Cerebral ischemia leading to an ischemic stroke is a possible complication of a transcatheter aortic valve replacement (TAVR) procedure. This is because embolic debris can become dislodged and travel through the aortic arch, where they either continue to the descending aorta and join the systemic circulation or travel into the cerebral vasculature through the three daughter vessels that branch off the top of the aortic arch. These three vessels are the brachiocephalic artery, the left subclavian artery, and the left common carotid artery. These three vessels lead either directly or indirectly to the cerebral vasculature, where the diameter of vessels become very small. If a large enough embolus travels into the cerebral vasculature, it can become stuck in the small cerebral vessels, blocking blood flow and cutting off the supply of oxygen to brain cells. The purpose of this study is to expand upon previous work in order to 1) create a more accurate physics simulation of blood and debris flow through the aortic arch 2) report on embolic debris distribution through the aortic arch and 3) analysis on which physical parameters affect embolic debris distribution. The physical parameters analyzed were particle diameter and particle density. This study was performed by creating a finite element model in COMSOL Multiphysics™ using a SolidWorks model of an aortic arch, with dimensions taken from a patient’s CT scan. Computational fluid dynamics was performed using a pulsatile pressure waveform throughout the aortic arch with a non-constant viscosity model. Once the velocity profile through the aortic arch matched with value ranges from literature, the particle tracing study was implemented. Both a pulsatile pressure waveform and a constant pressure model were analyzed, as well as a constant viscosity model and a non-constant viscosity model. The pulsatile pressure waveform influenced particle distribution and is recommended for future studies since this model leads to pulsatile flow, which is representative of flow through the aorta. It was seen that the non-constant viscosity model did not have a large effect on the velocity profile, but more than doubled the surface average value of viscosity. It also had an effect on the particle distribution through the aortic arch. Small diameter emboli were more likely to flow into the descending aorta, the brachiocephalic artery, and the left subclavian artery; larger emboli were more likely to flow into the left common carotid. Lower density emboli were more likely to flow into the descending aorta and the brachiocephalic artery. Averaging all densities and sizes, it was determined 44.8% of emboli flow into the three daughter vessels, but ultimately only 30.61% of emboli flow into the cerebral vasculature and have the potential to cause an ischemic stroke.

Blood flow velocity is an important parameter that can give information on several pathologies including atherosclerosis, glaucoma, Raynaud’s phenomenon, and ischemic stroke [2,5,6,10]. Present techniques of measuring blood flow velocity involve expensive procedures such as Doppler echocardiography, Doppler ultrasound, and magnetic resonance imaging [11,12]. They cost from $8500-$20000. It is desired to find a low-cost yet equally effective solution for measuring blood flow velocity. This thesis has a goal of creating a proof of concept device for measuring blood flow velocity. Finger blood flow velocity is investigated in this project. The close proximity to the skin of the finger’s arteries makes it a practical selection. A Red Green Blue (RGB) color sensor is integrated with an Arduino Uno microcontroller to analyze color on skin. The initial analysis involved utilization of red RGB values to measure heart rate; this was performed to validate the sensor. This test achieved similar results to an experimental control as the measurements had error ranging from 0% to 6.67%. The main analysis was to measure blood flow velocity using 2 RGB color sensors. The range of velocity found was 5.20cm/s to 12.22cm/s with an average of 7.44cm/s. This compared well with the ranges found in published data that varied from 4cm/s to 19cm/s. However, there is an error associated with the device that affects the accuracy of the results. The apparatus has the limitation of collecting data between sensors every 102-107ms, so there is a maximum error of 107ms. The average finger blood flow velocity of 7.44cm/s may actually be between 6.17cm/s and 9.39cm/s due to the sampling error. In addition, mean squared error analysis found that the most likely time difference between pulses among those found is 739ms, which corresponds to 5.21cm/s. Although there is error in the system, the tests for heart rate along with the obtained range and average for finger blood velocity data provided a method for analyzing blood flow velocity. Finger blood velocity was examined in a much more economical manner than its traditional methods that cost between $8500-$20000. The cost for this entire thesis was $99.66, which is a maximum of 1.17% of the cost.

