The current approach for using cone penetration test data to estimate soil behavior during seismic loading involves the comparison of the seismic stresses imparted into a soil mass during an earthquake to the penetration resistance measured during an in-situ test. The approach involves an indirect empirical correlation of soil density and other soil related parameters to the behavior of the soil during the loading and does not involve a direct measurement of the dynamic behavior of the soil in-situ. The objective of this research was to develop an approach for evaluating the in-situ behavior of soil during dynamic loading directly through the use of a vibrating piezocone penetrometer. Cone penetration tests were performed in a large calibration chamber in saturated sand samples prepared at different densities and stress levels. A total of 118 tests were performed as part of the study. The piezocone penetrometer used in the investigation was subjected to a vibratory load during the penetration test. The vibratory units used in the investigations were mounted on top of a 1m section of drill rod that was attached at the lower end to the cone penetrometer. Pneumatic impact, rotary turbine, and counter rotating mass vibrators were used in the investigation. The vibration properties generated by the vibratory unit and imparted into the soil were measured during the penetration test by a series of load cells and accelerometers mounted below the vibrator and above the cone penetrometer, respectively. The tip resistance, sleeve friction and pore water pressure were also measured during the test by load cells and transducers in the cone itself. The vibration and cone data were compiled and compared to evaluate the effect of the vibration on the penetration resistance and pore water pressure in the soil mass. The results of the testing revealed that the influence of the vibration on the penetration resistance value decreased as the density and the mean effective stress in the soil increased, mainly because the pore water pressure was not significantly elevated throughout the entire zone of influence of the cone penetometer at the elevated stress and density conditions. An analysis of the soil response during the testing resulted in the generation of a family of curves that relates the soil response during the vibratory and static penetration to the vertical effective stress and density of the soil. The data used to generate the curves seem to agree with the proposed values estimated through the empirical relationship. An evaluation of the effects of the frequency of vibration was also performed as part of the study. The largest reduction in penetration resistance occurred when the input vibration approximated the natural frequency of the soil deposit, suggesting that resonance conditions existed between the input motion and the soil. An energy-based approach was developed to compare the energy imparted into the soil by the vibrator to the energy capacity of the soil. The input energy introduced into the soil mass prior to the reduction in penetration resistance agrees well with the energy capacity of the soil, especially in tests at the low effective stress level where a high excess pore water pressure was observed. / Ph. D.

Porous ceramics have successfully been used in a wide variety of highly advanced applications. Current routes to porous ceramics are limited in the types of porosity they can create and no one process is flexible enough to create any desired structure. This study introduces the use of ice particles as pore forming agents to fabricate porous materials. This novel method possesses several advantages over current industrial techniques including environmental friendliness, low cost, and flexibility in size and shape of resulting pores. Porous ceramic structures were created by adding preformed ice particles to an alumina slurry which was quickly frozen, air dried, and then sintered. Porosity was characterized using Scanning Electron Microscopy (SEM), Archimedes measurements, and gas sorption techniques. Small spherical pores were successfully created in the 20-200?m range and larger spherical pores were also created in the 2-3 mm range. Amount of porosity was controlled through specifying the amount of ice added to the ceramic slurry. Samples were prepared with porosity levels ranging from 30-75%. As a completely new process, these initial results are quite promising and further development will allow for even greater morphology control. / Master of Science

Lateral swelling pressure induced in expansive soils upon wetting can adversely impact the performance and integrity of earthen structures and foundations. The yearly cost associated with damage to structures from expansive clays in the United States is estimated to exceed the loss associated with natural disasters such as earthquakes, floods, and hurricanes. The main objective of this dissertation is to provide new insight into the evolution of lateral swelling pressure in variably saturated expensive soils under infiltration via physical testing. In the first part of this study, a new laboratory-scale testing apparatus was built to measure lateral and vertical swelling pressures under anisotropic conditions. The testing apparatus was used to investigate the effect of compaction level on lateral swelling pressure in an expansive clay collected from central Arkansas. Results show that the higher the compaction, the higher the lateral swelling pressure. In contrast, compaction was found to have an insignificant effect on the vertical swelling pressure at a compaction level of less than 90%. In the second part, the laboratory-scale testing apparatus was employed to test the effects of four additives (lime, lime kiln dust, cement, and cement kiln dust). The results showed that the addition of a high calcium additive could significantly reduce the swelling pressures of expansive clay. The third part of the dissertation involved full-scale testing of lateral pressures in an expansive clay upon infiltration. A heavily instrumented 3-m high masonry wall backfilled with an expansive clay was built and subjected to infiltration. The degree of saturation, pore-water pressure, temperature, suction, and lateral and vertical pressures were monitored at different locations during the test. Results showed that the development of lateral pressure is rapid during initial saturation and levels out as the clay approaches saturation levels. This finding highlights the importance of monitoring lateral pressure over time to accurately predict its behavior. The study also found that lateral pressure develops prior to vertical pressure, depending on the area and restraint.

