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Modeling the Effect of Mechanical Deformation on Electrical Stimulation of Peripheral Nerve Fibers

Description

There are many challenges in designing neuroprostheses and one of them is to maintain proper axon selectivity in all situations. This project is based on an electrode that is implanted into a fascicle in a peripheral nerve and used to provide tactile sensory feedback of a prosthetic arm. This fascicle…

There are many challenges in designing neuroprostheses and one of them is to maintain proper axon selectivity in all situations. This project is based on an electrode that is implanted into a fascicle in a peripheral nerve and used to provide tactile sensory feedback of a prosthetic arm. This fascicle can undergo mechanical deformation during every day motion. This work aims to characterize the effect of fascicle deformation on axon selectivity and recruitment when electrically stimulated using hybrid modeling. The main framework consists of combining finite element modeling (FEM) and simulation environment NEURON. A suite of programs was developed to first populate a fascicle with axons followed by deforming the fascicle and rearranging axons accordingly. A model of the fascicle with an implanted electrode is simulated to find the electrical potential profile through FEM. The potential profile is then used to compare which axons are activated in the two conformations of the fascicle using NERUON.

ContributorsDileep, Devika (Author) / Abbas, James (Thesis director) / Sadleir, Rosalind (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

Fetal Growth Models of Cardiac Size and Function, and Prediction of Congenital Cardiomyopathy in Fetuses with Diabetic Mothers

Description

2D fetal echocardiography (ECHO) can be used for monitoring heart development in utero. This study’s purpose is to empirically model normal fetal heart growth and function changes during development by ECHO and compare these to fetuses diagnosed with and without cardiomyopathy with diabetic mothers. There are existing mathematical models describing…

2D fetal echocardiography (ECHO) can be used for monitoring heart development in utero. This study’s purpose is to empirically model normal fetal heart growth and function changes during development by ECHO and compare these to fetuses diagnosed with and without cardiomyopathy with diabetic mothers. There are existing mathematical models describing fetal heart development but they warrant revalidation and adjustment. 377 normal fetuses with healthy mothers, 98 normal fetuses with diabetic mothers, and 37 fetuses with cardiomyopathy and diabetic mothers had their cardiac structural dimensions, cardiothoracic ratio, valve flow velocities, and heart rates measured by fetal ECHO in a retrospective chart review. Cardiac features were fitted to linear functions, with respect to gestational age, femur length, head circumference, and biparietal diameter and z-scores were created to model normal fetal growth for all parameters. These z-scores were used to assess what metrics had no difference in means between the normal fetuses of both healthy and diabetic mothers but differed from those diagnosed with cardiomyopathy. It was found that functional metrics like mitral and tricuspid E wave and pulmonary velocity could be important predictors for cardiomyopathy when fitted by gestational age, femur length, head circumference, and biparietal diameter. Additionally, aortic and tricuspid annulus diameters when fitted to estimated gestational age showed potential to be predictors for fetal cardiomyopathy. While the metrics overlapped over their full range, combining them together may have the potential for predicting cardiomyopathy in utero. Future directions of this study will explore creating a classifier model that can predict cardiomyopathy using the metrics assessed in this study.

ContributorsMishra, Shambhavi (Co-author) / Numani, Asfia (Co-author) / Sweazea, Karen (Thesis director) / Plasencia, Jonathan (Committee member) / Economics Program in CLAS (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

Rapid 3D phase contrast magnetic resonance angiography through high-moment velocity encoding and 3D parallel imaging

Description

Phase contrast magnetic resonance angiography (PCMRA) is a non-invasive imaging modality that is capable of producing quantitative vascular flow velocity information. The encoding of velocity information can significantly increase the imaging acquisition and reconstruction durations associated with this technique. The purpose of this work is to provide mechanisms for reducing…

Phase contrast magnetic resonance angiography (PCMRA) is a non-invasive imaging modality that is capable of producing quantitative vascular flow velocity information. The encoding of velocity information can significantly increase the imaging acquisition and reconstruction durations associated with this technique. The purpose of this work is to provide mechanisms for reducing the scan time of a 3D phase contrast exam, so that hemodynamic velocity data may be acquired robustly and with a high sensitivity. The methods developed in this work focus on the reduction of scan duration and reconstruction computation of a neurovascular PCMRA exam. The reductions in scan duration are made through a combination of advances in imaging and velocity encoding methods. The imaging improvements are explored using rapid 3D imaging techniques such as spiral projection imaging (SPI), Fermat looped orthogonally encoded trajectories (FLORET), stack of spirals and stack of cones trajectories. Scan durations are also shortened through the use and development of a novel parallel imaging technique called Pretty Easy Parallel Imaging (PEPI). Improvements in the computational efficiency of PEPI and in general MRI reconstruction are made in the area of sample density estimation and correction of 3D trajectories. A new method of velocity encoding is demonstrated to provide more efficient signal to noise ratio (SNR) gains than current state of the art methods. The proposed velocity encoding achieves improved SNR through the use of high gradient moments and by resolving phase aliasing through the use measurement geometry and non-linear constraints.

