Functional neuroimaging techniques such as near-infrared spectroscopy (NIRS) have been studied in brain-computer interface (BCI) development. Previous research has suggested that the addition of a second brain-monitoring modality may improve the accuracy of a NIRS-BCI. The objective of this study was to determine whether the classification accuracies achievable by a multimodal BCI, which combines NIRS and transcranial Doppler ultrasonography (TCD) signals, can exceed those attainable using a unimodal NIRS-BCI or TCD-BCI. Nine able-bodied subjects participated in the study. Simultaneous measurements were made with NIRS and TCD instruments while participants were prompted to perform a verbal fluency task or to remain at rest, within the context of a block-stimulus paradigm. In five of nine (55.6%) participants, classification accuracies with the NIRS-TCD system were significantly higher (p<0.05) than with NIRS or TCD systems alone. Our results suggest that multimodal neuroimaging may be a promising approach towards improving the accuracy of future BCIs.

There are two contributions of this thesis. The first contribution, described in chapters one through six, involves studing the relationship between the protein packing structure of bacteriorhodopsin (bR) and its function as a proton pump. In 2002, a novel crystallization method published by Bowie and Farham resulted in an unusual antiparallel monomeric packing structure of bicelle bacteriorhodopsin (bcbR) crystals, the spectroscopic properties of which had not been studied. In this thesis, these bicelle bR crystals are investigated to better understand how the changes in the protein tertiary structure affect the function. Specifically: Does the retinal Schiff base retain its ability to isomerize in this unusual protein packing structure of bR? How is the hydration of its binding pocket affected? Does the protein retain the ability to undergo the photocycle and pump protons? If so, how are the rates of the deprotonation/reprotonation of the Schiff base affected by the antiparallel monomer packing structure of the protein? Is Asp85 still the proton acceptor during the deprotonation process of the photocycle? The second contribution of the thesis, described in chapter seven, describes the surface attachment and growth of the biofilm formed by the pathogenic bacterium Streptococcus pneumoniae using attenuated total reflection/Fourier transform infrared spectroscopy (ATR/FTIR). This organism was chosen for its clinical significance; it is one of the organisms suspected in forming biofilms in individuals who develop otitis media, one of the most common causes of ear infections of childhood. In contrast to previous ATR/FTIR experiments examining the formation of biofilms on surfaces, this method is unique in that it combines two techniques - ATR/FTIR and Epifluorescence microscopy which when used together allow for the simultaneous monitoring of the IR spectrum of the S. pneumoniae biofilm as it develops and as provides a method for quantifying total and viable cell counts at various stages during the development.

An alkyl-containing self-assembled monolayer is grafted on the silicon surface by a nature process in solutions. The alkyl thin film was used as the lubricant for the silica interface, usually applied to the MEMS or NENS domains. The ability of reducing friction for silica device at room temperature was improved, but little was known as the thin films existed at higher temperature during device was working or operating. In this study, we used Hexyltrichlorosilane (C6), Dodecyltrichlorosilane (C12), and Octadecyltrichlorosilane (C18) molecules to form self-assembled monolayers (SAMs) on silicon, and these monolayers exhibited different molecular packing properties due to different interactions between the molecules. Fourier transform infrared spectroscopy (FTIR) revealed that the short chain-length (C6) molecules exhibited poor packing on the surface at room temperature, and that the molecular packing of C6 was thermally stable up to 500 K. But the C12 and C18 monolayers exhibited abrupt blue shifts in FTIR at temperatures between 300 and 575 K, with stable packing observed over several temperature ranges. Furthermore, water contact angle measurements showed the C6, C12, and C18 molecular films changed from hydrophobic to hydrophilic as the sample temperature was increased. Atomic force microscopy (AFM) images revealed that pits had formed in the C18 monolayer after the temperature was increased to 460 K, which were caused by the molecular reorganization of C18 on the surface. This resulted in an abrupt change in the friction coefficient for the C18 monolayer at 460K as compared to the short C6 and C12 monolayers. However, the friction coefficients for all the SAM films still increased with temperature. Understanding the temperature-dependent behavior of SAM film molecules will assist in the design of better anti-wear monolayers to improve performance and increase lifetimes in modern MEMS and NEMS devices.

