Coarse Wavelength Division Multiplexing (CWDM) is becoming a popular way to increase the optical throughput of fibers for short to medium haul networks at a reduced cost. The International Telecommunications Union (ITU) has defned the CWDM network to consist of eighteen channels with channel spacings of 20 nm starting at 1270 nm and ending at 1610 nm.Four and eight channel AWGs on InP, suitable for CWDM, were fabricated using a novel and versatile S-shape design. The standard horseshoe layout will not work on semiconductor for AWGs with a free spectral range (FSR) larger than 30 nm. The AWG design provides operation insensitive to thermal and polarization fluctuations, which is key for low cost operation and packaging. It will be shown thatrefractive index changes over the large operating wavelength band produced negligible effects in the transmission spectrum.Standard AWG design assumes refractive index is a constant over the operating wavelength band. As a result, the output waveguide separations are held constant on the second star coupler. As the channel number increases, secondary focal dispersion causedfrom a changing refractive index can have detrimental effects on performance. A new design method will be introduced which includes refractive index dispersion by allowing the output waveguide separations to vary. The new design is consistent with standard design but is applicable in materials with a linear index dispersion over an arbitrarily large wavelength band.Lastly, a method for increasing the transmission using multimode waveguides is discussed. Traditionally, single mode waveguides are required in order to prevent higher order waveguide modes creating ghost images in the output spectrum. Using bend loss and waveguide junction offsets, higher order modes can be filtered from the output,thereby eliminating ghost images and at the same time, increase transmission.

The purpose of this study was to examine instructional experiences of students with visual impairment in an guided inquiry-based science classroom. Drawing from social constructive perspectives about teaching and learning, I focused on the initial attempts of students to participate fully in an inquiry-based astronomy unit. The astronomy unit incorporated features of project-based science inquiry and aligned with national standards. This study described the opportunities provided to and challenges faced by students with visual impairment as they participated in the guided inquiry-based learning environment. Additionally, discursive practices of students including student-generated questions, student discussions, and students' science notebook writing were examined. Also, students' alternative conceptions about scientific phenomena and changes in students' thinking during the course of instruction, if any, were described. Methods of data collection included classroom observations, video records, pre- and post- curriculum assessments, attitudes toward science measurement, student interviews, and student artifacts (i.e., science notebook entries, student-constructed models). Findings showed that student learning was enhanced when the instructor-researcher guided students in accomplishing inquiry tasks and in making sense of their inquiry experiences. Additionally, the use of appropriate reflective prompts assisted students with visual impairment to fully participate in the writing tasks of the inquiry-based learning environment. Results suggested that the quantity and quality of student-generated questions increased with extended inquiry instruction. Also, students used questions to not only establish verbal communication, but to elaborate on their own thinking and expand or explain the thinking of others. Findings suggested also that students with visual impairment have similar alternative frameworks about scientific phenomena (i.e, causes of lunar phases, reason for the seasons) as do their peers with sight. This study contributes to the literature about inquiry-based instructional strategies for all students and initiates the conversation about best practice for science instruction with students with visual impairment.

Prostate cancer is a worldwide health concern for men. Needle biopsy is the most definitive form of cancer diagnosis. Target-specific biopsies can be performed under magnetic resonance imaging (MRI) guidance. However, needle placements are often inaccurate due to intra-operative prostate motion and the lack of motion compensation techniques. As a result, malignant tumors can be missed, which in turn will lead to an increased number of repeated biopsies and delaying of treatment. To increase the needle targeting accuracy, intra-operative prostate motion and deformation need to be studied so that motion compensation techniques can be developed accordingly. This thesis intends to make three main contributions: 1. A comprehensive survey of the state-of-art in image-guided prostate needle placement interventions. 2. Retrospective clinical accuracy validation of a MRI-guided robotic prostate biopsy system that was used in the U.S. National Cancer Institute for over 6 years. A 3D-3D registration algorithm consists of an initial two-step rigid alignment followed by a B-spline deformable transform was developed to align the pre- and post-needle insertion images. A total of 90 biopsies from 24 patients were studied. The mean target displacement, needle placement error, and clinical biopsy error were 5.2, 2.5, and 4.3 mm, respectively. 3. Development of a multi-slice-to-volume registration for intra-operative target localization. The algorithm aligns the planning volume with three orthogonal image slices of the prostate acquired immediately before needle insertion. It consists of a rigid registration followed by a deformable step using only the prostate region. The algorithm was validated on 14 clinical images sets from Brigham and Women's Hospital in Boston, Massachusetts. All registration errors were well below the radius of a clinically significant tumour (5 mm), and are considered clinically acceptable. The results show that there was a substantial amount of biopsy error caused by prostate motion and deformation during MRI-guided biopsy. This error can be reduced by using quantitative imaging techniques for prostate registration and motion compensation. In particular, the multi-slice-to-volume registration algorithm demonstrated the feasibility of intra-operative target localization and motion compensation; which in turn may improve the quality of MRI-guided prostate interventions. / Thesis (Ph.D, Computing) -- Queen's University, 2014-03-01 11:45:55.8