The intricate task of segmenting and quantifying cell nuclear pores in high-resolution 3D microscopy data is critical for cellular biology and disease research. This thesis introduces a deep learning pipeline crafted to automate the segmentation and quantification of nuclear pores from high-resolution 3D cell organelle images. Our aim is to refine computational methods capable of handling the data's complexity and size, thus improving accuracy and reducing manual labor in biological image analysis. The developed pipeline incorporates data preprocessing, augmentation strategies, random block sampling, and a three-stage post-processing algorithm. It utilizes a 3D U-Net with a VGG-16 backbone, optimized through cyclical data augmentation and random block sampling to tackle the challenges posed by limited labeled data and the processing of large-scale 3D images. The pipeline has demonstrated its capability to effectively learn and predict nuclear pore structures, achieving improvements in validation metrics compared to baseline models. Our experiments suggest that cyclical augmentation helps prevent overfitting, and random block sampling contributes to managing data imbalance. The post-processing phase successfully automates the quantification of nuclear pores without the need for manual intervention. The proposed pipeline offers an efficient and scalable approach to segmenting and quantifying nuclear pores in 3D microscopy images. Despite the ongoing challenges of computational intensity and data volume, the techniques developed in this study provide insights into the automation of complex biological image analysis tasks, with potential applications extending beyond the detection of nuclear pores. / Master of Science / This thesis outlines a computer program developed to automatically segment and count nuclear pores in 3D cell images, aiding cell and disease research. This program aims to handle large, complex image data more effectively, boost accuracy, and cut down the need for manual labor. We created a system that prepares data, applies a technique called augmentation to enrich it, selects specific image sections, and carries out a three-step final analysis. At the core of our program is a 3D U-Net model, a type of deep learning network, that has been enhanced to address the challenges of scarce labeled data and the processing of very large images. The system developed is capable of learning and identifying the structure of nuclear pores in cell images. Our experiments indicate that using augmentation in a cyclical manner during training can prevent overfitting, which is when a model learns the training data too well, and cannot suitably generalize. Selecting certain parts of the images for processing proves helpful with imbalanced data. Additionally, the program can automatically count nuclear pores in the final step. The proposed program is effective for analyzing and counting nuclear pores in 3D cell images and has the potential for broader applications in cell analysis. Despite the challenges of managing large datasets and the significant computational power required, our methods open new possibilities for automating cell studies, with uses extending beyond just nuclear pores.