The story of a typical spiral galaxy like the Milky Way is a tale of the transformation of metal-poor hydrogen gas to heavier elements through nuclear burning in stars. This gas is thought to arrive in early times during the assembly phase of a galaxy and at late times through a combination of hot and cold “flows” representing external evolutionary processes that continue to the present. Through a somewhat still unclear mechanism, the atomic hydrogen is converted to molecules that collect into clouds, cool, condense, and form stars. At the end of these stars’ lives, much of their constituent gas is returned to the galaxy to participate in subsequent generations of star formation. In earlier times in the history of the universe, frequent and large galaxy mergers brought additional gas to further fuel this process. However, major merger activity began an ongoing decline several Gyr ago and star formation is now diminishing; the universe is in transitioning to an era in which the structural evolution of disk galaxies is dominated by slow, internal (“secular”) processes. In this evolutionary regime, stars and the gas from which they are formed participate in resonant gravitational interactions within disks to build ephemeral structures such as bars, rings, and small scale-height central bulges. This regime is expected to last far into the future in a galaxy like the Milky Way, punctuated by the periodic accretion of dwarf satellite galaxies but lacking in the “major” mergers that kinematically scramble disks into ellipticals. This thesis examines details of the story of gas from infall to structure-building in three major parts. The High- and Intermediate-Velocity Clouds (HVCs/IVCs) are clouds of H i gas at velocities incompatible with simple models of differential Galactic rotation. Proposed ideas explaining their observed properties and origins include (1) the infall of low-metallicity material from the Halo, possibly as cold flows along filaments of a putative “Cosmic Web”; (2) gas removed from dwarf satellite galaxies orbiting the Milky Way via some combination of ram pressure stripping and tidal disruption; and (3) the supply and return feeds of a “Galactic Fountain” cycling gas between the Disk and Halo. Numerical values of their observed properties depend strongly on the Clouds’ distances. In Chapter 2, we summarize results of an ongoing effort to obtain meaningful distances to a selection of HVCs and IVCs using the absorption-line bracketing method. We find the Clouds are not at cosmological distances, and with the exception of the Magellanic Stream, they are generally situated within a few kiloparsecs of the Disk. The strongest discriminator of the above origin scenarios are the heavy element abundances of the Clouds, but to date few reliable Cloud metal- licities have been published. We used archival UV spectroscopy, supplemented by new observations with the Cosmic Origins Spectrograph aboard the Hubble Space Telescope and H I 21 cm emission spectroscopy from a variety of sources to compute elemental abundances relative to hydrogen for 39 HVC/IVC components along 15 lines of sight. Many of these are previously unpublished. We find support for all three origin scenarios enumerated above while more than doubling the number of robust measurements of HVCs/IVCs in existence. The results of this work are detailed in Chapter 3. In Chapter 4 we present the results of a spectroscopic study of the high-mass protostellar object NGC 7538 IRS 9 made with the Texas Echelon Cross Echelle Spectrograph (TEXES), a sensitive, high spectral resolution, mid-infrared grating spectrometer and compare our observations to published data on the nearby object NGC 7538 IRS 1. Forty-six individual lines in vibrational modes of the molecules C₂H₂, CH₄, HCN, NH₃ and CO were detected, including two isotopologues (¹³CO, ¹²C¹⁸O) and one combination mode ([nu]₄+[nu]₅ C₂H₂). Fitting synthetic spectra to the data yielded the Doppler shift, excitation temperature, Doppler b parameter, column density and covering factor for each molecule observed; we also computed column density upper limits for lines and species not detected, such as HNCO and OCS. We find differences among spectra of the two objects likely attributable to their differing radiation and thermal environments. Temperatures and column densities for the two objects are generally consistent, while the larger line widths toward IRS 9 result in less saturated lines than those toward IRS 1. Finally, we compute an upper limit on the size of the continuum-emitting region (~2000 AU) and use this constraint and our spectroscopy results to construct a schematic model of IRS 9. In Chapters 5 and 6, we describe studies of the bright, nearby, edge-on spiral galaxies NGC 4565 and NGC 5746, both previously classified as type Sb spirals with measured bulge-to-total luminosity ratios B/T ≃ 0.4. These ratios indicate merger-built, “classical” bulges but in reality represent the photometric signatures of bars seen end-on. We performed 1-D photometric decompositions of archival Hubble Space Telescope, Spitzer Space Telescope, and Sloan Digital Sky Survey images spanning a range of wavelengths from the optical to near-infrared that penetrate the thick midplane dust in each galaxy. In both, we find high surface brightness, central stellar components that are clearly distinct from the boxy bar and from the disk; we interpret these structures as small scale height “pseudobulges” built from disk material via internal, resonant gravitational interactions among disk material − not classical bulges. The brightness profiles of the innermost component of each galaxy is well fitted by a Sersic function with major/minor axis Sersic indices of n = 1.55±0.07 and 1.33±0.12 for NGC 4565 and n = 0.99±0.08 and 1.17 ± 0.24 for NGC 5746. The true “bulge-to-total” ratios of these galaxies are considerably smaller than once believed: 0.061+0.009 and 0.136 ± 0.019, −0.008, respectively. Therefore, more galaxies than we thought contain little or no evidence of a merger-built classical bulge. We argue further that a classical bulge cannot hide behind the dust lane of either galaxy and that other structures built exclusively through secular evolution processes such as inner rings, both revealed through the infrared imagery, argue strongly against any merger violence in the recent past history of these objects. From a formation point of view, NGC 4565 and NGC 5746 are giant, pure-disk galaxies, and we do not understand how such galaxies form in a ΛCDM universe. This presents a challenge to our picture of galaxy formation by hierarchical clustering because it is difficult to grow galaxies as large as these without making big, classical bulges. We summarize the work presented in this thesis in Chapter 7 and conclude with speculations about the future direction of research in this field. / text