Colorectal cancer is the second most common cause of cancer-related deaths in the United States, with the relative 5-year survival rate for distant stage cancer being only 14%. The most common treatment for colorectal cancer is with chemotherapeutic drugs; however, the discovery of these drugs is costly, time-consuming, and often requires the use of animal models that do not yield results that translate to clinical trials. Due to these shortcomings, researchers seek to develop physiologically relevant in vitro tumor models that more accurately mimic the tumor microenvironment for cheaper and faster high-throughput drug screening. The aim of this research was to develop a colorectal cancer tumor model co-cultured with endothelial and stromal cells, followed by validation with clinically relevant chemotherapeutic agents within microfluidic devices. The first experiment consisted of a lipofection of fibroblasts to yield fluorescently tagged cells that could be later imaged using a fluorescence microscope. The next experiment consisted of a co-culture of tumor, endothelial, and fibroblast cells at varying densities in a twodimensional (2D) culture to determine the optimal plating densities that would yield quantifiable tumor and endothelial network formation. The following experiment used these optimal densities to test the effects of the chemotherapeutic agents oxaliplatin and SN38 on the tumor and endothelial cells in 2D. After the various densities and drug concentrations were tested in 2D, the model was introduced into microfluidic devices. The first experiment in the devices was similar to the first experiment plated in 2D, as it involved the establishment of optimal plating densities of all three cell types within the devices. Similarly, the goal of this experiment was to yield quantifiable tumor and endothelial network formation within the devices. The final experiment performed in this research was the introduction of oxaliplatin and SN38 to the optimized densities v of cells determined from the previous experiment, with the aim of evaluating the effects of these chemotherapeutic agents on the tumor and endothelial cells within microfluidic devices. The two experiments plated in 2D established plating densities to be tested in the devices. These experiments also showed that increasing drug concentrations resulted in reduced tumor count and size and revealed no disruption in the endothelial networks when exposed to oxaliplatin concentrations as high as 50 µM. The final two experiments in microfluidic devices revealed that endothelial network formation is not yet possible within the devices with the current protocols, but that tumor cells still showed dose-dependent responses to drug exposure as they did in 2D. Due to the lack of network formation in this device model, future work is required to allow for endothelial cell organization into networks, to further increase the physiological relevancy of this model to in vivo tumor conditions.

<p>Microinjection is an established and reliable method to deliver transgenic constructs and other reagents to specific locations in the animal. Specifically, microinjection of a desired DNA construct into the distal gonad is the most widely used method to generate germ-line transformation of <em>C. elegans</em>. Although, current <em>C. elegans</em> microinjection method is an effective manner for creating transgenic worms, it requirements such as expensive multi DOF micromanipulator, detailed injection alignment procedure and skilled operator which makes the microinjection process slow and not suitable for scale to high throughput. Although many microfabricated microinjectors exist, none of them are capable of immobilizing a freely mobile animal such as <em>C.elegans</em> worm. In this research, a microfluidic microinjector was developed to simultaneously immobilize a freely mobile animal such as <em>C.elegans</em> and perform microinjection by using a simple and fast mechanism for needle actuation. The entire process of the microinjection takes ~30 seconds which includes 10s for worm loading and aligning, 5s needle penetration, 5s reagent injection and 5s worm unloading. The capability of the microinjector chip for creating transgenic <em>C. elegans</em> was illustrated (with success rate between 4% to 20%)</p> / Master of Science (MSc)

The product of this thesis aims to enable the study of the biochemical and physical dynamics of the lower limbs at high levels of muscle tension and fast contraction speeds. This is accomplished in part by a magnetic resonance (MR) compatible ergometer designed to apply a load as a torque of up to 420 Nm acting against knee extension at speeds as high as 4.7 rad/s. The system can also be adapted to apply the load as a force of up to 1200 N acting against full leg extension. The ergometer is designed to enable the use of magnetic resonance spectroscopy and imaging in a three Tesla Siemens Skyra MRI system. Due to the electromagnetic limitations of having the device operate inside the magnet, the design is split into two components. One designed to fit inside the 70 cm bore of the scanner. This component is electromagnetically passive; made out of materials exhibiting minimal magnetic interference, and having no electrically powered parts. The other component is electromagnetically active; it contains all of the powered elements and actuates the passive part from another room. A tensioned cable transmits power through a waveguide; a pipe through the wall of the MRI room with an RF shield. The device was tested applying a sagittal plane moment on the knee joint during isometric, isokinetic, isotonic, and constant power contractions.