ContributorsZwart, Nicholas R (Author) / Frakes, David H (Thesis advisor) / Pipe, James G (Thesis advisor) / Bennett, Kevin M (Committee member) / Debbins, Josef P (Committee member) / Towe, Bruce (Committee member) / Arizona State University (Publisher)

Created2011

Analytical control grid registration for efficient application of optical flow

Description

Image resolution limits the extent to which zooming enhances clarity, restricts the size digital photographs can be printed at, and, in the context of medical images, can prevent a diagnosis. Interpolation is the supplementing of known data with estimated values based on a function or model involving some or all…

Image resolution limits the extent to which zooming enhances clarity, restricts the size digital photographs can be printed at, and, in the context of medical images, can prevent a diagnosis. Interpolation is the supplementing of known data with estimated values based on a function or model involving some or all of the known samples. The selection of the contributing data points and the specifics of how they are used to define the interpolated values influences how effectively the interpolation algorithm is able to estimate the underlying, continuous signal. The main contributions of this dissertation are three fold: 1) Reframing edge-directed interpolation of a single image as an intensity-based registration problem. 2) Providing an analytical framework for intensity-based registration using control grid constraints. 3) Quantitative assessment of the new, single-image enlargement algorithm based on analytical intensity-based registration. In addition to single image resizing, the new methods and analytical approaches were extended to address a wide range of applications including volumetric (multi-slice) image interpolation, video deinterlacing, motion detection, and atmospheric distortion correction. Overall, the new approaches generate results that more accurately reflect the underlying signals than less computationally demanding approaches and with lower processing requirements and fewer restrictions than methods with comparable accuracy.

ContributorsZwart, Christine M. (Author) / Frakes, David H (Thesis advisor) / Karam, Lina (Committee member) / Kodibagkar, Vikram (Committee member) / Spanias, Andreas (Committee member) / Towe, Bruce (Committee member) / Arizona State University (Publisher)

Created2013

The effects of endovascular treatment parameters on cerebral aneurysm hemodynamics

Description

A cerebral aneurysm is an abnormal ballooning of the blood vessel wall in the brain that occurs in approximately 6% of the general population. When a cerebral aneurysm ruptures, the subsequent damage is lethal damage in nearly 50% of cases. Over the past decade, endovascular treatment has emerged as an…

A cerebral aneurysm is an abnormal ballooning of the blood vessel wall in the brain that occurs in approximately 6% of the general population. When a cerebral aneurysm ruptures, the subsequent damage is lethal damage in nearly 50% of cases. Over the past decade, endovascular treatment has emerged as an effective treatment option for cerebral aneurysms that is far less invasive than conventional surgical options. Nonetheless, the rate of successful treatment is as low as 50% for certain types of aneurysms. Treatment success has been correlated with favorable post-treatment hemodynamics. However, current understanding of the effects of endovascular treatment parameters on post-treatment hemodynamics is limited. This limitation is due in part to current challenges in in vivo flow measurement techniques. Improved understanding of post-treatment hemodynamics can lead to more effective treatments. However, the effects of treatment on hemodynamics may be patient-specific and thus, accurate tools that can predict hemodynamics on a case by case basis are also required for improving outcomes.Accordingly, the main objectives of this work were 1) to develop computational tools for predicting post-treatment hemodynamics and 2) to build a foundation of understanding on the effects of controllable treatment parameters on cerebral aneurysm hemodynamics. Experimental flow measurement techniques, using particle image velocimetry, were first developed for acquiring flow data in cerebral aneurysm models treated with an endovascular device. The experimental data were then used to guide the development of novel computational tools, which consider the physical properties, design specifications, and deployment mechanics of endovascular devices to simulate post-treatment hemodynamics. The effects of different endovascular treatment parameters on cerebral aneurysm hemodynamics were then characterized under controlled conditions. Lastly, application of the computational tools for interventional planning was demonstrated through the evaluation of two patient cases.