Thesis (MTech. degree in Pharmaceutical Sciences)--Tshwane University of Technology, 2009. / Quality control procedures are vital in the pharmaceutical industry to guarantee the authenticity and quality of products. A major challenge in quality assurance of herbal material is the vast variation of active constituents in plants from the same species. As a result of this variation, the selection of only a few compounds as criteria for quality control is inadequate. Pelargonium (P.) sidoides is indigenous to South Africa and highly valued by traditional healers as a remedy to treat coughs, upper respiratory tract irritations and gastrointestinal conditions. An ethanolic extract of P. sidoides is used in the proprietary herbal tincture known as Umckaloabo®. The composition and concentration of polyphenols are parameters which determine the quality of this herbal medicine because it provides several therapeutic benefits in the non-specific medicinal treatment of infectious diseases. Despite the commercial development of P. sidoides very few studies have been conducted to document the full phytochemical range of variation for natural populations and no study has been published on the development of a fast accurate quality control method for the validation of raw material.

Les naines brunes sont des astres incapables de déclencher et soutenir des réactions nucléaires dans leur cœur. En l’absence de cette source d’énergie, leur luminosité diminue avec le temps jusqu’à leur extinction complète. Leur flux aux longueurs d’onde de 0,8 à 2,35 μm est particulièrement altéré par l’humidité contenue dans l’atmosphère terrestre, ce qui complique l’étude de ces astres. Le but de la présente recherche est de vérifier si la division par un spectre d’étoile A0 est un moyen de corriger l’altération causée par l’atmosphère terrestre sur cette partie de leur spectre. Tout d’abord, des notions, pertinentes à la compréhension de ce travail, sont abordées. L’introduction présente quelques notions sur les naines brunes et sur l’atmosphère terrestre. Le deuxième chapitre concerne le traitement des données. Il traite de la calibration, de la mise en évidence du problème de non-répétabilité de la position de la fente du spectromètre SIMON ainsi que de ses causes. Il porte aussi sur l’uniformisation de la réponse des pixels et de la soustraction du ciel pour extraire les spectres. La méthode employée pour étudier l’effet de l’atmosphère terrestre sur les spectres de naines brunes y est présentée. Le troisième chapitre analyse les résultats obtenus par l’utilisation de l’étoile de référence de type A0 comme calibration pour corriger le spectre de naine brune, en assumant un même effet de l’atmosphère terrestre sur les deux types d’astres. Nous ne pouvons conclure, avec certitude, que l’absorption tellurique affecte de la même façon les deux spectres ni de quelle façon exactement ils sont affectés. Une recherche supplémentaire nécessitant de nouvelles prises de données à des masses d’air et à des taux d’humidité variés est requise. / Brown dwarfs are celestial bodies unable to sustain nuclear reactions. For this reason their luminosity declines until complete extinction. Their flux, particularly in the band between 0,8 and 2,35 μm, is absorbed by the water vapor in the terrestrial atmosphere. The goal of this research is to find a way to correct this part of their spectra affected by this effect. First, general notions needed to understand the project are exposed. The second chapter concerns the data reduction. The calibration, the problem of the position repeatability of the slit of the spectrometer SIMON and his cause are exposed. It discusses techniques to even up the pixels’ response and the substraction of the sky from the spectra. The method used to study the atmosphere effect on brown dwarf spectra is presented. The third chapter analyses the results that use the A0 reference star to correct the brown dwarf spectrum. We cannot conclude that the A0 spectrum is affected in the same way as the brown dwarf spectrum by the terrestrial atmosphere. The data from a single night do not allow a good analysis of this effect as a function of air mass and humidity level. Others missions are needed.

