<p>This thesis provides new regression methods for the removal of structured noise in datasets. With multivariable data, the variables and the noise can be both temporally correlated (i.e. auto correlated in time) and contemporaneously correlated (i.e. cross-correlated at the same time). In many occasions it is possible to acquire measurements of the noise, or some function of it, during the data collection. Several new constrained latent variable methods (LVM) that are built upon previous LVM regression frameworks are introduced. These methods make use of the additional information available about the noise to decompose a dataset into basis for the noise and signal. The properties of these methods are investigated mathematically, and through both simulation and application to actual biomedical data.</p> <p>In Chapter Two, linear, constrained LVM methods are introduced. The performance of these methods are compared to the other similar LVM methods as well as ordinary PLS throughout several simulation studies. In Chapter Three, a NIPALS type algorithm is developed for the soft constrained PLS method which is also able to account for missing data as well as datasets with large covariance matrices. Chapter Four introduces the nonlinear-kernelized constrained LVM methods. These methods are capable of handling severe nonlinearities in the datasets. The performance of these methods are compared to nonlinear kernel PLS method. In Chapter Five the constrained methods are used to remove ballistocardiographic and muscle artifacts from EEG datasets in combined EEG-fMRI as well as single EEG experiments on patients. The results are shown and compared to the standard noise removal methods used in the field. Finally in Chapter Six, the overall conclusion and scope of the future work is laid out.</p> / Doctor of Philosophy (PhD)

<p>High-content screening (HCS) produces an immense amount of data, often on the scale of Terabytes. This requires considerable processing power resulting in long analysis time. As a result, HCS with a single-core processor system is an inefficient option because it takes a huge amount of time, storage and processing power. The situation is even worse because most of the image processing software is developed in high-level languages which make customization, flexibility and multi-processing features very challenging. Therefore, the goal of the project is to develop a multithreading model in C language. This model will be used to extract subcellular localization features, such as threshold adjacency statistics (TAS) from the HCS data. The first step of the research was to identify an appropriate dye for use in staining the MCF-7 cell line. The cell line has been treated with staurosporin kinase inhibitor, which can provide important physiological and morphological imaging information. The process of identifying a suitable dye involves treating cells with different dye options, capturing the fluorescent images of the treated cells with the Opera microscope, and analyzing the imaging properties of the stained cells. Several dyes were tested, and the most suitable dye to stain the cellular membrane was determined to be Di4-Anepps. The second part of the thesis was to design and develop a parallel program in C that can extract TAS features from the stained cellular images. The program reads the input cell images captured by Opera microscopes, converts it to TIFF format from the proprietary Opera format, identifies the region-of-interest contours of each cell, and computes the TAS features. A significant increase in speed in the order of four fold was obtained using the customized program. Different scalability tests using the developed software were compared against software developed in Acapella scripting language. The result of the test shows that the computational time is proportional to number of cells in the image and is inversely proportional to number of cores in a processor.</p> / Master of Applied Science (MASc)

<p>A microfluidic device capable of drug delivery to multiple wells in a concentration gradient was designed for automated high content and high throughput screening. The design was proposed to utilize a nanoporous polycarbonate membrane to spatially and temporally control drug dosage from the microchannels below to the wells above. Microchannels were to hold to the drugs or reagents, while wells were to culture cells. An array of 16 wells was to fit in the equivalent area of a single well of a 96 well plate. Two simpler devices were created to validate electrokinetic drug delivery to a single well and to characterize cell proliferation and viability in micro-wells. The first device tested drug delivery to a single well with methylene blue dye at applied voltages of 100V, 125V, and 150V. It was validated that the dosage of dye could be controlled by increasing the voltage and by increasing the duration the voltage was applied. The second devices were a series of 9-well arrays, each testing a different diameter (1.2 mm – 0.35 mm). These devices were cultured with MCF-7 breast cancer cells over 5 days. At the end of the 5 day study, all diameters except for 0.5 mm and 0.35 mm measured a cell viability of 99% and exhibited cell growth patterns similar to coverslip glass controls. The proposed integrated cell culture and drug delivery device could have application towards early stage drug discovery and could have compatibility with lab equipment originally designed for well plates.</p> / Master of Applied Science (MASc)

