Water is a major factor limiting cotton production and farmers must aim to optimise crop water use through timely irrigation scheduling decisions. Airborne video imagery when calibrated with a low density of ground based observations, offers the potential for near real time monitoring of crop condition, through sequential coverages of entire cotton fields. Using commercially available video equipment mounted on a light aircraft images were acquired of field experiments that were established in commercial cotton fields to test if the imagery could monitor changes in crop condition. Ground data collected from these experiments were used to evaluate green, red, near infrared and thermal band imagery for irrigated crop management. Prior to acquiring imagery, a ground radiometer study was conducted to investigate if canopy reflectance changed with the onset of crop water stress. Canopy reflectance decreased in the near infrared and green bands during the five day period prior to the crop's normal irrigation date. Red reflectance increased only after the crop irrigation was due, when the crop was suffering from water stress. The greatest change in canopy reflectance was in the near infrared region, attributable in part to a decrease in ground cover caused by canopy architectural changes including leaf wilting. The results of this experiment were used to select spectral filters for the video cameras. A range of crop conditions were identified in the imagery including; crop waterlogging, wheeltrack soil compaction, crop nitrogen status, different varieties, crop maturity, canopy development, soil moisture status, cotton yield and nutgrass weeds. Thermal imagery was the most successful for distinguishing differences in the crop soil moisture status. Near infrared imagery was most closely related to crop canopy development and is recommended for monitoring crop growth. Linear relationships were found between spectral responses in the imagery, crop reflectance (%) and crop temperature measured on the ground. Near infrared reflectance linearly increased, while spectral responses in the green, red and thermal bands exhibited an inverse relationship with plant height and ground cover. Imagery collected early in the season was affected by the soil background. Final lint yield was related to imagery in the red band. As the soil moisture level declined, crop temperature increased while reflectance in the green band decreased. To ensure an accurate relationship between soil moisture and thermal imagery, separate calibration equations are recommended for different stages in the season. Green, red and near infrared imagery were affected by the sun angle that caused one side of the imagery to appear brighter than the other. This problem was greatest in the green and red bands, but was not evident in the thermal imagery. Changes in solar radiation and air temperature on some occasions caused greater variation to the imagery between flights, than changes in crop condition per se. Therefore, it is not aIways possible to directly determine the soil moisture status from canopy temperature. Further research is required to correct imagery for environmental variables such as solar radiation, air temperature and vapour pressure deficit. Thermal imagery offers many improvements to current irrigation scheduling techniques including the facilitation of locating more representative ground sampling points. Thermal imagery also enables cotton fields on a farm to be ranked according to their soil moisture status. This then provides farmers with a visual picture of the crop water status across the whole farm, which is not possible using conventional ground scheduling techniques. At this stage, airborne video imagery will not replace soil moisture data collected for irrigation scheduling, however offers potential to enhance irrigation scheduling methods by addressing the problem of crop variability within cotton fields.