Natural products have been a source of many pharmaceutical drugs and a number of drugs that are currently used in the treatment of cancer are derivatives of compounds originally isolated from natural products. There is evidence that extracts of Tulbaghia violacea can be used to treat cancer. The activation of apoptosis in cancer cells is a target for the development of novel anti-cancer drugs since one of the characteristics of cancer cells is resistance to apoptosis due to the deregulation of biochemical pathways leading to apoptosis. In fact, many current anti-cancer drugs exert their effects through the activation of apoptosis. Previous studies showed that extracts of T.violacea induce apoptosis in cancer cells and one study reported on the isolation of a compound (methyl-ԃ-D-glucopyranoside), which is responsible for the pro-apoptotic activity of the T.violacea extract. Therefore the aim of this study was to investigate the anti-cancer activity of methyl-ԃ-Dglucopyranoside and extracts prepared from T.violacea. In this study the pro-apoptotic activity of methyl-ԃ-D-glucopyranoside and extracts prepared from T.violacea were investigated on a panel of human cancer cell lines, which included HepG2, MCF7, H157, HT29 and the non-cancerous cell line, KMST6. The induction of apoptosis was evaluated by flow cytometry using several bioassays which measures biochemical events (caspase activation, phosphatidylserine externalisation and reactive oxygen species (ROS) production that is associated with the induction of apoptosis. The results demonstrated that the effects of methyl--D-glucopyranoside on cultured cells are transient and that the cells recover from the effects of methyl--D-glucopyranoside. This suggested thatmethyl-ԃ-D-glucopyranoside is not the compound responsible for the pro-apoptotic bioactivity in the T.violacea extract. This study also showed that cytotoxic and pro-apoptotic bioactivity of the leaf-extract was significantly higher in comparison to the tuber-extract. The bioactivity of the organic solvent extracts (dichloromethane, hexane, methanol and 50% methanol/water) of T.violacea leaves was also significantly higher than water extracts of T.violacea leaves. A comparison of the different organic extracts prepared from the T.violacea leaves showed that the highest activity was observed for the dichloromethane and hexane extracts. In an effort to identify the bioactive compound(s) the dichloromethane extract was subjected to Versaflash® column chromatography. However, due to problems experienced with the solubility of the dichloromethane sub-fractions, these compounds could not be tested for their bioactivity. Palmitone (16-hentriacontanone) was identified as one of the major compounds present in the dichloromethane sub-fractions. This compound was previously shown to have anticonvulsant bioactivity but there is no evidence in the literature that it has anti-cancer or pro-apoptotic activities. Fingerprinting of the methanol extract showed the presence of long chain fatty acid derivatives, flavonoids and allicin derivatives in the methanol extract. Although, this study failed to isolate the pro-apoptotic bioactive compound(s) present in the extracts of T.violacea, it confirmed that extracts of this plant induce apoptosis in cultured human cancer cell lines.