ACL injury has been shown to have long-lasting and severe consequences on the different structures of the knee such as the articular cartilage and meniscus. Cartilage thickness changes in particular are indicative of osteoarthritic changes in the tibiofemoral joint. While there has been significant research focused on cartilage changes of the tibia and femur, there has been little work looking at patellar cartilage. The following goals were set forth for this study. First, to establish a robust coordinate system to accurately determine the location and orientation of the patella. Secondly, to determine the effects of ACL injury on patellar cartilage thickness. Twenty-one individuals (10 males, 11 females) were studied. All individuals had suffered first time ACL injuries to one of their knees. MRI data from both the healthy and injured knees were collected an average of 4 ± 0.9 years. Using MRI data, the bone and cartilage surfaces were manually segmented and imported into MATLAB for study. Differences in cartilage thickness values between the healthy and unhealthy knees within individuals was the primary measure of analysis. Analysis revealed a total of 9 square millimeters of cartilage surface area that were statistically significant. Four square millimeters of significant difference were found in males in the medial superior compartment, (mean thickness difference = -0.381 mm, with SD = 0.084mm, indicating thinning). Five square millimeters of significant difference were found in females in the medial inferior compartment (mean thickness difference = 0.551 mm, SD = 0.015mm, indicating thickening). This suggests regional and sex related cartilage thickness changes occur following ACL injury, surgery, and 4 year follow-up.

One of the most recent advancements in laser technology is the development of ultrashort pulsed femtosecond lasers (FSLs). FSLs are improving many fields due to their unique extreme precision, low energy and ablation characteristics. In the area of laser medicine, ophthalmic surgeries have seen very promising developments. Some of the most commonly performed surgical operations in the world, including laser-assisted in-situ keratomileusis (LASIK), lens replacement (cataract surgery), and keratoplasty (cornea transplant), now employ FSLs for their unique abilities that lead to improved clinical outcome and patient satisfaction. The application of FSLs in medical therapeutics is a recent development, and although they offer many benefits, FSLs also stimulate nonlinear optical effects (NOEs), many of which were insignificant with previously developed lasers. NOEs can change the laser characteristics during propagation through a medium, which can subsequently introduce unique safety concerns for the surrounding tissues. Traditional approaches for characterizing optical effects, laser performance, safety and efficacy do not properly account for NOEs, and there remains a lack of data that describe NOEs in clinically relevant procedures and tissues. As FSL technology continues to expand towards new applications, FSL induced NOEs need to be better understood in order to ensure safety as FSL medical devices and applications continue to evolve at a rapid pace. In order to improve the understanding of FSL-tissue interactions related to NOEs stimulated during laser beam propagation though corneal tissue, research investigations were conducted to evaluate corneal optical properties and determine how corneal tissue properties including corneal layer, collagen orientation and collagen crosslinking, and laser parameters including pulse energy, repetition rate and numerical aperture affect second and third-harmonic generation (HG) intensity, duration and efficiency. The results of these studies revealed that all laser parameters and tissue properties had a substantial influence on HG. The dynamic relationship between optical breakdown and HG was responsible for many observed changes in HG metrics. The results also demonstrated that the new generation of therapeutic FSLs has the potential to generate hazardous effects if not carefully controlled. Finally, recommendations are made to optimize current and guide future FSL applications.