Field-based liquefaction evaluation procedures include the stress-based, strain-based, and energybased based approaches. The existence of a volumetric threshold shear strain, γtv, under which there is no development of excess pore pressures, and the unique relationship between pore pressure ratio and cyclic shear strain, γc, make a compelling argument for using a strain-based approach. However, the cyclic strain approach has not yet been standardized for field evaluations. The primary objective of this thesis is to use published databases of 415 shear-wave velocity and 230 Standard Penetration Test liquefaction field case histories to investigate the performance of the cyclic strain approach for the evaluation of initial liquefaction relative to the cyclic stress approach. Additionally, the concept of the γtv is expressed in terms of the peak ground surface acceleration and defined as the threshold amax. Computing (amax)t could provide a fast and simple evaluation for initial liquefaction, where no liquefaction is expected for a minimum computed (amax)t determined from the case histories. The variant of the strain-based procedure proposed herein avoids the direct need for laboratory cyclic testing by employing pore pressure generation models that are functions of cyclic shear strain, number of equivalent cycles, and relative density to predict initial liquefaction. The results from the proposed procedure are compared with those of the stress-based approach to determine which better matches the field observations of the case histories. It was found that the cyclic strain approach resulted in 70% to 77% correct predictions. In contrast, the cyclic stress approach yielded 87% to 90% correct predictions. The reasons why the predictions were not always correct with the cyclic strain approach are due to inherent limitations of the cyclic strain approach. Most significantly, an inherent and potentially fatal limitation of the strain-based procedure is it ignoring the softening of the soil stiffness due to excess pore pressure in representing the earthquake loading in terms of γc and neqγ. / Master of Science / Earthquakes can cause heavy damage when they occur. One of the ways in which this happens is when the earthquake shaking causes the soil to behave like a liquid. This is the phenomenon known as liquefaction. An example of liquefaction is a person sinking in quicksand. Relating this to earthquakes, liquefaction can be thought of as a building sinking in quicksand that formed as a consequence of earthquake shaking. Destructive cases of liquefaction have been reported in almost all major earthquakes. When cases of liquefaction are properly documented, they can provide information that will help engineers and scientists assess the efficacy of existing liquefaction evaluation procedures and/or to develop new procedures. There are different methods to evaluate the occurrence of liquefaction, with the cyclic stress approach being the most widely used. This study assesses the efficacy of an alternative approach to see if it yields better predictions of liquefaction triggering than the cyclic stress approach. The approach under consideration is called the cyclic strain approach. To examine the effectiveness of the cyclic strain approach, sites that experienced liquefaction in the past were analyzed to see if the predictions made with the approach matched the past field observations. Due to potential shortcomings in implementing the strain based procedure, as well as inherent limitations of the procedure, the strain-based procedure yielded predictions that were inferior to the more widely used stress-based procedure.

Free-fall penetrometers (FFPs) are an attractive tool for the rapid characterization of sediments in the nearshore and coastal areas. To improve their measurement capabilities, modern FFPs can be equipped with pore pressure sensors. Pore pressure measurements are extensively used in traditional cone penetration testing, but their usage and interpretation is still limited for FFP testing. This thesis represents an effort to advance the interpretation of pore pressure measurements from FFP testing. Data was collected using the torpedo-shaped FFP BlueDrop during surveys at Herschel Island, YT, Yakutat, AK, Clay Bank, VA, and Yorktown, VA. Additionally, test deployments in the laboratory were performed in kaolin clay. Data analysis was focused on pore pressure measurements during these deployments. Two major advancements regarding current data analysis of FFP pore pressure measurements were explored: 1) a method based on fluid dynamic principles was proposed to correct the pressure recordings for the dynamic flow effects due to the high-velocity fall and impact. The results show that using Bernoulli’s theorem coupled with the concept of pressure coefficients results in good agreement between measured and hydrostatic pressures during the free-fall and initial penetration stage. 