Natural products have been a source of many pharmaceutical drugs and a number of drugs that are currently used in the treatment of cancer are derivatives of compounds originally isolated from natural products. There is evidence that extracts of Tulbaghia violacea can be used to treat cancer. The activation of apoptosis in cancer cells is a target for the development of novel anti-cancer drugs since one of the characteristics of cancer cells is resistance to apoptosis due to the deregulation of biochemical pathways leading to apoptosis. In fact, many current anti-cancer drugs exert their effects through the activation of apoptosis. Previous studies showed that extracts of T.violacea induce apoptosis in cancer cells and one study reported on the isolation of a compound (methyl-ԃ-D-glucopyranoside), which is responsible for the pro-apoptotic activity of the T.violacea extract. Therefore the aim of this study was to investigate the anti-cancer activity of methyl-ԃ-Dglucopyranoside and extracts prepared from T.violacea. In this study the pro-apoptotic activity of methyl-ԃ-D-glucopyranoside and extracts prepared from T.violacea were investigated on a panel of human cancer cell lines, which included HepG2, MCF7, H157, HT29 and the non-cancerous cell line, KMST6. The induction of apoptosis was evaluated by flow cytometry using several bioassays which measures biochemical events (caspase activation, phosphatidylserine externalisation and reactive oxygen species (ROS) production that is associated with the induction of apoptosis. The results demonstrated that the effects of methyl--D-glucopyranoside on cultured cells are transient and that the cells recover from the effects of methyl--D-glucopyranoside. This suggested thatmethyl-ԃ-D-glucopyranoside is not the compound responsible for the pro-apoptotic bioactivity in the T.violacea extract. This study also showed that cytotoxic and pro-apoptotic bioactivity of the leaf-extract was significantly higher in comparison to the tuber-extract. The bioactivity of the organic solvent extracts (dichloromethane, hexane, methanol and 50% methanol/water) of T.violacea leaves was also significantly higher than water extracts of T.violacea leaves. A comparison of the different organic extracts prepared from the T.violacea leaves showed that the highest activity was observed for the dichloromethane and hexane extracts. In an effort to identify the bioactive compound(s) the dichloromethane extract was subjected to Versaflash® column chromatography. However, due to problems experienced with the solubility of the dichloromethane sub-fractions, these compounds could not be tested for their bioactivity. Palmitone (16-hentriacontanone) was identified as one of the major compounds present in the dichloromethane sub-fractions. This compound was previously shown to have anticonvulsant bioactivity but there is no evidence in the literature that it has anti-cancer or pro-apoptotic activities. Fingerprinting of the methanol extract showed the presence of long chain fatty acid derivatives, flavonoids and allicin derivatives in the methanol extract. Although, this study failed to isolate the pro-apoptotic bioactive compound(s) present in the extracts of T.violacea, it confirmed that extracts of this plant induce apoptosis in cultured human cancer cell lines.

Modern image-guided surgery aids minimally-invasive, high-precision procedures that increase efficacy of treatment. This thesis investigates two research aims to improve precision and integration of intraoperative cone-beam CT (CBCT) imaging in guidance of head and neck (H&N) surgery. First, marker configurations were examined to identify arrangements that minimize target registration error (TRE). Best arrangements minimized the distance between the configuration centroid and surgical target while maximizing marker separation. Configurations of few markers could minimized TRE with more markers providing improved uniformity. Second, an algorithm for automatic registration of image and world reference frames was pursued to streamline integration of CBCT with real-time tracking and provide automatic updates per scan. Markers visible to the tracking and imaging systems are automatically co-localized and registered with equivalent accuracy and superior reproducibility compared to conventional registration. Such work helps the implementation of CBCT in H&N surgery to maximize surgical precision and exploit intraoperative image guidance.

This thesis presents the first work, to our knowledge, to evaluate the potential of Optical Coherence Tomography (OCT) as an intravascular imaging modality to characterize and guide interventions on chronic total occlusions (CTOs) in arteries. An ex vivo imaging study using OCT is presented that characterizes various pathologies associated with peripheral CTOs and illustrates the ability to differentiate between the vessel wall and the occluded lumen. We also found that, while OCT could image approximately 1mm through tissue, it was effective for imaging deeper through clarified microchannels seen within the occluded lumen. While others had reported observing such microchannels within the lumen before, little was known about the global architecture of these channels. This motivated a study of the global morphology of microchannels in occlusions using micro computed tomography (microCT). In this microCT study, we found that microchannels within the occluded lumen of the artery appeared to be continuous over several millimeters. However, these channels also exited the artery frequently, suggesting the need for some form of imaging guidance. As a potential intravascular imaging set-up, a forward-viewing OCT catheter was built. This catheter uses a novel scanning mechanism that combines high voltage and a dissipative polymer to achieve fast compact actuation. Doppler OCT results are presented using this catheter to image flow in the forward direction. Doppler OCT imaging of microchannels in vivo is also shown in a surgically exposed occluded artery in situ.