The prevalence of work-related muscle pain (WRMP) is large in the general population in the industrialized world. Despite significant advances over recent years in some research areas, the mechanisms of why WRMP occurs and the pathophysiological mechanisms behind the disorders are still unclear. One suggested explanation is that WRMP is caused initially by a limitation of the local muscle circulation and oxidative metabolism. There is a lack of objective methods to gauge the development and diagnosis of WRMP. Near infrared spectroscopy (NIRS) is a non-invasive technique that allows for determinations of oxygenation and blood flow. The purpose of this thesis was to evaluate NIRS (1) as a method for measuring muscle oxygenation and hemodynamics for the extensor carpi radialis (ECR) and trapezius descendens muscles (TD), and (2) to investigate whether variables measured by NIRS differed between patients diagnosed with WRMP and healthy subjects. Several variables of NIRS were produced and investigated. These included muscle oxygenation (StO2%), changes during contractions (ΔStO2%) and StO2% recovery (Rslope), total hemoglobin (HbT) as an indication of blood volume and its changes during contractions (ΔHbT). In addition, for the ECR, by applying an upper arm venous occlusion (VO) HbTslope increase as a surrogate of blood flow, and for both VO and arterial occlusion (AO) HHbslope increase (i.e. deoxyhemoglobin slope) as a surrogate of oxygen consumption were variables of interest. A first objective was to determine how StO2% and HbT responded to various contraction forces and how it related to muscle activation measured by electromyography (EMG). For both muscles isometric contractions of 10, 30, 50 and 70% of maximal voluntary contraction (MVC) were maintained for 20 s each by healthy males and females; additionally a 10% MVC contraction was sustained for 5 min. For the different contraction levels, predictable relationships were seen between ΔStO2% and force, and between ΔStO2% and EMG RMS amplitude. The general trend was a decrease in ΔStO2% with increasing force and increasing EMG. Females showed a tendency for a higher oxygen use (i.e., drop in StO2%) for the ECR over force levels than males and a higher RMS% MVC for the TD. For the 10% MVC contraction sustained for 5 min gender specific changes over time for HbT and RMS for the ECR, and for StO2% for the TD muscle were seen. A second objective was to determine the day-to-day reliability of NIRS variables for the ECR and TD muscles at group level (Pooled data) and at gender level (males and females). Measurements were performed on two occasions separated by 4-6 days and intraclass correlation coefficients (ICC) and limits of agreement (LOA) were determined as reliability and reproducibility indicators, respectively. Variables tested were ΔStO2% during submaximal isometric contractions of 10, 30, 50 and 70% MVC and StO2% recovery (Rslope) after contractions and after AO. For the ECR, HbTslope as an indication of blood flow (using VO) and HHbslope as a surrogate of oxygen consumption for both VO and AO were computed. For ΔStO2% for the ECR the highest ICC was at 30% MVC for both the pooled data and at gender level. For the TD ICCs were comparably high for 30, 50, 70 % MVC (for both muscles the ΔStO2% at 10% MVC showed the lowest ICC). Further, females showed a higher ICC than males for contraction levels of 50 and 70% MVC. For both muscles, LOA for ΔStO2% was lowest at 10% and highest at 50 and 70% MVC. For the ECR Rslope ICCs were high for all contraction levels, but was lower for AO; LOA was lowest at 70% MVC. For the TD, Rslope ICCs were also high for all contraction levels and LOA was lowest at 30 % MVC. ICC for HbTslope was the lowest of all variables tested. For HHbslope ICC was higher for AO than for VO, and LOA was lower for AO. A third objective was to determine if there were differences between healthy subjects and patients diagnosed with WRMP in ΔStO2% and ΔHbT responses during varying submaximal contractions (10, 30, 50 and 70% MVC), and StO2% recovery (Rslope) immediately after contractions and AO. Additional variables tested in the ECR at rest were HHbslope to indicate oxygen consumption (using AO) and HbTslope as an indication of blood flow. There were no differences between groups in ΔStO2% and ΔHbT variables during the contractions or Rslope in the recovery after contractions or AO. Furthermore, HbTslope was not different between groups However, oxygen consumption for the ECR and StO2% for the TD at rest were significantly greater for healthy subjects compared to patients. A fourth objective was to determine if there were differences in StO2% and HbT between healthy subjects and WRMP patients during a 12 min sustained contraction of 15 % MVC. In addition, the protocol included a recovery period of 30 min. Prior to contraction, as well as during the recovery period, HbTslope as a surrogate of blood flow was determined for the ECR. Neither the ECR nor the TD exhibited significant differences between groups for StO2% and HbT during the contraction. For the TD patients showed a lower StO2% value at rest and throughout the contraction than healthy subjects. For the ECR HbT during the sustained contraction the general trend was an initial decrease with gradual increase throughout the contraction for both groups. For HbTslope no differences were seen between patients and healthy subjects before the sustained contraction and during the recovery period for both muscles. NIRS is deemed a suitable technique for assessing physiological measurements of the upper extremity, including for day-to-day testing. NIRS was not able to distinguish between the patients with WRMP and controls. A concern in the thesis is the characteristics of the patient group in being equally active in recreational sports, actively working, and similar in muscle strength as controls. Thus, applying NIRS for studying a more severe patient group could yield different results.

