About MacSphere

MacSphere is McMaster University's Institutional Repository (IR). The purpose of an IR is to bring together all of a University's research under one umbrella, with an aim to preserve and provide access to that research. The research and scholarly output included in MacSphere has been selected and deposited by the individual university departments and centres on campus.

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Students wishing to deposit their PhD or Masters thesis, please follow the instructions outlined by the School of Graduate Studies.

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Advances In FIB-SEM Nanotomography of Biological Systems
(2026) Williams, Alyssa M.
FIB-SEM nanotomography is a powerful 3D nanoscale characterization tool that performs iterative ion milling and electron imaging to produce high-resolution and large volume imaging. However, for biological samples, FIB-SEM nanotomography requires development and optimization to mitigate artifacts, drift and misalignments to ensure accurate volumetric data acquisitions. The research within this thesis seeks to optimize, analyze and evaluate the use of FIB-SEM nanotomography in biological systems consisting of bone, fossilized bone and bone cells. Bone tissue has a hierarchical organization with distinct hard and soft components at the macro- to nanoscale level. The fundamental nanoscale features of bone, mineral ellipsoids and collagen fibrils constitute the building blocks of bone, and how these components organize and change during external processes, including fossilization, is of high interest. FIB-SEM was optimized to visualize the organization of ellipsoidal mineral clusters and collagen fibrils within highly mineralized human bone tissue, where the twisted plywood organization of mineral ellipsoids was unveiled. Similarly, fossilized Albertosaurus sarcophagus bone tissue was imaged using FIB-SEM to analyze the microstructural organization of the bone, which revealed preserved mineral and organic fundamental components but also diagenetic changes in the specimen. Lastly, FIB-SEM was evaluated with a created semiconductor and Saos-2 (osteosarcoma) cell sample. Through post-acquisition analysis, deviations and errors were identified and corrected, thereby providing a customizable and biologically relevant standard that can be used for 3D FIB-SEM data validation. This thesis advances the utilization of FIB-SEM nanotomography as a reliable nanoscale characterization tool for bone imaging by providing in-depth details on the structural organization of key bone components and insight into the FIB-SEM acquisition behaviour during biological acquisitions. These insights advance the broader bioimaging field, where enhanced nanometer-scale 3D imaging over large volumes provides greater understanding of biological building blocks.
AN INVESTIGATION OF PARAMETERS AFFECTING THE SPURIOUS VARIATION OF PHOTON FLUENCE IN INTENSITY MODULATED RADIATION THERAPY
(2003-12) FABIOLA VALLEJO-CASTANEDA
The parameters that influence the amount of spurious variation in a set of optimized fluence maps (FMs) for intensity modulated radiation therapy (IMRT) were investigated. For this purpose, several simple geometries were used for testing various approaches. The FMs were characterized in term of the mean, standard deviation and first and second derivatives in the two cardinal directions. The peripheral and interior regions of the FMs were analyzed. The parameters tested and the results of the investigations were as follows. (1) The effect of the field margin: it was found that a margin of less than or equal to 0.5cm from the planning target volume (PTV) to the field edge increases the variation of a FM. (2) Incident beam direction: changing to a different but equivalent beam direction caused a small change in the variation of the FM. (3) Minimum transmission: small increases in the minimum transmission values reduce the amount of spurious variation. (4) Sequence of application of objectives: the sequence in which the objectives were applied influenced the smoothness of the fluence map to a small degree. (5) The influence of organ at risk separation from the PTV: the proximity of the PTV to organ at risk (OAR) affects the variation in a fluence map, independent of the thickness of the phantom or the beam direction. (6) The effect of different smoothing strategies on the optimized fluence maps: intelligent smoothing did not appreciably raise the composite objective value whereas a smooth-filter algorithm did. (7) The effect of different dose calculation grids: the amount of variation was reduced when the superior-inferior grid size was a factor of the pencil beam size. The factors that influenced the spurious variation the most were field margin size, ROI separation, minimum transmission and dose calculation grid dimensions. Strategic smoothing algorithms may reduce spurious variation while maintaining acceptable composite objective values. These results were applied to a very limited set of phantom geometries. In order to generalize this work, experiments will need to be done in clinically relevant geometries.
THE AGE OF NARCISSISM: A CULTURAL CRITIQUE OF THE NEW AGE MOVEMENT
(1993-04) Lanna Nakoneshny
The aim of this thesis is to show that the few theories surrounding the New Age movement are inaccurate, unfounded and even dangerous. By looking at the larger cultural contexts of advanced industrial societies, I argue that the New Age is a product of the culture of narcissism. The growing holistic healing practices, which New Age ideas and practices can best be understood, show the desperate need for us to make some sense of things. The search to unite body, mind and spirit emerges as a protective shield to guard off any unpleasant things that the world gives us. Even though the New Age movement has narcissistic tendencies, these leanings are solely brought about by survivalism: that self-awareness is the initial step to try to make a difference in the world. The result of this study is to dispel the myths that we, as participants of popular culture, have about the New Age movement and to judge it with sound facts, data and observation.
Stabilizing Effects of Prey Growth Delay in a Delayed Predator-Prey System
(2026) Lenz Gil, Konstantin
Approved Minutes: November 2025 Graduate Council
(2025) School of Graduate Studies

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