Children and adolescents are thought to use oxidative metabolism to a greater extent than adults during high intensity exercise. The studies reported in this thesis examine the nature and implications of age-related differences in muscle metabolism during high intensity exercise and recovery. Chapter 4 concluded that during heavy intensity exercise, phosphocreatine (PCr) kinetics did not differ with age or sex, while Chapter 5 revealed that during very heavy intensity exercise, the fundamental τ was slower and slow component amplitude greater in men compared with adolescent boys, indicating that exercise intensity might play a role in determining age-related differences in muscle metabolism. In Chapter 6, two bouts of very heavy intensity exercise were completed, and prior exercise reduced the PCr slow component amplitude in men but not boys. Deoxyhaemoglobin (HHb) kinetics was faster in adolescents compared with adults during both heavy and very heavy intensity exercise, indicating that matching of oxygen delivery to oxygen utilisation is less precise at the onset of exercise in adolescents compared with adults. PCr recovery from high intensity exercise was faster in boys than men, but not different in girls and women, as described in Chapter 7. The speed of PCr recovery was correlated with maturity in adolescents, but was not correlated with end-exercise [PCr] or pH. Two different tests to measure mitochondrial capacity in adolescents were evaluated in Chapter 8, and a fitted curve and gated test were both used to determine PCr recovery kinetics. Finally, in Chapter 9, age-related differences in muscle metabolism and oxygenation during fatiguing exercise were examined; a strong trend for greater fatigue in adults compared with adolescents was accompanied by greater metabolic perturbation in adults. Overall, these data show that muscle metabolism and oxygenation differs between adolescents and adults during and following very high intensity exercise.

This thesis presents a unique design for an infrared spectrometer based on a MEMS Binary Fresnel Zone Plate for the purpose of assessing the health of oil-impregnated high voltage (HV) equipment. It does so by measuring dissolved gases within it. These gases include carbon monoxide, carbon dioxide, methane, ethane, ethylene, and acetylene. These gases are currently measured using numerous technologies such as gas combustion, gas chromatography, photoacoustic spectroscopy, and FTIR spectroscopy. Each of these technologies have their advantages and disadvantages. The design presented in this thesis consists of an analysis of how the various Binary Zone Plate parameters affect its spectral resolution and transmission efficiency. Simulations show that increasing the number of zones and the focal length, as well as decreasing the aperture diameter, increases the spectral resolution of the spectrometer. Simulations also show that transmission efficiency is proportional to the number of zones and the aperture diameter. This thesis presents a theoretical argument for how one zone plate lens can be used to measure all dissolved gases present in HV equipment. Lenses for the visible and infrared ranges were fabricated in the University of Manitoba NSFL Cleanroom. The lenses were then tested in an optical setup. The results show that the visible light experiments were successful in achieving appropriate spectral discrimination by changing the distance between the aperture and the lens. The results from the infrared experiment show that a detector was able to discriminate between full and no incident radiation. / May 2017

Variability in neural activity has historically been treated as noise, in favour of deriving estimates based on central tendency (e.g., mean). Recently, researchers have shown that variability and mean confer different sources of information and that increased variability in neural activity is associated with superior behavioural performance and that it decreases during late-life. Although mounting evidence suggests that neural variability is beneficial, it is less clear whether these findings are driven by within- or between-person factors and whether they are apparent during higher-order cognitive tasks. Further, variability can be derived in several different ways, drawing into question its congruence across operationalizations. The present investigation sought to separate within- and between-person sources of variance in order to ascertain what was driving any observable effects in three operationalizations of cerebral oxygenation, computed based on central tendency (mean), variability (standard deviation) and signal complexity (multivariate multiscale entropy). 25 older adults (71-81 years of age) completed two tasks of executive functions while undergoing assessment using functional near infrared spectroscopy. Time-varying covariation models were employed to estimate the effects of cerebral oxygenation on behavioural performance, as well as the moderating effects of age and fall status. Findings suggest that mean and variability are differentially associated with behavioural performance and are increased in older adults at greater fall risk. Whereas mean based computations were positively associated with more accurate and faster responding, variability based computations were primarily associated with faster responding only and occurred in non-overlapping regions of prefrontal cortex. Future studies of neural variability may consider examining within- and between-person factors and operationalizing signal complexity in cerebral oxygenation over longer time periods to examine its effects over multiple time scales. / Graduate / drewh@uvic.ca

Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to monitor organometallic reactions. It is fast at generating spectrum, soft to fragile organometallic compounds and sensitive to intermediates in low concentration. When coupled with the pressurized sample infusion (PSI) that helps to continuously inject reacting solution to the MS, both an inert-gas atmosphere and real-time reaction monitoring can be achieved. Also collision induced dissociation (CID) of MS can be used to probe the relative binding affinities of phosphine ligands in ruthenium complexes. PSI ESI-MS can be coupled with Fourier transform infrared spectroscopy (FTIR) to monitor the rhodium-catalyzed hydroacylation simultaneously. This technique expands the dynamic range to 5 magnitudes. The effect of mass-transfer in heterogeneous hydrogenation of charge-tagged alkyne was also studied by PSI ESI-MS. In this study cross area, stirring effect, catalyst loading and hydrogen concentration were considered and tested. Also in the study an interesting finding reveals in heterogeneity of the solution. Relative binding affinities of different phosphine ligands were attained from comparing the relative intensities of fragmentation products from MS/MS. And the phosphine ligand substitution reaction was monitored by the ESI-MS in a real-time manner. A competitive dissociative substitution mechanism was proposed and confirmed by the simulation and modeling of COPASI. / Graduate

The Composite Infrared Spectrometer (CIRS) instrument onboard the Cassini spacecraft will be used to probe the atmosphere and surface of Saturn's giant moon Titan. This thesis describes an investigation of the capabilities of CIRS as a remote sounding instrument. To enable infrared spectra to be computed, a radiative transfer code has been adapted for Titan's atmosphere. The atmospheric model, including gases and aerosol particles, was refined by comparison of synthetic spectra with results from the IRIS instrument of the Voyager 1 spacecraft. Characteristics of the instrument have been deduced from laboratory measurements. The size and shape of the field of view was found for the mid-infrared detectors. A Fourier code was developed to transform the raw data (interferograms). Blackbody spectra taken with the flight instrument were analysed to calculate the noise equivalent radiance for the detectors of all three focal planes. Finally, the data regarding instrument performance was used in combination with the predictive radiative transfer code to consider in detail the extent to which gaseous bands and other spectral features will be observable for a variety of limb and nadir viewing modes. Current observing strategies are reviewed and recommendations for scientific emphasis in the light of the actual instrument performance are made.

Fourier Transform Infrared spectroscopy is used as a diagnostic tool in biological and physical sciences by characterizing the samples based on infrared light-matter interaction. In the case of biological samples, Activation of Jurkat T-cells in culture following treatment with anti-CD3 (Cluster of Differentiation 3) antibody is detectable by interrogating the treated T-cells using the Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) Spectroscopy technique. Cell activation was detected within 75 minutes after the cells encountered specific immunoglobulin molecules. Spectral markers noted following ligation of the CD3 receptor with anti CD3 antibody provides proof-of-concept that ATR-FTIR spectroscopy is a sensitive measure of molecular events subsequent to cells interacting with anti-CD3 Immunoglobulin G (IgG). ATR-FTIR spectroscopy is also used to screen for Colitis in chronic (Interleukin 10 knockout) and acute (Dextran Sodium Sulphate-induced) models. Arthritis (Collagen Antibody Induced Arthritis) and metabolic syndrome (Toll like receptor 5 knockout) models are also tested as controls. The marker identified as mannose uniquely screens and distinguishes the colitic from the non-colitic samples and the controls. The reference or the baseline spectrum could be the pooled and averaged spectra of non-colitic samples or the subject’s previous sample spectrum. The circular dichroism of titanium-doped silver chiral nanorod arrays grown using the glancing angle deposition (GLAD) method is investigated in the visible and near infrared ranges using transmission ellipsometry and spectroscopy. The characteristics of these circular polarization effects are strongly influenced by the morphology of the deposited arrays. Studies of optical phonon modes in nearly defect-free GaN nanowires embedded with intrinsic InGaN quantum dots by using oblique angle transmission infrared spectroscopy is described here. These phonon modes are dependent on the nanowire fill-factor, doping densities of the nanowires and the presence of InGaN dots. These factors can be applied for potential phonon based photodetectors whose spectral responses can be tailored by varying a combination of these three parameters. The optical anisotropy along the growth (c-) axis of the GaN nanowire contributes to the polarization agility of such potential photodetectors.