Low-load repetitive work (LLRW) and mental load are important risk factors for the development of workrelated muscle pain. The link between these risk factors and the development of pain is still not understood, but stimulation of chemo-sensitive receptors in the muscle probably plays an important role. It has been suggested that sensitising substances may accumulate in the muscle during LLRW, especially when combined with mental load. The overall purpose of this thesis was to try to shed some light on the effects of LLRW on the concentration of sensitising substances (glutamate, prostaglandin E2 (PGE2), norepinephrine (NE)) and on metabolism (lactate, pyruvate and oxygenation) in the trapezius muscle of healthy controls (CON) and subjects with trapezius myalgia (TM). A first step was to investigate whether females with TM exhibit higher absolute concentrations of glutamate and PGE2 in the affected muscle during rest. Using Microdialysis (MD) females with TM and asymptomatic controls were studied during four hours of rest. [Glutamate] and [PGE2] during rest did not differ between groups. A second step was to investigate, in a simulated occupational setting, the effects of LLRW on the concentration of sensitising substances and metabolism in the trapezius muscle of TM and CON, and whether increased work duration resulted in a progressive effect. Asymptomatic females were studied during baseline rest, 30 versus 60 min work and recovery, using MD and near infrared spectroscopy (NIRS). Subjects with TM were studied during baseline rest, 30 min work and recovery. [Glutamate] and [lactate] increased in response to work, but not progressively with increased work duration. [Glutamate] was at all time points significantly lower in TM. [PGE2]and oxygenation remained unchanged during work for CON, while for TM oxygenation decreased significantly during work. In TM [pyruvate] increased during both work and recovery, and a significant interaction between groups was found for [pyruvate] during recovery; while moderately increased in CON it increased progressively in TM. The effects of LLRW with and without superimposed mental load on intramuscular [NE], muscle activity and oxygen saturation in the trapezius were also investigated and compared. Using MD, electromyography and NIRS, healthy females were studied on two occasions; during 30 min LLRW and during 30 min LLRW with superimposed mental load. During work [NE], and muscle activity, were increased, while oxygenation decreased, but no differences between occasions. However, recovery of [NE] to baseline was slower after LLRW with superimposed mental load. The findings of the present thesis suggest: (i) no inflammation, or increased interstitial [glutamate] in TM; (ii) LLRW causes an increased anaerobic metabolism in both TM and CON; (iii) no effect of work duration was found; (iv) a significant difference in the effects of LLRW on the interstitial milieu of the trapezius muscle in TM as compared to CON; (v) LLRW causes a significant increase in [NE], but superimposed mental load does not cause a further increase; (vi) LLRW with a superimposed mental load may result in a slower recovery to baseline [NE] as compared with LLRW alone.

Carbocyanine dyes are organic compounds containing chains of conjugated methine groups with electron-donating and electron-withdrawing substituents at the terminal heterocycles of the general formula [R1-(CH)n-R2]+X-. The synthetic methodology and optical properties of carbocyanines will be discussed. This thesis consists of two parts: (A) synthesis and optical properties of novel carbocyanine dyes substituted with various amines and the synthesis of unsymmetrical carbocyanine dyes containing monofunctional groups for bioconjugation. (B) synthesis of heptamethine carbocyanine dyes to be used for image-guided surgery. In part A, the synthesis of carbocyanine dyes functionalized with various amines and studies of their optical properties with respect to absorbance, fluorescence, quantum yield and extinction coefficient will be presented. These property studies will aid in designing efficient dyes for future biomedical applications. Part A will also include a one pot synthesis of unsymmetrical carbocyanine dyes functionalized with mono carboxylic acid chains, useful for biomolecule (i.e. proteins, amino acids, etc.) conjugation. Part B will describe the synthesis of novel carbocyanine dyes to be used for cancer image-guided surgery. Cancers are thus far incurable diseases, i.e. there are no drugs currently available to cure cancer; however, by designing a dye to visualize tumor cells will greatly increase the efficiency of cancer removal and hopefully increase the survival rate of cancer patients. The dyes reported in this thesis are superior to commercially available dyes used to visualize and identify various tumors invisible to the naked eye of surgeons with regards to biodistribution and clearance through kidney filtration.

A brain-computer interface (BCI) allows individuals to communicate through the modulation of regional brain activity. Clinical near-infrared spectroscopy (NIRS) is used to monitor changes in cerebral blood oxygenation due to functional activation. It was hypothesized that visually-cued emotional induction tasks can elicit detectable activity in the prefrontal cortex. Data were collected from eleven participants as they performed positively and negatively-valenced emotional induction tasks. Baseline and activation trials were classified offline with accuracies from 75.0-96.7% after applying a feature selection algorithm to determine optimal performance parameters for each participant. Feature selection identified common discriminatory features across participants and relationships between performance parameters. Additionally, classification accuracy was used to quantify NIRS hemodynamic response latency. Significant increases in classification rates were found as early as 2.5 s after initial stimulus presentation. These results suggest the potential application of emotional induction as a NIRS-BCI control paradigm.