A combined attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR)-atomic force microscopy (AFM) platform was used to visualize and characterize membranolytic protein- and peptide-membrane interactions, allowing spectroscopic details to be correlated with structural features. Modifications to a previous combined platform permitted IR results for physiologically-relevant protein or peptide concentrations as well as provided nanometer-resolution height data for AFM. This combination provides greater insight than individual techniques alone. The interactions of hemolytic sticholysin proteins on a model red blood cell membrane showed evidence of conformational changes associated with a membrane-induced organization. In addition, the examination of a de novo cationic antimicrobial peptide on a model bacterial membrane showed that the peptide adopted a helical structure upon interaction with the membrane, and also provided evidence of membrane disruption and peptide aggregation. These results demonstrate that ATR-FTIR-AFM can be a powerful tool for understanding protein- and peptide-membrane interactions.

The eldana stalk borer (Eldana saccharina Walker) is the most serious pest of the Southern African sugarcane industry, and it is imperative that effective control measures are available to minimize economic damage. Because conventional control methods have had limited success, cultivar resistance is seen as the most viable method of controlling infestation. However, due to the space- and time-consuming nature of the present screening methods, only small numbers of cultivars can be tested relatively late in the Plant Breeding selection programme. Increased resistance in breeding and selection populations is therefore slow. Buds are a preferred entry point of eldana larvae as they are softer than the rind that is present on the rest of the stalk surface. Preliminary results by other workers suggested that near infrared spectroscopy (NIRS) could provide a rapid screening method for the chemical profile in bud scales, the outer coating of buds and therefore the first contact point of an invading larva. If feasible, analysis of samples using this method could be done in the South African Sugar Experiment Station's (SASEX) stage two selection trials, providing an early indication of eldana resistance on large numbers of cultivars, without the necessity of separate trials. However, knowledge of how environments, position of bud scales on the stalk and age affect NIRS is required in order to determine the feasibility of the method. Planting of a trial with an identical set of genotypes across a range of environments, sampled at a number of ages, would provide the necessary information on environmental effects, whilst simultaneously providing the necessary range of samples to develop a calibration between bud scale chemical profiles and eldana resistance ratings. Inheritance patterns of the characteristics being measured is also required if they are to be used in a breeding programme. The original work by Rutherford (1993) was carried out on only five calibration sets (a set of standard clones with relatively well-known eldana resistance ratings), and different sets were not comparable due to what was assumed to be environmental differences between calibration sets. One aspect of the current experiment was to examine more closely the effect of genotype x environment interaction (G x E) on the performance of the NIRS technique under a range of conditions. Two sites were chosen to represent the conditions encountered in trials carried out by SASEX. The crops were sampled at three ages, representing the range of ages at which sugarcane is harvested in South Africa. Two locations on the stalk were also examined, top and bottom, for removal of bud scales, based on the assumption that aging of bud scales may affect chemical composition. A new NIRSystems 6500 instrument was acquired during the course of this study. Data from the new instrument indicated that there were no longer differences between the different calibration sets, and therefore no longer differences between environments. Spectra for different samples were very close, the differences being of the same scale as those recorded with repeated measures of the same samples, or between the readings for the standard solvent solution. This led to the conclusion that the differences observed on the original NIRSystems 5000 instrument were due to instrument error, not environmental differences. More importantly, the different calibration sets were not comparable despite being similar to each other. Prediction from one calibration set to another was low. These observations led to the conclusion that NIRS was not a suitable method for determining chemical compounds associated with tolerance of sugarcane genotypes to eldana borer. The original NIRS instrument was subject to error, and the small number of calibration sets included in the study led to the erroneous conclusion that NIRS was suitable for the prediction of varietal tolerance to eldana. With the acquisition of the new instrument, the errors generated by the old instrument became apparent. With the increase in number of calibration sets included in the study, it also became apparent that a global calibration covering all environments was not possible. An analysis of the heritability of the chemical compounds associated with eldana resistance was also included in this study. A biparental progeny design of 24 crosses with 33 unselected offspring per cross was used. This trial would have been analysed once the calibration had been developed using the environmental trial, and it would have provided knowledge of the breeding behaviour of the chemical compounds associated with tolerance to eldana. Because the NIRS technique proved to be unsuitable for detection of chemical compounds associated with eldana resistance, the heritability of these chemical compounds could not be studied. As the NIRS study did not produce data, the G x E interaction analysis and determination of heritability was applied to the bud scale mass data set. This study showed a relatively low positive correlation between bud scale mass and resistance to eldana. The broad sense heritability estimate for bud scale mass from the G x E interaction analysis was 0.45, and the narrow sense heritability estimate from parent-offspring regression analysis was approximately 0.27, suggesting a low degree of genetic determination in bud scale mass. The G x E interaction analyses gave varying results depending on the method used. The ANOVA analysis suggested that ages, sites and years had an effect on bud scale mass, while deviation from maximum plot showed no significance for G x E interactions. The number and choice of genotypes selected as unstable also varied with the method used to determine the stability of individual genotypes. Regression analysis and rank order analysis revealed a number of unstable genotypes, whilst stability variance and ecovalence, which produced similar results, detected only two unstable genotypes. In the rank order analysis correction of data to remove genotype effect, reduced the number of unstable genotypes, suggesting that the G x E interaction effect was partially confounded with the bud scale mass of the genotypes. This was a more reliable method than the uncorrected rank order analysis, and would be the preferred analysis type of all those tried. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2003.