Challenges encountered in pathogen identification and detection include the genetic heterogeneity of strains within species of some foodborne pathogens, isolation of injured cells, mixed strains or mixed species contamination of foods, and differentiation between viable and dead cells. The first objective of this research was to evaluate an isolation medium that was based on time-delayed release (5 to 6 h) of selective agents in tablet format to a modified Listeria recovery enrichment broth (mLRB) medium for enhanced and rapid recovery of injured Listeria. The second objective involved the use of Fourier transform infrared (FT-IR) spectroscopy and chemometric analysis for the differentiation of: Listeria monocytogenes epidemic clones (ECs); viable versus heat-killed populations; different mixed strains and mixed species of Listeria; and different injury treatments and repair in Listeria populations. Nitrite- or acid-injured Listeria at approximately 10 CFU/ml were recovered in mLRB medium, and cell populations enumerated at various times (12 to 48 h) of incubation at 37oC. Analysis of variance revealed that acid-injured Listeria populations in mLRBS6 (mLRB plus the selective agents at 6 h) were significantly higher (P < 0.05) than those in mLRBS0 (mLRB plus the selective agents at 0 h) at 24 h; however, the differences in populations on these two media were not significant for nitrite-injured Listeria. Cell populations of four strains of Listeria recovered in mLRBTD (mLRB plus the time-delayed release tablets of the selective agents) were significantly higher than when those strains were enriched in the U.S. Food and Drug Administration (FDA), International Organization for Standardization (ISO), and U.S. Department of Agriculture (USDA) broths at 24 h. Comparison between artificially contaminated milk and meat samples with a four-strain cocktail of Listeria resulted in cell populations that were significantly higher (P < 0.05) on mLRBTD for contaminated meat than on mLRBTD for contaminated milk at 24 h. FT-IR spectroscopy in the mid-infrared region (4000 to 600 cm-1) and chemometrics was successfully applied to discriminate L. monocytogenes strains belonging to the same EC (ECII or ECIV) (100% accurate spectral classification), intact and heat-killed populations of each EC strain (100% accurate spectral classification), and spectral wavenumbers 1650 to 1390 cm-1 were used to differentiate heat-killed from intact populations. FT-IR spectroscopy and chemometrics in the wavelength region 1800 to 900 cm-1 could successfully discriminate different mixed strains of L. monocytogenes (98.15% accurate spectral classification) and different mixed species of L. monocytogenes and L. innocua (92.06% accurate spectral classification) from individual strains; Wavelength range 1800 to 900 cm-1 was successfully used to discriminate between intact, acid-injured, and heat-injured Listeria, with repaired cells from acid and heat treatments clustering closer to intact cells (93.33% of spectra accurately classified). Delayed-addition of selective agents to broth medium improves recovery of injured Listeria by allowing repair time, could minimize contamination through manual addition of selective agents, and saves analyst time; FT-IR spectroscopy is a highly discriminatory and reproducible technique that can be used for the differentiation of strains and various physiological states of Listeria.