L’utilisation de nano-objets luminescents en milieu biologique est devenue très répandue, notamment en vue d’applications biomédical est elles que l’imagerie, la thérapie et le diagnostic. Jusqu’à récemment, les principaux travaux réalisés dans ce domaine concernaient les nanoparticules de silice dopées ou fonctionnalisées avec des molécules organiques, les nanoparticules d’or et les nanoparticules semi-conductrices (quantum dots, i.e., QDs). Toutefois, un certain nombre de limitations demeurent pour les applications dans le domaine du vivant, en lien notamment avec des problèmes de stabilité, de biocompatibilité et de toxicité ou encore de biodégradabilité. En parallèle,un certain nombre de molécules organiques fluorescentes non-toxiques ont été utilisées comme sondes fluorescentes en milieu biologique, mais leur brillance demeure limitée. L’idée directrice de la thèse est de concevoir et synthétiser de nouveaux chromophores organiques présentant une émission modulable (du visible au proche infrarouge) et adaptés à la préparation de nanoparticules organiques fluorescentes (FONs) combinant à la fois une brillance extrêmement élevée, une excellente stabilité colloïdale et une photostabilité adaptée à leur utilisation en imagerie in vitro et in vivo. De tels nanoobjets ultra-brillants pourraient alors représenter une alternative très intéressante aux nanoparticules actuellement les plus utilisées en imagerie de fluorescence du vivant (QDs). Le manuscrit décrit la synthèse et les propriétés de plusieurs classes de molécules fluorescentes spécifiquement conçues pour former des telles FONS par auto-assemblage dans l’eau. La préparation de ces FONs est présentée et leurs propriétés étudiées et discutées. Enfin des applications concrètes en bio-imagerie sont présentées. / Nowadays the use of bright luminescent nano-objects in biological environment is a topic that is gaining more and more importance, especially for biomedical applications such as imaging, the rapyand diagnostic. So far, numerous studies have been conducted with gold nanoparticles, silica nanoparticles (doped or functionalized with organic molecules), as well as semiconductor nanoparticles (quantum dots, i.e., QDs). However, most of these nanoparticles suffer from drawbacks (in terms of stability, biocompatibility, eco-toxicity or degradability). On the other hand, several nontoxic fluorescent molecular probes have been widely used, but most of the time their brightness remain modest in biological environments compared to QDs. Our idea is to engineer new organicchromophores with tunable emission wavelength (from visible to near infrared) for further preparation of organic fluorescent nanoparticles (so called FONs) that display giant one-photon and two-photonbrightness, as well as good colloidal and chemical stability, and suitable photostability for in vitro andin vivo imaging. As such, these FONs would represent interesting alternatives to QDs for use in bioimaging. This manuscript describes the synthesis and characterization of new classes of fluorescent molecules specifically engineered as building blocks for the fast preparation of such nanoparticles byself-aggregation in water. The FONs were fully characterized from both morphological and photophysical points of view and further used in bioimaging.

O trabalho apresentado nessa dissertação concentra-se na área de espectroscopia de íons terras raras com aplicação em biofotônica e foi desenvolvido através da síntese de partículas de fluoreto de bário e gadolínio dopada com o par Yb3+/Tm3+ para estudos conversão ascendente de energia, além da tentativa de crescimento desse material nos poros de uma nanoesfera de sílica. Os materiais a base de fluoretos foram sintetizados através de metodologia hidrotermal com agente complexante citrato de sódio variando a concentração de dopagem do par Yb3+/Tm3+ produzindo três diferentes materiais luminescentes que apresentou conversão ascendente em energia e emissões características do íon túlio a partir da excitação em 980 nm (BaGdF5YbTm nos quais a razão (porcentagem mol/mol) Yb/Tm foi igual à 18/0,5; 20/1 e 10/0,5), além de um quarto material dopado com o íon Eu3+ para estudos estruturais e espectroscópicos acerca da matriz (BaGdF5Eu Gd/Eu 1% mol/mol). Todos os materiais obtidos pela metodologia são cristalinos e apresentaram fase cúbica da solução sólida de BaGdF5. Ademais, dois materiais híbridos, contendo sílica e fluoreto, foram preparados. O primeiro, recobrimento das partículas de fluoreto com sílica (SiO2), apresentou resultados diferentes do que foi previamente reportado por esse grupo de pesquisa, direcionando os estudos ao segundo material, que consistiu no crescimento de partículas de fluoreto dentro dos poros de uma nanoesfera de sílica (SiO2). Neste último, os materiais apresentaram manutenção da morfologia esférica precursora das nanoesferas de sílica além de, para uma amostra sintetiza hidrotermicamente na ausência de citrato de sódio, promover o aparecimento da banda 1D4 5H6 e serão conduzidas para testes biológicos subsequentes como citotoxicidade. / The work presented herein focuses on the area of rare earth spectroscopy with application in biophotonics and it was developed through the synthesis of barium and gadolinium fluoride particles doped with the Yb3+/Tm3+ pair for upconversion studies and the attempt to grow the material in the pores of a silica nanosphere. Biophotonic has been an area of growing interest for the last 30 years, it studies the interaction between light and living matter seeking new technologies in order to characterize, image, diagnose and treat a complexity of dysfunctions in biological material. The search and development of new materials for bioimaging is a need that involves several areas of knowledge. In this work, fluoride-based materials were synthesized by hydrothermal method by varying the doping concentration of Yb3+/Tm3+ pair producing 3 different luminescent materials (BaGdF5YbTm - in which the ratio (mole/mole percentage) Yb/Tm was equal to 18/0,5; 20/1 and 10/0,5). In addition, a fourth material doped with Eu3+ was synthetized for structural and spectroscopic studies on the matrix (BaGdF5Eu - Gd / Eu 1 mol% mol). All materials obtained by this method were crystalline and presented cubic phase of BaGdF5 solid solution. Moreover, two multifunctional materials were prepared. The first was obtained by coating the fluoride particles with silica (SiO2) presented different results than previously reported by this research group, directing the studies to the second material, which consisted of the growth of fluoride particles inside the pores of a nanosphere of silica (SiO 2). In the latter, the materials showed maintenance of the precursor spherical morphology of silica nanospheres and, for a hydrothermally synthesized sample in the absence of sodium citrate, promote the appearance of the 1D4 5H6 band and will be conducted for subsequent biological tests as cytotoxicity.

