Biomedical Engineering and Bioengineering Commons^™

Region-Of-Interest Material Decomposition From Truncated Energy-Resolved Ct, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Purpose: Energy-resolved CT using photon-counting detectors has the potential to provide improved material decomposition compared to dual-kVp approaches. However, available photon-counting detectors are susceptible to pulse-pileup artifacts, especially at the periphery of the field of view (FOV) where the object attenuation is low compared to the center of the FOV. Pulse pileup may be avoided by imaging a region-of-interest (ROI) where the dynamic range is expected to be limited. This work investigated performing material decomposition and reconstructing ROI basis images from truncated energy-resolved data.

Methods: A method is proposed to reconstructimages of basis functions primarily contained within the ROI, such …

A Compressed Sensing Algorithm For Sparse-View Pinhole Single Photon Emission Computed Tomography, Paul Arthur Wolf, Emil Y. Sidky, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Single Photon Emission Computed Tomography (SPECT) systems are being developed with multiple cameras and without gantry rotation to provide rapid dynamic acquisitions. However, the resulting data is angularly undersampled, due to the limited number of views. We propose a novel reconstruction algorithm for sparse-view SPECT based on Compressed Sensing (CS) theory. The algorithm models Poisson noise by modifying the Iterative Hard Thresholding algorithm to minimize the Kullback-Leibler (KL) distance by gradient descent. Because the underlying objects of SPECT images are expected to be smooth, a discrete wavelet transform (DWT) using an orthogonal spline wavelet kernel is used as the sparsifying …

Comparison Of Four Chip-Seq Analytical Algorithms Using Rice Endosperm H3k27 Trimethylation Profiling Data., Brandon M. Malone, Feng Tan, Susan M. Bridges, Zhaohua Peng

BCoE Publications

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology laboratories.Here we profile H3K27me3 enrichment sites in rice young endosperm using the ChIP-Seq approach and analyze the data using four peak calling algorithms (FindPeaks, PeakSeq, USeq, and MACS). Comparison …

Reducing Selection Bias In Case-Control Studies From Rare Disease Registries, J. Alexander Cole, John S. Taylor, Thomas N. Hangartner, Neal J. Weinreb, Pramod K. Mistry, Aneal Khan

Biomedical, Industrial & Human Factors Engineering Faculty Publications

Background: In clinical research of rare diseases, where small patient numbers and disease heterogeneity limit study design options, registries are a valuable resource for demographic and outcome information. However, in contrast to prospective, randomized clinical trials, the observational design of registries is prone to introduce selection bias and negatively impact the validity of data analyses. The objective of the study was to demonstrate the utility of case-control matching and the risk-set method in order to control bias in data from a rare disease registry. Data from the International Collaborative Gaucher Group (ICGG) Gaucher Registry were used as an example.

Methods: …

Soft Tissue Cutting With Ultrasonic Mechanical Waveguides, Mark Wylie, Garrett Mcguinness, Graham Gavin

Conference Papers

The use of ultrasonic vibrations transmitted via small diameter wire waveguides represents a technology that has potential for minimally invasive procedures in surgery. This form of energy delivery results in distal tip mechanical vibrations with amplitudes of vibration of up to 50 μm and at frequencies between 20-50 kHz commonly reported. This energy can then be used by micro-cutting surgical tools and end effectors for a range of applications such as bone cutting, cement removal in joint revision surgery and soft tissue cutting. One particular application which has gained regulatory approval in recent years is in the area of cardiovascular …

Impact Isolation Of Training Shoes, Nicci Daly, Stephen Tiernan

Conference Papers

ABSTRACT The increase in popularity of physical activities from fun runs to competitive marathons has lead to a huge industry in sports footwear, which is now worth $20bn annually. There is a resultant increase in injuries, largely due to the repeated and prolonged nature of the impact forces experienced by the leg. Clinical data indicates that the knee is the most common site of running related injury, followed by the lower leg and foot. The complexity of the ankle structure means that injuries are acute and the success rates of replacements are very low. Therefore research in this area is …

