The divalent Ca2+ metal ion acts as a universal second messenger in virtually all eukaryotic cells from fungi to plants to mammals. In mammals, Ca2+ signaling is vital to a variety of physiological processes including fertilization, cell proliferation, secretion, and muscular contraction. In electrochemically non-excitable tissues, the release of Ca2+ from intracellular stores such as the endoplasmic reticulum is tightly regulated by the inositol 1,4,5-trisphosphate receptor (IP3R). The IP3R Ca2+ release channel is activated by the binding of the small molecule inositol 1,4,5-trisphosphate (IP3) in response to extracellular stimuli such as hormones, growth factors, and neurotransmitters. The conformational changes accompanying IP3 binding were investigated using a biophysical approach. A specific focus of this work is to decipher how signals of ligand binding are transmitted from the N-terminal IP3-binding core to the C-terminal channel domain. To such end, biophysical studies of the ligand-induced conformational changes within the N-terminal domain of IP3R (a.a. 1 – 604) were performed. The results implicated the presence of two flexible linkers which join stably folded domains. This prompted the proposal of a model in which an equilibrium mixture of conformational substrates containing compact and more extended structures co-exist. Determinants within the N- and C-terminal regions of IP3R have previously been reported to be critical to channel function. Employing nuclear magnetic resonance (NMR) as well as biochemical methods, an intermolecular interaction between the S4-S5 linker, the cytoplasmic loop between the fourth and fifth transmembrane helices of IP3R, and the suppressor domain was identified. The determination of the crystal structure of the suppressor domain from isoform type 3 IP3R (IP3R3SUP) allowed us to map the residues involved in this interaction to one face of the molecule. The characterization of this interaction provides insight into the N- and C-terminal determinants essential to the IP3R channel gating mechanism.

Radiation therapy is often offered as the primary treatment for head and neck cancer(HNC). Accurate target delineation is essential for the success of radiation therapy. The current target definition technique - manual delineation using Computed Tomography(CT) - is subject to high observer variability. Functional imaging modalities such as 2-[18F]-fluoro-2-deoxy-D-glucose Positron Emission Tomography(FDG-PET) can greatly improve the visualization of tumor. FDG-PET co-registered with CT has shown potential to improve the accuracy of target localization and reduce observer variability. Unfortunately, due to the limitation of PET, the degree of improvement obtained by qualitative and simple quantitative (e.g. thresholding) use of FDG-PET is not ideal. However, both PET and CT images contain a wealth of texture information that could be used to improve the accuracy of target definition. This thesis has investigated using texture analysis techniques to automatically delineate radiation targets. Firstly, PET and CT texture features with high discrimination ability were identified and a texture analysis technique- a decision tree based K Nearest Neighbour(DTKNN) classifier – was developed. DTKNN could accurately classify head and neck tissue with an area under curve(AUC) of a Receiver Operator Characteristic(ROC) of 0.95. Subsequently, an automated target delineation technique - CO-registered Multi-modality Pattern Analysis Segmentation System(COMPASS) - was developed that can delineate tumor on a voxel-by-voxel basis. COMPASS was found to accurately delineate HNC with 84% sensitivity and 95% specificity on a voxel basis per patient. To accurately evaluate the utility of the COMPASS in radiation targeting, a validation method which can combine biased observers' contours to generate a probabilistic reference for validation was developed. The method was based on maximum likelihood analysis using a simulated annealing(SA) algorithm. The results from this thesis show that texture features of both PET and CT images can enhance the discrimination between HNC and normal tissue, and an automated delineation method of HNC using texture analysis of PET and CT images can accurately and consistently define radiation targets in head and neck. This suggests that automated segmentation of radiation targets based on texture analysis techniques may significantly reduce observer variability and improve the accuracy of radiation targeting.

There is a clear need for improved methods (e.g. computer modelling, imaging) to characterize the substrate of abnormal rhythms like ventricular tachycardia (VT) developed by patients who have suffered a heart attack. Progress leading to improved disease management and treatment planning (based on predictive models) as well as outcomes assessment will have immediate impact on the quality of life in this large patient population. Prior to integration into clinical applications, the predictive models have to be properly validated using experimental techniques selected to reflect the electrophysiological phenomena at spatio-temporal scales similar to those considered in simulations. This thesis advanced us toward this goal by addressing the challenge of building more accurate models of electrophysiology for individual hearts. A novel construction of a realistic 3D cardiac model from Magnetic Resonance Images (MRI), with a long-term aim to predict propagation of the electrical impulse in normal and pathologic large hearts (translatable to human hearts), and associated inducibility of VT is described. To parameterize the model, an original evaluation method of electrophysiological (EP) characteristics of the heart tissue was used. The method combined state-of-the-art experimental physiology tools like optical fluorescence imaging using voltage-sensitive dyes and a CARTO electro-anatomical system, with a cardiac computer model generated from high resolution MR scans of explanted normal and pathologic porcine hearts. Several input model parameters (e.g., conductivity, anisotropy, restitution) were successfully adjusted using the ex-vivo measurements of action potential to yield close correspondence between model output and experiments. Moreover, a simple, fast, and macroscopic mathematical model was used with computation times less than 1h, attractive for clinical EP applications.

In this thesis focused ultrasound thrombolysis was investigated in vitro and in vivo. At high intensities it was demonstrated that clot breakdown only arises under the presence of inertial cavitation for longer pulse lengths, consistent with observations at significantly shorter pulse durations, and that the majority of clot debris is sub-capillary in size. Evidence of flow restoration was demonstrated in vivo by partially restoring flow to an occluded rabbit femoral artery. At slightly lower intensities it was observed that steady- state clot displacements scale linearly with power for clots treated with focused ultrasound pulses, and in some cases can reach magnitudes up to several hundred microns. It was demonstrated that the shear strain exerted on the clot by a focused ultrasound pulse scale with power, which may be implicated in enhancing drug permeation for studies in combination with lytic agents.

