Impact induced dynamic cracks are produced with a Split Hopkinson Pressure Bar (SHPB) apparatus in two rocks (Kuru granite and Flamboro limestone) with impact velocities ranging from 8 to 12 m/s. Impact bit (tungsten carbide) diameters range from 8mm to 15mm. Dye impregnation combined with UV imaging, CAT scans and Optical scans were employed to study the resulting crack patterns. The resulting damage is quantified in terms of radial crack density on impact surface, crater, crushed zone and crack density with depth. In both rocks ‘total’ damage obtained is directly proportional (exponential) with bit diameter and impact velocity. The ‘total’ damage in Kuru granite is found to be greater than Flamboro limestone at all impact velocities; however, the crushed zone in the latter is found to consistently greater than the former. 2D simulations of dynamic fractures with AUTODYN have also been carried out showing good qualitative agreement with experimental results.

Recent developments in instrumentation, communication and software have enabled the integration of real-time data into the decision-making process of hydrocarbon production. Applications of real-time data integration in drilling operations and horizontal-well lateral placement are becoming industry common practice. In reservoir management, the use of real-time data has been shown to be advantageous in tasks such as improving smart-well performance and in pressure-maintenance programs. Such capabilities allow for a paradigm change in which reservoir management can be looked at as a strategy that enables a semi-continuous process of model updates and decision optimizations instead of being periodic or reactive. This is referred to as closed-loop reservoir management (CLRM). Due to the complexity of the dynamic physical processes, large sizes, and huge uncertainties associated with reservoir description, continuous model updating is a large-scale problem with a highly dimensional parameter space and high computational costs. The need for an algorithm that is both feasible for practical applications and capable of generating reliable estimates of reservoir uncertainty is a key element in CLRM. This thesis investigates the validity of Markov Chain Monte Carlo (MCMC) sampling used in a Bayesian framework as an uncertainty quantification and model-updating tool suitable for real-time applications. A 3-phase, dual-porosity, dual-permeability reservoir model is used in a synthetic experiment. Continuous probability density functions of cumulative oil production for two cases with different model updating frequencies and reservoir maturity levels are generated and compared to a case with a known geology, i.e., truth case. Results show continuously narrowing ranges for cumulative oil production, with mean values approaching the truth case as model updating advances and the reservoir becomes more mature. To deal with MCMC sampling sensitivity to increasing numbers of observed measurements, as in the case of real-time applications, a new formulation of the likelihood function is proposed. Changing the likelihood function significantly improved chain convergence, chain mixing and forecast uncertainty quantification. Further, methods to validate the sampling quality and to judge the prior model for the MCMC process in real applications are advised.

The feasibility and success of petroleum development projects depend to a large degree on well construction costs. Well construction cost estimates often contain high levels of uncertainty. In many cases, these costs have been estimated using deterministic methods that do not reliably account for uncertainty, leading to biased estimates. The primary objective of this work was to improve the reliability of deterministic well construction cost estimates by incorporating probabilistic methods into the estimation process. The method uses historical well cost estimates and actual well costs to develop probabilistic correction factors that can be applied to future well cost estimates. These factors can be applied to the entire well cost or to individual cost components. Application of the methodology to estimation of well construction costs for horizontal wells in a shale gas play resulted in well cost estimates that were well calibrated probabilistically. Overall, average estimated well cost using this methodology was significantly more accurate than average estimated well cost using deterministic methods. Systematic use of this methodology can provide for more accurate and efficient allocation of capital for drilling campaigns, which should have significant impacts on reservoir development and profitability.

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Detecting the presence of insects at low densities can avoid total deterioration of stored grains because corrective actions can be implemented early. Tribolium castaneum (Herbst) and Cryptolestes ferrugineus (Stephens) are the major insect pests of the Canadian grain handling industry. Identification of the volatile organic compounds released by insects can be used to detect insects in stored grains. An attempt was made to identify the volatile organic compounds released by T. castaneum and C. ferrugineus by headspace analysis. The volatiles in the head space of vials with insects, insects and wheat flour, and insects and wheat, were analyzed using a GC-MS coupled with an automatic headspace sampler. Wheat with fifteen percent moisture content was used in this study along with two different insect densities. Feasibility of the automatic headspace sampler in headspace analysis was found to be positive. The sampler can do sample conditioning, absorption, trap cleaning and desorption of the volatiles into the GC-MS and speed up the process. The samples extracted at 20 strokes with 1000 µL per stroke, and desorbed at 250°C gave a clear peak of compounds. The amount of volatiles produced by T. castaneum adults varied based on insect densities, the concentration of Methyl-1, 4-benzoquinone; Ethyl-1, 4-benzoquinone; and 1-Tridecene released by ten adult insects were 355, 390 and 530 µg/L compared to 300,310 and 210 µg/L of Methyl-1, 4-benzoquinone; Ethyl-1, 4-benzoquinone; and 1-Tridecene produced by five adult insects. Extreme high and low temperature leading to death produced very high amounts of volatiles compared to insects kept at 35°C. The larvae of the T. castaneum insects did not produce any volatiles at ambient condition as well as at extreme cold and warm conditions. The C. ferrugineus adults did not produced any detectable amount of volatiles even at the higher insect density after up to 3 days. The results of the combination of T. castaneum and C. ferrugineus insects gave the same volatile organic compounds as produced by T. castaneum insects alone. The 1-Tridecene produced by T. castaneum was not reported previously in other studies.