2) Pore pressure dissipation curves measured by the penetrometer at rest at maximum penetration depth were also studied. The mechanisms behind the non-standard dissipation curves were explored. The results suggest that non-standard dissipation curves can be interpreted by correcting according to Sully et al.’s (1999) extrapolation technique. The technique can also be used with data from an unsaturated or clogged filter. / Master of Science / An increasing use of nearshore and offshore areas for the development of infrastructure such as pipelines, cables, renewable energy harvesting devices, and measures against coastal erosion warrants the development of specialized methods for investigating the stability of the seabed. Portable free-fall penetrometers represent a cost-efficient approach to characterize shallow seabed sediments, but there are challenges associated with deriving geotechnical design parameters from these novel instruments. This study aims at developing a better understanding of the pore pressure (the pressure developed in the water in the soil’s voids) data obtained during free-fall penetration testing. The pore pressures developed during the penetration of the penetrometer is dependent on the soil type, and is often used to correlate to it. This study used data obtained from field surveys at Herschel Island, YT, Clay Bank, VA, Yakutat, AK, and Yorktown, VA. Additionally, controlled tests were performed in the laboratory in an instrumented seabed. This study resulted in a novel method to correct the pressure data from the penetrometer for dynamic fluid flow effects and validation of an interpretation technique for dissipation curves to obtain the time required for consolidation, based on initial results.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

L'ischémie-reperfusion (IR) rénale entraîne des lésions de nécrose tubulaire aigue, nécessitant parfois une épuration extra rénale transitoire voir définitive. La mitochondrie joue un rôle important dans la physiopathologie de ces lésions d'IR en entrainant la mort cellulaire. L'étude de l'IR dans la cellule cardiaque a permis de mettre en évidence le rôle central du pore de transition de perméabilité mitochondriale (mPTP) dans le déclenchement de cette mort cellulaire. La ciclosporine (CsA) a été proposée comme thérapeutique pour protéger la cellule des lésions d'IR en retardant l'ouverture de ce mPTP. Cependant la CsA a des effets rénaux vasoconstricteurs aigus, nécessitant une validation expérimentale de sa protection dans l'IR rénale. Au cours de ce travail de thèse, nous avons mis au point un modèle murin d'IR rénale. Ensuite nous avons montré que le post-conditionnement à la CsA, ainsi que le post-conditionnement ischémique, permettent d'améliorer la fonction rénale avec un retard à l'ouverture du mPTP. Dans un deuxième travail, nous montrons que le pré conditionnement à la CsA est dose et temps dépendant, et médié en partie par l'augmentation d'expression d'une protéine chaperonne, l'Heat Shock Protéine 70 (HSP70). L'injection en bolus de CsA permet également d'améliorer la fonction rénale dans ce modèle d'IR avec un retard à l'ouverture du mPTP. Nos résultats ouvrent de nouvelles perspectives dans la protection rénale, notamment dans la réduction des épisodes d'insuffisance rénale aigue après chirurgie aortique ou en transplantation rénale / Ischemia-reperfusion (IR) is a situation encountered in transplantation or during aortic surgery, which can result in renal damages, requiring sometimes transient or definitive dialysis. Mitochondria play a crucial role in the pathophysiology of IR causing cell death. Previous studies of cardiac IR highlighted the role of mitochondrial permeability transition pore (mPTP). Cyclosporin A (CsA) has been proposed as a treatment to protect the kidney from IR by the delay of the opening of the mPTP. However, CsA has acute renal hemodynamic effects and a long-term toxicity, requiring an experimental validation of its protection in the renal IR. In this work, we developed a mouse model of renal IR. In a first study, we showed that the post-conditioning with CsA and ischemic postconditioning improve renal function with a delay of the opening of the mPTP. In a second study, we showed that a high dose of CsA injected just before the ischemia improves renal function and leads to the delay of the opening of mPTP mediated by an increase of HSP70. Our results open new perspectives in renal protection, especially for reducing episodes of acute renal failure in aortic surgery or in renal transplantation