ContributorsBabiker, M. Haithem (Author) / Frakes, David H (Thesis advisor) / Adrian, Ronald (Committee member) / Caplan, Michael (Committee member) / Chong, Brian (Committee member) / Vernon, Brent (Committee member) / Arizona State University (Publisher)

Created2013

Video deinterlacing using control grid interpolation frameworks

Description

Video deinterlacing is a key technique in digital video processing, particularly with the widespread usage of LCD and plasma TVs. This thesis proposes a novel spatio-temporal, non-linear video deinterlacing technique that adaptively chooses between the results from one dimensional control grid interpolation (1DCGI), vertical temporal filter (VTF) and temporal line…

Video deinterlacing is a key technique in digital video processing, particularly with the widespread usage of LCD and plasma TVs. This thesis proposes a novel spatio-temporal, non-linear video deinterlacing technique that adaptively chooses between the results from one dimensional control grid interpolation (1DCGI), vertical temporal filter (VTF) and temporal line averaging (LA). The proposed method performs better than several popular benchmarking methods in terms of both visual quality and peak signal to noise ratio (PSNR). The algorithm performs better than existing approaches like edge-based line averaging (ELA) and spatio-temporal edge-based median filtering (STELA) on fine moving edges and semi-static regions of videos, which are recognized as particularly challenging deinterlacing cases. The proposed approach also performs better than the state-of-the-art content adaptive vertical temporal filtering (CAVTF) approach. Along with the main approach several spin-off approaches are also proposed each with its own characteristics.

ContributorsVenkatesan, Ragav (Author) / Frakes, David H (Thesis advisor) / Li, Baoxin (Committee member) / Reisslein, Martin (Committee member) / Arizona State University (Publisher)

Created2012

Observing effects of drug modulation on electrophysiological response of Aplysia neurons

Description

The effect of three different drug modulators on the electrophysiological response of Aplysia neurons was observed through the use of extracellular and intracellular recordings. Extracellular recordings captured the effects of magnesium chloride and glutamate at a variety of concentrations for each. Intracellular recordings displayed the effects of magnesium chloride, glutamate,…

The effect of three different drug modulators on the electrophysiological response of Aplysia neurons was observed through the use of extracellular and intracellular recordings. Extracellular recordings captured the effects of magnesium chloride and glutamate at a variety of concentrations for each. Intracellular recordings displayed the effects of magnesium chloride, glutamate, and GABA for two concentrations each. For extracellular recordings, the average firing rate, average peak-to-peak voltage, average SNR, and sorted units were considered. For intracellular recordings, average firing rate, average peak voltage, and average resting potential were considered. Significance of data could not be determined using statistical analysis due to having a sample size of 1 for every experiment.

ContributorsEyster, Kyle (Co-author) / Moore, Amanda (Co-author) / Muthuswamy, Jitendran (Thesis director) / Sadleir, Rosalind (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor)

Created2014-05

Mathematical Analysis of Glioma Growth in a Murine Model

Description

Five immunocompetent C57BL/6-cBrd/cBrd/Cr (albino C57BL/6) mice were injected with GL261-luc2 cells, a cell line sharing characteristics of human glioblastoma multiforme (GBM). The mice were imaged using magnetic resonance (MR) at five separate time points to characterize growth and development of the tumor. After 25 days, the final tumor volumes of…

Five immunocompetent C57BL/6-cBrd/cBrd/Cr (albino C57BL/6) mice were injected with GL261-luc2 cells, a cell line sharing characteristics of human glioblastoma multiforme (GBM). The mice were imaged using magnetic resonance (MR) at five separate time points to characterize growth and development of the tumor. After 25 days, the final tumor volumes of the mice varied from 12 mm³ to 62 mm³, even though mice were inoculated from the same tumor cell line under carefully controlled conditions. We generated hypotheses to explore large variances in final tumor size and tested them with our simple reaction-diffusion model in both a 3-dimensional (3D) finite difference method and a 2-dimensional (2D) level set method. The parameters obtained from a best-fit procedure, designed to yield simulated tumors as close as possible to the observed ones, vary by an order of magnitude between the three mice analyzed in detail. These differences may reflect morphological and biological variability in tumor growth, as well as errors in the mathematical model, perhaps from an oversimplification of the tumor dynamics or nonidentifiability of parameters. Our results generate parameters that match other experimental in vitro and in vivo measurements. Additionally, we calculate wave speed, which matches with other rat and human measurements.