Heptamethine cyanine dyes are attractive compounds for imaging purposes in biomedical applications because of their chemical and photophysical properties exhibited in the near-infrared region. A series of meso amino-substituted heptamethine cyanine dyes with indolenine, benz[e]indolenine and benz[c,d]indolenine heterocyclic moieties were synthesized and their spectral properties including fluorescence quntum yield were investigated in ethanol and ethanol/water mixture. Upon substitution with amines, the absorption maxima of the dyes shifted to the lower wavelength region (~600 nm), showed larger Stokes shifts and stronger fluorescence which can be attributed to an excited state intramolecular charge transfer (ICT). High quantum yields were observed for primary amine derivatives and lower quantum yields were observed for secondary amine derivatives. Fluorescence quantum yields are greater for dyes with 3H-indolenine terminal moieties than for dyes with benz[e]indolenine end groups. Benz[c,d]indolenine based heptamethine cyanine dyes exhibited the lowest quantum yield due to aggregation in solution. In general, the benz[e]indolenine hepatemethine cyanines showed high Stokes shifts compared to indolenine dyes. For the meso-chloro dyes, the absorption maxima for the dyes shifted bathochromically in the order of indolenine, benz[e]indolenine and benz[c,d]indolenine.

The main objective of the study was to determine the effects of enzymes on quality of breads baked in halogen lamp-microwave combination, microwave and conventional oven. It was also aimed to determine the optimum processing conditions in these ovens. In the first part of the study, as independent variables, baking time, baking temperature for conventional oven / microwave power for microwave oven and microwave power and halogen power for combination oven was used. Weight loss, specific volume, firmness and color of the breads were measured during the study. The optimum baking conditions were determined as 13 min at 200&deg / C in conventional oven, 0.75 min at 100% power in microwave oven, 10 min at 60% power in halogen lamp oven, and 3 min at 30% microwave power and 70% halogen lamp power in halogen lamp-microwave combination oven. In the case of combination oven, specific volume and color values of breads were comparable with the conventionally baked breads but weight loss and firmness of them were still higher. The effects of different enzymes (&amp / #945 / -amylase, xylanase, lipase &amp / protease) were studied to reduce the quality problems of breads baked in microwave and halogen lamp-microwave combination oven. The optimum baking conditions determined for each type of oven in the first part of the study were used in the investigation of the functions of enzymes on bread quality during baking and staling. As a control, no enzyme added breads baked at 200&deg / C for 13 min in conventional oven were used. All the enzymes were found to be effective in reducing initial firmness and increasing specific volume of breads baked in microwave and halogen lamp-microwave combination ovens. However, in conventional baking, the effects of enzymes on crumb firmness were seen mostly during storage. The usage of enzyme protease in the bread formulation resulted in breads with higher volume and darker color in all of the ovens. All of the enzymes were found to be effective to retard the staling of breads baked in conventional, microwave and halogen lamp-microwave combination ovens.

A brain-computer interface (BCI) allows individuals to communicate through the modulation of regional brain activity. Clinical near-infrared spectroscopy (NIRS) is used to monitor changes in cerebral blood oxygenation due to functional activation. It was hypothesized that visually-cued emotional induction tasks can elicit detectable activity in the prefrontal cortex. Data were collected from eleven participants as they performed positively and negatively-valenced emotional induction tasks. Baseline and activation trials were classified offline with accuracies from 75.0-96.7% after applying a feature selection algorithm to determine optimal performance parameters for each participant. Feature selection identified common discriminatory features across participants and relationships between performance parameters. Additionally, classification accuracy was used to quantify NIRS hemodynamic response latency. Significant increases in classification rates were found as early as 2.5 s after initial stimulus presentation. These results suggest the potential application of emotional induction as a NIRS-BCI control paradigm.

Regional tissue temperature dynamics in the brain are determined by the balance of the metabolic heat production rate and heat exchange with blood flowing through capillaries embedded in the brain tissue, the surrounding tissues and the environment. Local changes in blood flow and metabolism during functional activity can upset this balance and induce transient temperature changes. Invasive experimental studies in animal models have estab- lished that the brain temperature changes during functional activity are observable and a definitive relationship exists between temperature and brain activity. We present a theoreti- cal framework that links tissue temperature dynamics with hemodynamic activity allowing us to non-invasively estimate brain temperature changes from experimentally measured blood- oxygen level dependent (BOLD) signals. With this unified approach, we are able to pinpoint the mechanisms for hemodynamic activity-related temperature increases and decreases. In addition to these results, the potential uses and limitations of optical measurements are dis- cussed.

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