Impact induced dynamic cracks are produced with a Split Hopkinson Pressure Bar (SHPB) apparatus in two rocks (Kuru granite and Flamboro limestone) with impact velocities ranging from 8 to 12 m/s. Impact bit (tungsten carbide) diameters range from 8mm to 15mm. Dye impregnation combined with UV imaging, CAT scans and Optical scans were employed to study the resulting crack patterns. The resulting damage is quantified in terms of radial crack density on impact surface, crater, crushed zone and crack density with depth. In both rocks ‘total’ damage obtained is directly proportional (exponential) with bit diameter and impact velocity. The ‘total’ damage in Kuru granite is found to be greater than Flamboro limestone at all impact velocities; however, the crushed zone in the latter is found to consistently greater than the former. 2D simulations of dynamic fractures with AUTODYN have also been carried out showing good qualitative agreement with experimental results.

The paper sheds light upon a specific issue: carbon leakage. Leakage can be understood as an unanticipated net carbon loss or gain, attributable to a climate policy, or reduction activities. Benign leakage effects are harmless. Unsettling are the ones that pose a threat to project’s environmental integrity. The Clean Development Mechanism (CDM) is no exception to such risk. In order to investigate leakage and the corresponding leakage calculation methods addressed in the CDM projects, a qualitative content analysis is conducted on 203 methodologies. Methodology documents serve as ideal textual data for examining CDM related leakage because the development of any new project must be based on methodologies. In relation to the research question, the content analysis synthesizes 11 types of leakage sources. Excluding the case where no leakage is considered, 10 type of leakage sources are then broadly classified as Activity Shift, Market Effects and Life Cycle Leakage. Their corresponding leakage calculation methods are described and reviewed in terms of their geographic reach, and leakage characteristics. A percentage pattern is presented in relation to each sector. The findings are that the vast majority of the CDM leakage calculation methods address primary leakage specific to each individual project at a localized scale, among which, methods addressing Life Cycle Leakage are in the predominant majority. Market Effects as secondary sources are acknowledged as a potential threat to the overall benefit, but the CDM methodologies offer no quantitative method.

In 2012, more than 1.6 million new cases of breast cancer were diagnosed and about half a million women died of breast cancer. The incidence has increased in the developing world. The mortality, however, has decreased. This is thought to partly be the result of advances in diagnosis and treatment. Studying tissue samples from biopsies through a microscope is an important part of diagnosing breast cancer. Recent techniques include camera-equipped microscopes and whole slide scanning systems that allow for digital high-throughput scanning of tissue samples. The introduction of digital pathology has simplified parts of the analysis, but manual interpretation of tissue slides is still labor intensive and costly, and involves the risk for human errors and inconsistency. Digital image analysis has been proposed as an alternative approach that can assist the pathologist in making an accurate diagnosis by providing additional automatic, fast and reproducible analyses. This thesis addresses the automation of conventional analyses of tissue, stained for biomarkers specific for the diagnosis of breast cancer, with the purpose of complementing the role of the pathologist. In order to quantify biomarker expression, extraction and classification of sub-cellular structures are needed. This thesis presents a method that allows for robust and fast segmentation of cell nuclei meeting the need for methods that are accurate despite large biological variations and variations in staining. The method is inspired by sparse coding and is based on dictionaries of local image patches. It is implemented in a tool for quantifying biomarker expression of various sub-cellular structures in whole slide images. Also presented are two methods for classifying the sub-cellular localization of staining patterns, in an attempt to automate the validation of antibody specificity, an important task within the process of antibody generation.  In addition, this thesis explores methods for evaluation of multimodal data. Algorithms for registering consecutive tissue sections stained for different biomarkers are evaluated, both in terms of registration accuracy and deformation of local structures. A novel region-growing segmentation method for multimodal data is also presented. In conclusion, this thesis presents computerized image analysis methods and tools of potential value for digital pathology applications.