Ion sensitive field effect transistors (ISFETs) are semiconductor sensors that have the capability to determine the selected concentration of a specific ion in a solution. Most modern ISFETs utilize their ion selective properties for glucose monitors for diabetics. However, in this thesis, the ISFET fabricated is for the selective detection of K+. The goals of this thesis are to develop a functioning ion-selective polymer membrane, manufacture a working FET device, and implement the two aspects together into a working bench-top K+ selective ISFET device. Properties of a polymer composed of 33 wt.% polyvinyl chloride (PVC) 66 wt.% dioctyl sebacate (DOS) and 1 wt.% valinomycin applied to an ion-sensitive electrode (ISE) were investigated. The membrane generated a sensitivity value of -9.864E-08 Ω/log10(CK). Though this data set was affected by both the maximum resolution of the I-V curve tracing device and the thin-membrane effect. Selectivity tests following the IUPAC two-solution method in the presence of Na+ as the interfering ion, provided selectivity values of 0.228 and 0.443 with higher ratios of primary ion to interfering ion resulting in higher selectivity coefficients. Additionally, utilizing an illumination test, dielectric constants of 17.71 and 10.88 were calculated dependent on the amount of solvent used during formulation. Fabrication of the FET device also resulted in developments in metal contact materials, nitride film processing, and physical vapor deposition (PVD) processes. With further improvements, it is possible to fabricate a biocompatible, wearable K+-selective monitor for continuously testing dialysis patients.

Snoring is a sleep disruption that can lead to obstructive sleep apnea (OSA), which interrupts breathing by obstructing the airway. Injecting a protein crosslinker, such as genipin, into the soft palate could decrease the severity of snoring and OSA by stiffening the soft palate. Equine soft palates modeled human palates due to a high incidence of awake snoring and apnea. The pilot in vivo study treated six horses with two 100 mM injections of the buffered genipin reagent. The efficacy phase horses underwent respiratory audio recordings to document snoring changes using Matlab and ImageJ in the time and frequency domains. Histological analysis was completed on the safety phase palates post treatment. All horses were successfully treated with the genipin injections. At least one horse showed high frequency amplitude reductions, and all horses had low frequency amplitude reductions, correlating to a reduction in palatal displacement and snoring loudness. One efficacy horse appears to have been completely cured. The histological analysis presented tissue damage, mucosal tissue damage, and mild inflammation due to palate expansion and errant injections. Different injection volumes and techniques should be investigated next. Applying this treatment to human studies for snoring and OSA applications is the ultimate goal.

In this study we design a succession of three increasingly adept diffuse optical devices towards the simultaneous 3D imaging of blood flow and fluorescence contrasts in relatively deep tissues. These metrics together can provide future insights into the relationship between blood flow distributions and fluorescent or fluorescently tagged agents. A noncontact diffuse correlation tomography (ncDCT) device was firstly developed to recover flow by mechanically scanning a lens-based apparatus across the sample. The novel flow reconstruction technique and measuring boundary curvature were advanced in tandem. The establishment of CCD camera detection with a high sampling density and flow recovery by speckle contrast followed with the next instrument, termed speckle contrast diffuse correlation tomography (scDCT). In scDCT, an optical switch sequenced coherent near-infrared light into contact-based source fibers around the sample surface. A fully noncontact reflectance mode device finalized improvements by combining noncontact scDCT (nc_scDCT) and diffuse fluorescence tomography (DFT) techniques. In the combined device, a galvo-mirror directed polarized light to the sample surface. Filters and a cross polarizer in stackable tubes promoted extracting flow indices, absorption coefficients, and fluorescence concentrations (indocyanine green, ICG). The scDCT instrumentation was validated through detection of a cubical solid tissue-like phantom heterogeneity beneath a liquid phantom (background) surface where recovery of its center and dimensions agreed with the known values. The combined nc_scDCT/DFT identified both a cubical solid phantom and a tube of stepwise varying ICG concentration (absorption and fluorescence contrast). The tube imaged by nc_scDCT/DFT exhibited expected trends in absorption and fluorescence. The tube shape, orientation, and localization were recovered in general agreement with actuality. The flow heterogeneity localization was successfully extracted and its average relative flow values in agreement with previous studies. Increasing ICG concentrations induced notable disturbances in the tube region (≥ 0.25 μM/1 μM for 785 nm/830 nm) suggesting the graduating absorption (320% increase at 785 nm) introduced errors. We observe that 830 nm is lower in the ICG absorption spectrum and the correspondingly measured flow encountered less influence than 785 nm. From these results we anticipate the best practice in future studies to be utilization of a laser source with wavelength in a low region of the ICG absorption spectrum (e.g., 830 nm) or to only monitor flow prior to ICG injection or post-clearance. In addition, ncDCT was initially tested in a mouse tumor model to examine tumor size and averaged flow changes over a four-day interval. The next steps in forwarding the combined device development include the straightforward automation of data acquisition and filter rotation and applying it to in vivo tumor studies. These animal/clinical models may seek information such as simultaneous detection of tumor flow, fluorescence, and absorption contrasts or analyzing the relationship between variably sized fluorescently tagged nanoparticles and their tumor deposition relationship to flow distributions.