Multi-modality imaging is a possible solution for overcoming individual modality limitations. With the use of modality specific contrast agents, contrast-enhanced multi-modality imaging may provide a more comprehensive evaluation of tumour characteristics. This may be possible by combining ultrasound and magnetic resonance imaging, whose contrast agents behave differently within the microvasculature. A novel, microvascular, and leaky phantom is presented that permits ultrasound contrast agents to remain entirely within the mimicking vascular compartment while the magnetic resonance contrast agents may freely diffuse between the mimicking vasculature and tissue compartments. The results show that the phantom is a useful tool for investigating the combination of contrast-enhanced ultrasound and magnetic resonance imaging. This work motivates further combined contrast-enhanced imaging studies, with future work to incorporate additional modalities.

Variability between oncologists in defining the tumor during radiation therapy planning can be as high as 700% by volume. Robust, automated definition of tumor boundaries has the ability to significantly improve treatment accuracy and efficiency. However, the information provided in computed tomography (CT) is not sensitive enough to differences between tumor and healthy tissue and positron emission tomography (PET) is hampered by blurriness and low resolution. The textural characteristics of thoracic tissue was investigated and compared with those of tumors found within 21 patient PET and CT images in order to enhance the differences and the boundary between cancerous and healthy tissue. A pattern recognition approach was used from these samples to learn the textural characteristics of each and classify voxels as being either normal or abnormal. The approach was compared to a number of alternative methods and found to have the highest overlap with that of an oncologist's tumor definition.

In this thesis focused ultrasound thrombolysis was investigated in vitro and in vivo. At high intensities it was demonstrated that clot breakdown only arises under the presence of inertial cavitation for longer pulse lengths, consistent with observations at significantly shorter pulse durations, and that the majority of clot debris is sub-capillary in size. Evidence of flow restoration was demonstrated in vivo by partially restoring flow to an occluded rabbit femoral artery. At slightly lower intensities it was observed that steady- state clot displacements scale linearly with power for clots treated with focused ultrasound pulses, and in some cases can reach magnitudes up to several hundred microns. It was demonstrated that the shear strain exerted on the clot by a focused ultrasound pulse scale with power, which may be implicated in enhancing drug permeation for studies in combination with lytic agents.

Multi-modality imaging is a possible solution for overcoming individual modality limitations. With the use of modality specific contrast agents, contrast-enhanced multi-modality imaging may provide a more comprehensive evaluation of tumour characteristics. This may be possible by combining ultrasound and magnetic resonance imaging, whose contrast agents behave differently within the microvasculature. A novel, microvascular, and leaky phantom is presented that permits ultrasound contrast agents to remain entirely within the mimicking vascular compartment while the magnetic resonance contrast agents may freely diffuse between the mimicking vasculature and tissue compartments. The results show that the phantom is a useful tool for investigating the combination of contrast-enhanced ultrasound and magnetic resonance imaging. This work motivates further combined contrast-enhanced imaging studies, with future work to incorporate additional modalities.

Variability between oncologists in defining the tumor during radiation therapy planning can be as high as 700% by volume. Robust, automated definition of tumor boundaries has the ability to significantly improve treatment accuracy and efficiency. However, the information provided in computed tomography (CT) is not sensitive enough to differences between tumor and healthy tissue and positron emission tomography (PET) is hampered by blurriness and low resolution. The textural characteristics of thoracic tissue was investigated and compared with those of tumors found within 21 patient PET and CT images in order to enhance the differences and the boundary between cancerous and healthy tissue. A pattern recognition approach was used from these samples to learn the textural characteristics of each and classify voxels as being either normal or abnormal. The approach was compared to a number of alternative methods and found to have the highest overlap with that of an oncologist's tumor definition.

The use of polarized light for characterization of biological tissues has received increased attention in recent years due to the wealth of information available in the interactions of polarized light with tissue and the noninvasive nature of optical radiation. While the depolarizing effects of multiple scattering complicate the use of polarimetry in tissue, many biological constituents affect the polarization of light such as collagen, muscle fibers, and glucose. Thus, if the effects of scattering can be accounted for⎯or utilized in the analysis⎯polarized light can potentially be used as a probe of tissue status. This thesis presents advancements in the techniques for the simulation of polarized light in tissue-simulating media, and explores two biomedical applications. Previous Monte Carlo models for simulation of polarized light propagation in tissue-simulating media do not include the effects of birefringence and optical activity, two polarizing effects of useful diagnostic potential. To overcome this limitation, our model was extended to include both these effects simultaneously, and then experimentally validated using a novel polarization phantom system. The use of polarized light for characterization of the myocardium, and specifically towards monitoring stem cell regenerative treatments of myocardial infarction, was investigated experimentally as a novel application for polarimetry. The potential for this technique is based on the changes in myocardial structure that occur with infarction and subsequent regeneration, and the associated changes in tissue birefringence. The use of polarized light for noninvasive tissue analyte monitoring, particularly glucose, was also investigated based on the optical activity exhibited by many tissue analytes due to their chiral structure. In this study, a novel combined optical polarization and intensity approach was developed and tested on Monte Carlo simulated data. The studies presented in thesis introduce new methods for polarization simulation and analysis in biological tissue and demonstrate potential for polarimetry in monitoring myocardial regeneration and noninvasive measurements of tissue analytes.