Les études en laboratoires montrent que les propriétés de l'eau liquide sont perturbées lorsqu'elle est proche d'une surface (≈ 1nm) ou occluse dans des pores de taille inférieure à la dizaine de nanomètres : au-delà de ces seuils, ses propriétés sont supposées volumiques. Paradoxalement, des observations de terrains suggèrent que le comportement de l'eau peut s'écarter de son comportement volumique pour des tailles de pores de l’ordre de quelques microns. Nous présentons une étude expérimentale des effets, et de leur portée, d'une surface solide, paroi interne d’une cavité fermée, sur les propriétés vibrationnelles et thermodynamiques de l'eau occluse. D’abord, nous avons développé et calibré une fonction de partition prenant en compte les modes inter- et intramoléculaires de l'eau, afin de convertir ses propriétés vibrationnelles en propriétés thermodynamiques. Cette fonction nous permet de calculer la variation d’enthalpie libre que représente une déviation du spectre IR par rapport au spectre de référence. Des mesures IR dans des canaux ont été réalisées en fonction de leur hauteur, de 100 à 5 nm, qui ont mis en évidence que les propriétés de l'eau sont modifiées entre 5 et 20 nm. Si ces distances restent dans les valeurs admises pour l’influence interfaciale, l’intensité thermodynamique des variations (jusqu’à 1.5 kJ/mol) est surprenante, de même que leur sens de variation : l’activité de l’eau augmente. Le moteur de cette évolution pourrait être la restriction géométrique, et des effets de pression de disjonction. Au contraire, des mesures de micro-spectroscopie IR haute résolution et Raman ont été menée dans des micro-cavités fermées (inclusions fluides synthétiques), en fonction de la distance aux interfaces solide/liquide et liquide vapeur. Elles ont montré que les propriétés de l'eau sont progressivement perturbées sur une distance de 1 à 3 μm. Proche de la surface, la variation thermodynamique est au-delà du kJ/mol d’eau, et traduit une augmentation de l’activité de l’eau. Le moteur de ce qu’on appelle une « interphase », vu son épaisseur, associe la tension de surface solide-solution aqueuse et des effets osmotiques, liés à une stratification chimique de la solution depuis la surface jusqu’au centre de la cavité. D'un point de vue thermodynamique, l’eau confinée et l’eau impliquée dans l’interphase apparaissent plus réactives que l’eau volumique : ces mesures ouvrent donc des perspectives d’interprétation des interactions solide-solution dans les milieux naturels. Quelques applications à des observations sont évoquées. / Laboratory studies shows that water properties are disturbed when it is located close to a surface (≈1nm) or occluded in a pore with size less than ten nanometers: beyond these thresholds, its properties are supposed to be bulk. Paradoxically, field observations suggest that the water behavior can deviate with respect to its bulk one for pore sizes of few microns. We present an experimental study of the effects and the scope of a solid surface, internal wall of closed cavity, on the occluded water vibrational and thermodynamic properties. First, we have developed and calibrated a partition function, that takes into account the water inter- and intramolecular modes, to convert its vibrational properties into its thermodynamic counterparts. This function allows us to calculate the free enthalpy corresponding to an IR spectrum deviation with respect to a reference spectrum. IR measurements were performed in channel in function of their height, from 100 to 5 nm. They highlighted that water properties are modified between 5 and 20 nm. Although these distances are within the accepted values for the interfacial influence, the intensity of thermodynamic variations are surprising, as its variation direction: the water activity increases. This evolution could be drive by the geometrical restrictions and the disjoining pressure effects. On the contrary, high resolution IR and Raman micro-spectroscopies measurements were carried out in closed micro-cavities (synthetic fluid inclusions), in function of the distance to the solid/liquid and liquid/vapor interfaces. They demonstrated that water properties are progressively disturbed on a distance from 1 to 3 μm. Close to the surface, the thermodynamic variation is beyond kJ/mol of water, and reflects an increasing of water activity. The driver of the so-called interphase, because of its thickness, involves the solid-aqueous solution surface tension and osmotic effects, related to a chemical stratification of the solution from the surface to the cavity center. From a thermodynamics point of view, confined water and water in the interphase appear more reactive than bulk water: these measurements offer perspectives for the solid-solution interaction interpretation in the natural media. Some applications of the observations are discussed.