone (single task condition) and simultaneously with a colour monitoring task (dual task condition). In Study 5, 8 PWS and 8 PNS read aloud nonsense syllable sequences alone (single task condition) and simultaneously with a colour monitoring task (dual task condition). For both studies, each group's speed and accuracy of sequencing performance were compared in each of the two conditions. Compared to the PNS, PWS demonstrated significantly slower performance after practice in the single task finger tapping condition, but not in the syllable reading condition. Studies 4 and 5 single condition results were comparable to the results of Study 1. PWS were also significantly less accurate under dual task conditions for both the finger tapping and the syllable reading experiments relative to PNS. This result suggested that the performance of PWS reflected significantly reduced automaticity development over practice relative to PNS. Deficits in sequence skill learning and automaticity development may represent important etiological components in the development and maintenance of stuttering.