Dosage du polyisoprène et des résines de la biomasse de guayule (Parthenium argentatum) par spectroscopie proche infrarouge (SPIR) Méthodes d'extraction par solvant de référence Un protocole basé sur l'extraction accélérée (ASE) avec l'acétone (EA) (résine) puis l'hexane (EH) (polyisoprène, PI) a été sélectionné et optimisé (rendement maximal; adapté à l'analyse de séries) ; quantification d'abord basée sur le poids de l'extrait (gravimétrie). L'EH est maximal à 120°C après étapes avec l'acétone à 40°C (plan d'expérience). La contamination croisée a été confirmée par SEC et FTIR (5 à 29%), conduisant à une deuxième méthode basée sur résine et PI et non plus sur EA et EH, incluant le PI de faible masse molaire (Mw) de l'EA. Ces 2 méthodes de référence ont servi à calibrer la SPIR (chimiométrie/PLS, coeff. beta) afin de relier signature spectrale, PI, résine. ASE-SPIR, couplés ici pour la première fois, ont été plus performants (R² 0.96; 0.98; RPD 4.8; 4.6; EA et EH resp.) que les méthodes de la littérature, grâce aux 215 échantillons représentatifs (génotypes, saison, âge du guayule, climat). La méthode tenant compte de la contamination est moins performante (erreur exp. due aux analyses SEC et FTIR; variation de composition des résines). Ayant montré la dégradation du PI au cours de l'extraction, un autre protocole a été étudié (biomasse humide, un solvant, une seule étape, 20°C) afin d'accéder au Mw «natif », donnant 2.106 g au lieu de 6.105 avec la biomasse séchée; il faut donc être prudent face aux Mw de guayule de la littérature. Ce travail montre la nécessité de tenir compte de la complexité de la biomasse de guayule (échelle cellulaire/PI vacuolaire, résine des canaux; moléculaire/instabilité chimique) lors de l'extraction du PI pour l'analyse structurale. Ces méthodes analytiques ont contribué à produire des prototypes (gant non allergisant, pneu) à haut Mw et à l'acclimatation en Europe dans le cadre du projet EU-Pearls. / Measurement of resin and polyisoprene in Parthenium argentatum (guayule) biomass using near infrared spectroscopy (NIRS) -Associated solvent-based reference methods .A protocol based on sequential extraction with acetone (resin) and hexane (polyisoprene, PI) with accelerated solvent extraction (ASE) was optimized and selected (maximized yield; adapted to large series) instead of Soxhlet and homogenizer. Quantification was first based on extract weight (gravimetry). Hexane extract was maximized at 120°C, after acetone steps at 40°C, through an experimental design. Cross contamination was confirmed and quantified (5 to 29%; SEC and FTIR). This gave a second method based on resin and PI, instead of crude extracts, accounting for low average molar mass PI (Mw) extracted by acetone instead of hexane. Both reference methods were used for calibrating NIRS applied to powdered biomass, with chemometric tools (PLS loadings, beta coefficients) to interpret spectral bands vs PI-resin relationship. ASE, not used before as reference, is highly reliable, and calibration with gravimetry (R² 0.96; 0.98; RPD 4.8; 4.6; for acetone and hexane extract) better than published data, thanks to the 215 samples covering genotypes, harvest date, plant age, climate. The method using cross contamination was less efficient because of higher experimental error induced by additional SEC and FTIR, and change in resin composition. Having set NIRS methods, a new protocol (single solvent THF, minimized processing, 20°C, fresh biomass) was designed to avoid degradation, yielding PI extracts with Mw above 2.106g/mole, closer to in vivo structure (6.105 when using dried guayule); caution to sample preparation in literature dealing with guayule PI structure. This calls for considering the complex structure of guayule biomass (PI in cells; resin in ducts; chemical instability) when extracting PI. These methods allowed producing high PI Mw glove and tire prototypes and domesticating this new crop in Europe within the EU-Pearls project.

Doctor of Philosophy / Department of Chemical Engineering / Jennifer L. Anthony / Ionic liquids are low melting salts composed of an organic cation and an inorganic or organic anion. Ionic liquids are of interest for their wide range of applications and unique properties, such as the negligible vapor pressure of some types of ionic liquids, and the ability to modify ionic liquid properties by selection of the cation or anion. It has been hypothesized that over one million binary ionic liquids (meaning a single cation/anion pair) are possible. Due to the vast number of potential combinations, it should be possible to design ionic liquids specifically for an application of interest. One potential application is their use as protein solvents. However there is little understanding of how ionic liquids affect proteins. This research examined the solubility and secondary structure of the hydrophobic corn protein zein in seven ionic liquids and three conventional solvents as a function of temperature and solvent properties. Zein’s solubility in the solvents was measured gravimetrically from 30 to 60 degrees Celsius. Solubility was then related to solvent properties to gain an understanding of what solvent properties are important, and how to design an ionic liquid to dissolve zein. It was found that a good solvent for zein has a small molecular volume, a low polarity, and is a weak hydrogen bond acceptor. Infrared spectroscopy with curve fitting was used to examine the secondary structure of zein as a function of both solvent and temperature from 25 to 95 degrees Celsius. It was found that most of the ionic liquids change zein’s secondary structure, but those secondary structure changes were not affected by temperature. Aprotic ionic liquids increase the amount of β-turn secondary structure through non-polar interactions between the mixed aromatic-alkyl imidazolium cations and the non-polar portions of the zein. Strong hydrogen bond accepting molecules were found to increase the amount of β-turn secondary structure. It is hypothesized from this research that suitable solvents for zein will have a small molar volume, low polarity, and be poor hydrogen bond acceptors. This combination of properties will enhance zein’s solubility and limit secondary structure changes that can harm protein properties.

Master of Science / Department of Chemical Engineering / J.R. Schlup / The curing reaction for the amine epoxy resin system of phenyl glycidyl ether (PGE) with metaphenylene diamine (mPDA) was investigated using two-dimensional correlation spectroscopy in the near-infared region (2DNIR). Synchronous and asynchronous correlation maps were generated using 2Dshige© software. The characteristic NIR band assignments were made, including the identification of new peaks for the O-H combination band in the 4825-4750 cm[superscript]-1 region and the CH stretching vibration overtone at 6018 cm[superscript]-1. Finally, the data suggests the reaction proceeds as follows: the appearance of the OH groups and C-H backbone vibrations occurs before the primary amine reactions and epoxide rings disappear.