A combined attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR)-atomic force microscopy (AFM) platform was used to visualize and characterize membranolytic protein- and peptide-membrane interactions, allowing spectroscopic details to be correlated with structural features. Modifications to a previous combined platform permitted IR results for physiologically-relevant protein or peptide concentrations as well as provided nanometer-resolution height data for AFM. This combination provides greater insight than individual techniques alone. The interactions of hemolytic sticholysin proteins on a model red blood cell membrane showed evidence of conformational changes associated with a membrane-induced organization. In addition, the examination of a de novo cationic antimicrobial peptide on a model bacterial membrane showed that the peptide adopted a helical structure upon interaction with the membrane, and also provided evidence of membrane disruption and peptide aggregation. These results demonstrate that ATR-FTIR-AFM can be a powerful tool for understanding protein- and peptide-membrane interactions.

This study combines noninvasive hybrid diffuse optical spectroscopies [near-infrared spectroscopy (NIRS) and diffuse correlation spectroscopy (DCS)] with occlusive calibration for continuous measurement of absolute blood flow (BF), tissue blood oxygenation (StO2), and oxygen consumption rate (VO2) in exercising skeletal muscle. Subjects performed rhythmic dynamic handgrip exercise, while an optical probe connected to a hybrid NIRS/DCS flow-oximeter directly monitored oxy-, deoxy-, and total hemoglobin concentrations ([HbO2], [Hb], and [tHb]), StO2, relative BF (rBF), and relative VO2 (rVO2) in the forearm flexor muscles. Absolute baseline BF and VO2 were obtained through venous and arterial occlusions, respectively, and used to calibrate continuous relative parameters. Previously known problems with muscle fiber motion artifact in optical measurements were mitigated with a novel dynamometer-based gating algorithm. Nine healthy young subjects were measured and results validated against previous literature findings. Ten older subjects with fibromyalgia and thirteen age-matched healthy controls were then successfully measured to observe differences in hemodynamic and metabolic response to exercise. This study demonstrates a novel application of NIRS/DCS technology to simultaneously evaluate quantitative hemodynamic and metabolic parameters in exercising skeletal muscle. This method has broad application to research and clinical assessment of disease (e.g. peripheral vascular disease, fibromyalgia), treatment evaluation, and sports medicine.