This thesis presents the first work, to our knowledge, to evaluate the potential of Optical Coherence Tomography (OCT) as an intravascular imaging modality to characterize and guide interventions on chronic total occlusions (CTOs) in arteries. An ex vivo imaging study using OCT is presented that characterizes various pathologies associated with peripheral CTOs and illustrates the ability to differentiate between the vessel wall and the occluded lumen. We also found that, while OCT could image approximately 1mm through tissue, it was effective for imaging deeper through clarified microchannels seen within the occluded lumen. While others had reported observing such microchannels within the lumen before, little was known about the global architecture of these channels. This motivated a study of the global morphology of microchannels in occlusions using micro computed tomography (microCT). In this microCT study, we found that microchannels within the occluded lumen of the artery appeared to be continuous over several millimeters. However, these channels also exited the artery frequently, suggesting the need for some form of imaging guidance. As a potential intravascular imaging set-up, a forward-viewing OCT catheter was built. This catheter uses a novel scanning mechanism that combines high voltage and a dissipative polymer to achieve fast compact actuation. Doppler OCT results are presented using this catheter to image flow in the forward direction. Doppler OCT imaging of microchannels in vivo is also shown in a surgically exposed occluded artery in situ.

Modern image-guided surgery aids minimally-invasive, high-precision procedures that increase efficacy of treatment. This thesis investigates two research aims to improve precision and integration of intraoperative cone-beam CT (CBCT) imaging in guidance of head and neck (H&N) surgery. First, marker configurations were examined to identify arrangements that minimize target registration error (TRE). Best arrangements minimized the distance between the configuration centroid and surgical target while maximizing marker separation. Configurations of few markers could minimized TRE with more markers providing improved uniformity. Second, an algorithm for automatic registration of image and world reference frames was pursued to streamline integration of CBCT with real-time tracking and provide automatic updates per scan. Markers visible to the tracking and imaging systems are automatically co-localized and registered with equivalent accuracy and superior reproducibility compared to conventional registration. Such work helps the implementation of CBCT in H&N surgery to maximize surgical precision and exploit intraoperative image guidance.

This thesis presents a theoretical study of thermoelastic guided waves in cylinders in the context of Lord-Shulman generalized theory of thermoelasticity. Two different methods were formulated to study dispersion relations in infinite cylinders. One of them is a Semi Analytical Finite Element (SAFE) method and the other is an analytical method. In the SAFE method, the dispersion equation has been formulated as a generalized eigenvalue problem by treating radial displacement and temperature with a one dimensional finite element model through the thickness of the cylinder. In the analytical method, displacement potentials are introduced to obtain the dispersion relations of guided wave modes. This method is applicable to isotropic cylinders and has been developed primarily to cross check the SAFE formulation. Frequency spectra obtained by both methods for an isotropic cylinder have shown excellent agreement with each other. Since the SAFE method can be used for an anisotropic composite cylinder, guided wave modes for anisotropic and composite cylinders are presented. Transient analysis of ultrasonic guided waves generated by concentrated heating of the outer surface of an infinite anisotropic cylinder has also been studied. The SAFE method is employed to model the response of a cylinder due to a pulsed laser focused on its surface. Green’s functions were constructed numerically by superposition of guided wave modes in frequency and wave number domains. Time histories of the propagating modes are then calculated by applying an inverse Fourier transformation in the time domain. Transient radial displacements of longitudinal and flexural modes of a silicon nitride cylinder are presented. Propagation of thermoelastic waves in finite length circular cylinders have also been investigated. The SAFE method is used to simulate the guided wave modes in the cylinder. Frequency spectra obtained by the SAFE formulation, for a finite length transversely isotropic cylinder, are validated by comparing the numerical results with relevant publications. Frequency spectra for axisymmetric and asymmetric modes in a silicon nitride finite cylinder with both ends insulated and restrained by frictionless rigid walls are presented. The plain strain problem of circumferential guided waves is also studied and the results are validated for an isothermal case.