ContributorsRutter, Erica (Author) / Stepien, Tracy (Author) / Anderies, Barrett (Author) / Plasencia, Jonathan (Author) / Woolf, Eric C. (Author) / Scheck, Adrienne C. (Author) / Turner, Gregory H. (Author) / Liu, Qingwei (Author) / Frakes, David (Author) / Kodibagkar, Vikram (Author) / Kuang, Yang (Author) / Preul, Mark C. (Author) / Kostelich, Eric (Author) / College of Liberal Arts and Sciences (Contributor)

Created2017-05-31

Advanced methods in post cartesian imaging

Description

Magnetic resonance (MR) imaging with data acquisition on a non-rectangular grid permits a variety of approaches to cover k-space. This flexibility can be exploited to achieve clinically relevant characteristics -- fast yet full coverage for short scan times, center out schemes for short Te, over-sampled k-space for robustness to motion,…

Magnetic resonance (MR) imaging with data acquisition on a non-rectangular grid permits a variety of approaches to cover k-space. This flexibility can be exploited to achieve clinically relevant characteristics -- fast yet full coverage for short scan times, center out schemes for short Te, over-sampled k-space for robustness to motion, long acquisition time for improved signal-to-noise (SNR) performance and benign under-sampling (aliasing) artifact. This dissertation presents advances in Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction (PROPELLER) trajectory design and improved reconstruction for spiral imaging. Scan time in PROPELLER imaging can be reduced by tailoring the trajectory to the required Field-Of-View (FOV). A technique to design the PROPELLER trajectory for an elliptical FOV is described. The proposed solution is a set of empirically derived closed form equations that preserve the standard PROPELLER geometry and specify the minimum number of blades necessary. Reconstructing spiral scans requires accurate trajectory information. A simple method to measure the deviation from the designed trajectory due to gradient coupling is presented. A line phantom is used to force a uniform structure in a predetermined orientation in k-space. This uniformity permits measurements of zeroth order trajectory deviations due to gradient coupling. Spiral reconstruction is also sensitive to B0 inhomogeneities (variations in the external magnetic field). This sensitivity manifests itself as a spatially varying blur. An algorithm to correct for concomitant field and first order B0 inhomogeneity effects is developed based on de-blurring via convolution by separable kernels. To reduce computation time, an empirical equation for sufficient kernel length is derived. It is also necessary to know the noise characteristics of the proposed algorithm; this is investigated via Monte-Carlo simulations. The algorithm is further extended to correct for concomitant field artifacts by modeling these artifacts as blurring due to a temporally static field map. This approach has the potential for further reduction in computational cost by combining the B0 map with the concomitant field map to simultaneously correct for artifacts resulting from both field inhomogeneities and concomitant field map.

ContributorsDevaraj, Ajit (Author) / Pipe, James G (Thesis advisor) / Karam, Lina J (Thesis advisor) / Frakes, David H (Committee member) / Aberle, James T (Committee member) / Arizona State University (Publisher)

Created2010

Improving the Realism and Magnetic Resonance Imaging of Multicellular Tumor Spheroids

Description

Magnetic resonance imaging (MRI) of changes in metabolic activity in tumors and metabolic abnormalities can provide a window to understanding the complex behavior of malignant tumors. Both diagnostics and treatment options can be improved through the further comprehension of the processes that contribute to tumor malignancy and growth. By detecting…

Magnetic resonance imaging (MRI) of changes in metabolic activity in tumors and metabolic abnormalities can provide a window to understanding the complex behavior of malignant tumors. Both diagnostics and treatment options can be improved through the further comprehension of the processes that contribute to tumor malignancy and growth. By detecting and disturbing this activity through personalized treatments, it is the hope to provide better diagnostics and care to patients. Experimenting with multicellular tumor spheroids (MCTS) allows for a rapid, inexpensive and convenient solution to studying multiple in vitro tumors. High quality magnetic resonance images of small samples, such as spheroid, however, are difficult to achieve with current radio frequency coils. In addition, in order for the information provided by these scans to accurately represent the interactions and metabolic activity in vivo, there is a need for a perfused vascular network. A perfused vascular network has the potential to improve metabolic realism and particle transport within a tumor spheroid. By creating a more life-like cancer model and allowing the progressive imaging of metabolic functions of such small samples, a better, more efficient mode of studying metabolic activity in cancer can be created and research efforts can expand. The progress described in this paper attempts to address both of these current shortcomings of metabolic cancer research and offers potential solutions, while acknowledging the potential of future work to improve cancer research with MCTS.

ContributorsTobey, John Paul (Author) / Kodibagkar, Vikram (Thesis director) / Sadleir, Rosalind (Committee member) / Barrett, The Honors College (Contributor)

Created2016-12