Probiotics are marketed throughout the world to promote the health of the consumer by improving the microorganisms that normally occur in the intestinal tract (Tannock, 1997). It has also been suggested that probiotics can prevent pathogen infections by adhering to the intestinal mucosa (Lee, Lim, Teng, Ouwehand, Tuomola, & Salminen, 2000). While probiotics can be delivered to the infected areas in multiple fashions, microencapsulation is a newer form of delivering probiotics straight to the infected area. A whey protein microcapsule is thought to protect the probiotics from stomach acid and delivers the treatment to the affected area. To ensure this microencapsulation treatment is affective, the microcapsules will be stained and imaged to see if the microcapsules are constructed in a way which is consistent with the theory: a whey protein microcapsule surrounding bacteria and fat droplets. Through these experiments, it was shown that the microcapsule was not constructed as previously thought. Instead of a thin layer of protein surrounding the bacteria, it more closely resembled a solid ball of protein with bacteria and fat trapped inside. The bacteria are able to survive stomach like conditions (0.1M HCl for 8 hours) due to other forms of microencapsulation.

The application of high frequency ultrasound is the key to higher resolution intravascular ultrasound (IVUS) images. The need to further improve the IVUS spatial resolution may drive the transducer center frequency even higher than the current 40 MHz range. However, increasing the center frequency may be challenging as it leads to stronger scattering echoes from blood. The high level of blood scattering echoes may obscure the arterial lumen and make image interpretation difficult. Blood backscatter levels increase with transmission center frequency at a much greater rate compared to arterial tissue. These different frequency dependencies provide a potential method to distinguish blood from tissues by means of multi-frequency processing techniques. To obtain a good blood-tissue contrast with sufficient signal-to-noise ratio, a system with a wider bandwidth is highly desirable. The method described in this paper is based on the ratio of the received signal power between the high (60 MHz) and low (25 MHz) frequency ranges from a novel 40 MHz wideband IVUS catheter. In this paper we will present our in vitro experiment work on porcine blood and a tissue-mimicking arterial wall. Results of multi-frequency processing indicate that blood, at higher frequencies, has a greater backscatter power that is 8X greater than arterial tissue, suggesting this technique will provide a greater contrast between the blood-wall lumen boundary for coronary imaging.

Medical imaging can involve different modalities, such as computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. Each examination generated by these modalities has a set of unique instructions, the imaging protocol, which are imaging parameters determine the signal and contrast for creating a particular medical image. Properly managing imaging protocols is like systemically documenting an instruction handbook, which guarantees the quality of scans by providing the radiologist and technicians with appropriate procedures for a given indication. It also ensures patients’ safety by reducing repeated scans to acquire the desired image information. Radiology Protocols (RP) is a company that provides an online medical protocol database to improve protocol management. It recently developed RP Import, an imaging protocol import software, to automatically collecting elements from the medical imaging file – Digital Imaging and Communications in Medicine (DICOM) files, and mapping them to the specified protocol database. With the help of RP Import, protocol creation is much faster and eliminates manual definition of the parameters, thus this tool lays the foundation of the further development of imaging protocol management. Radiology Protocols also developed a series of Modality Calculators to assist radiologists and technicians to build or modify imaging protocols as they are needed. These calculators cover most of the essential medical parameter calculations associated with different modalities. By using them, computing specific parameters while editing protocols becomes more convenient, and determining the use and amount of certain medical parameters becomes more precise as well. In summary, RP Import and Modality Calculators are two meaningful tools in protocol management, and they also play very important roles in regulating procedure and dosage during the medical image practice.