Mass spectrometry has increasingly become the method of choice for the analysis of complex biological samples, including proteins and lipids. This thesis describes the development of MS-based analytical methodologies for the analysis of complex proteomic and lipidomic samples. Chapter 3 describes the development of microfluidic proteomic reactors, in the formats of SCX reactor, SCX 96-well plate reactor, and SAX reactor, for the enzymatic digestion of complex proteomic samples for subsequent LC-MS/MS analysis. These microfluidic proteomic reactors greatly simplified the enzymatic digestion of complex proteomic samples by combining multiple processing steps, such as rapid extraction and enrichment of proteins. Furthermore, chemical and enzymatic treatments of proteins were all performed in a few nanoliters effective volume, resulting in an increased protein digestion efficacy. After the protein digestion process, the resulting peptides were eluted in buffers that were compatible with HPLC-MS/MS analysis. In chapter 4, a methodology based on nano-HPLC-ESI-MS/MS for the analysis of PAF and LPC lipid species is described. In this method, lipid extracts from biological samples were separated by nano-flow HPLC prior to being introduced into a Q-TRAP 2000 mass spectrometer, where the lipid species of interest were detected using a precursor ion scan at m/z 184. Absolute quantitation of PAF family lipid species were performed with standard addition method, where 5 standard solutions containing 0.2-1 ng each of C16:0, C18:0 PAF and C16:0, C18:0 lyso-PAF were used in the experiment. Further, the spiking of identical amount of non-endogenous C13:0 LPC at time of extraction allow the relative comparisons of other LPC lipid species of interest between different samples. The developed methods were employed to analyze the changes of PAF and LPC lipid species in NGFdifferentiated PC12 cells, in the posterior/entorhinal cortex of AD patients and TgCRND8 transgenic mice, and over the course of 24 hour exposure of human hNT neurons to Aβ42 treatment, respectively, in comparison to controls. iii Chapter 5 describes the development of a novel shotgun lipidomic methodology for the determination of stereospecificity of diacyl glycerophospholipids including glycerophosphatidic acids (PA), glycerophosphoserines (PS), glycerophosphoglycerols (PG), glycerophosphoinositols(PI), and glycerophosphoethanolamines (PE), which can be conventionally ionized under negative ion mode. The stereospecificity of diacyl glycerophospholipids was determined based on the relative abundance of the lyso-form fragment ions, attributed to the neutral loss of fatty acyl moieties. The fragmentation patterns of a variety of diacyl glycerophospholipid standards were first fully examined over a wide range of collision energy. We observed that lyso-form fragment ions corresponding to the neutral loss of fatty acyl moieties attached to the sn2 position as free fatty acids ([M-Sn2]-) and as ketenes ([M-(Sn2-H2O)]-) exhibited consistently higher intensity than their counter part ions due to the neutral loss of fatty acyl moieties attached to the sn1 position ([M-Sn1]- and [M-(Sn1-H2O)]-). We then examined the product ion spectra of diacyl glycerophospholipids recorded from lipid extracts of rat hepatoma cells, where the stereospecific information of these lipids was conclusively determined.

Detecting the presence of insects at low densities can avoid total deterioration of stored grains because corrective actions can be implemented early. Tribolium castaneum (Herbst) and Cryptolestes ferrugineus (Stephens) are the major insect pests of the Canadian grain handling industry. Identification of the volatile organic compounds released by insects can be used to detect insects in stored grains. An attempt was made to identify the volatile organic compounds released by T. castaneum and C. ferrugineus by headspace analysis. The volatiles in the head space of vials with insects, insects and wheat flour, and insects and wheat, were analyzed using a GC-MS coupled with an automatic headspace sampler. Wheat with fifteen percent moisture content was used in this study along with two different insect densities. Feasibility of the automatic headspace sampler in headspace analysis was found to be positive. The sampler can do sample conditioning, absorption, trap cleaning and desorption of the volatiles into the GC-MS and speed up the process. The samples extracted at 20 strokes with 1000 µL per stroke, and desorbed at 250°C gave a clear peak of compounds. The amount of volatiles produced by T. castaneum adults varied based on insect densities, the concentration of Methyl-1, 4-benzoquinone; Ethyl-1, 4-benzoquinone; and 1-Tridecene released by ten adult insects were 355, 390 and 530 µg/L compared to 300,310 and 210 µg/L of Methyl-1, 4-benzoquinone; Ethyl-1, 4-benzoquinone; and 1-Tridecene produced by five adult insects. Extreme high and low temperature leading to death produced very high amounts of volatiles compared to insects kept at 35°C. The larvae of the T. castaneum insects did not produce any volatiles at ambient condition as well as at extreme cold and warm conditions. The C. ferrugineus adults did not produced any detectable amount of volatiles even at the higher insect density after up to 3 days. The results of the combination of T. castaneum and C. ferrugineus insects gave the same volatile organic compounds as produced by T. castaneum insects alone. The 1-Tridecene produced by T. castaneum was not reported previously in other studies.