Normal movement execution requires proper coupling of motor and sensory activation. An increasing body of literature supports the idea that incorporation of sensory stimulation into motor rehabilitation practices increases its effectiveness. Paired associative stimulation (PAS) studies, in which afferent and efferent pathways are activated in tandem, have brought attention to the importance of well-timed stimulation rather than non-associative (i.e., open-loop) activation. In patients with tetraplegia resulting from spinal cord injury (SCI), varying degrees of upper limb function may remain and could be harnessed for rehabilitation. Incorporating associative sensory stimulation coupled with self-paced motor training would be a means for supplementing sensory deficits and improving functional outcomes. In a motor rehabilitation setting, it seems plausible that sensory feedback stimulation in response to volitional movement execution (to the extent possible), which is not utilized in most PAS protocols, would produce greater benefits. This capability is developed and tested in the present study by implementing a brain-computer interface (BCI) to apply sensory stimulation synchronized with movement execution through the detection of movement intent in real time from electroencephalography (EEG). The results demonstrate that accurate sensory stimulation application in response to movement intent is feasible in SCI patients with chronic motor deficit and often precedes the onset of movement, which is deemed optimal by PAS investigations that do not involve a volitional movement task.

Since aggressive cancers are frequently hypermetabolic with angiogenic vessels, quantification of blood flow (BF) can be vital for cancer diagnosis. Our laboratory has developed a noncontact diffuse correlation tomography (ncDCT) system for 3-D imaging of BF distribution in deep tissues (up to centimeters). The ncDCT system employs two sets of optical lenses to project source and detector fibers respectively onto the tissue surface, and applies finite element framework to model light transportation in complex tissue geometries. This thesis reports our first step to adapt the ncDCT system for 3-D imaging of BF contrasts in human breast tumors. A commercial 3-D camera was used to obtain breast surface geometry which was then converted to a solid volume mesh. An ncDCT probe scanned over a region of interest on the breast mesh surface and the measured boundary data were used for 3-D image reconstruction of BF distribution. This technique was tested with computer simulations and in 28 patients with breast tumors. Results from computer simulations suggest that relatively high accuracy can be achieved when the entire tumor was within the sensitive region of diffuse light. Image reconstruction with a priori knowledge of the tumor volume and location can significantly improve the accuracy in recovery of tumor BF contrasts. In vivo ncDCT imaging results from the majority of breast tumors showed higher BF contrasts in the tumor regions compared to the surrounding tissues. Reconstructed tumor depths and dimensions matched ultrasound imaging results when the tumors were within the sensitive region of light propagation. The results demonstrate that ncDCT system has the potential to image BF distributions in soft and vulnerable tissues without distorting tissue hemodynamics. In addition to this primary study, detector fibers with different modes (i.e., single-mode, few-mode, multimode) for photon collection were experimentally explored to improve the signal-to-noise ratio of diffuse correlation spectroscopy flow-oximeter measurements.