Protective Effects Of Milk Phospholipids Against Uv Photodamage In Human Skin Equivalents, Zyra Achay

Master's Theses

The ultraviolet (UV) spectrum has been known to cause damage to skin in varying degrees. UVB radiation (290-320 nm) in particular, has been proven to be highly mutagenic and carcinogenic in many animal experiments compared to either UVA or UVC. The alarming rate of increase in skin cancer incidence has prompted many investigators to pursue other alternatives to sunscreens including changes in lifestyle habits and dietary consumption in order to boost our efforts in tackling this widespread disease. Previous studies employing confocal reflectance, MTT assay and histology suggest that milk phospholipids may possess protective properties against UVB-mediated damage but the …

Spatial And Temporal Variation Of Rod Photoreceptor Reflectance In The Human Retina, Robert F. Cooper, Adam M. Dubis, Ashavini M. Pavaskar, Jungtae Rha, Alfredo Dubra, Joseph Carroll

Biomedical Engineering Faculty Research and Publications

Using adaptive optics imaging tools to image the living retina, numerous investigators have reported temporal fluctuation in the reflectivity of individual cone photoreceptors. In addition, there is cone-to-cone (spatial) variation in reflectivity. As it has only recently become possible to image the complete rod photoreceptor mosaic in the living human retina, we sought to characterize the reflectivity of individual rods and compare their behavior to that of foveal/parafoveal cones. Across two subjects, we were able to successfully track the reflectance behavior of 1,690 rods and 1,980 cones over 12 hours. Rod and cone photoreceptors showed similar regional and temporal variability …

Computational Simulations Demonstrate Altered Wall Shear Stress In Aortic Coarctation Patients Previously Treated By Resection With End-To-End Anastomosis, John F. Ladisa, Ronak Jashwant Dholakia, Alberto Figueroa, Irene E. Vignon-Clementel, Frandics P. Chan, Margaret M. Samyn, Joseph Richard Cava, Charles A. Taylor, Jeffrey A. Feinstein

Biomedical Engineering Faculty Research and Publications

Background.  Atherosclerotic plaque in the descending thoracic aorta (dAo) is related to altered wall shear stress (WSS) for normal patients. Resection with end-to-end anastomosis (RWEA) is the gold standard for coarctation of the aorta (CoA) repair, but may lead to altered WSS indices that contribute to morbidity.

Methods.  Computational fluid dynamics (CFD) models were created from imaging and blood pressure data for control subjects and age- and gender-matched CoA patients treated by RWEA (four males, two females, 15 ± 8 years). CFD analysis incorporated downstream vascular resistance and compliance to generate blood flow velocity, time-averaged WSS (TAWSS), and oscillatory shear …

Computational Simulations For Aortic Coarctation: Representative Results From A Sampling Of Patients, John F. Ladisa, Alberto Figueroa, Irene E. Vignon-Clementel, Hyun Jin Kim, Nan Xiao, Laura M. Ellwein, Frandics P. Chan, Jeffrey A. Feinstein, Charles A. Taylor

Biomedical Engineering Faculty Research and Publications

Treatments for coarctation of the aorta (CoA) can alleviate blood pressure (BP) gradients(D), but long-term morbidity still exists that can be explained by altered indices of hemodynamics and biomechanics. We introduce a technique to increase our understanding of these indices for CoA under resting and nonresting conditions, quantify their contribution to morbidity, and evaluate treatment options. Patient-specific computational fluid dynamics (CFD) models were created from imaging and BP data for one normal and four CoA patients (moderate native CoA: D12 mmHg, severe native CoA: D25 mmHg and postoperative end-to-end and end-to-side patients: D0 mmHg). Simulations incorporated vessel deformation, downstream vascular …

Effects Of Wrist Tendon Vibration On Arm Tracking In People Poststroke, Megan O. Conrad, Robert A. Scheidt, Brian D. Schmit

Biomedical Engineering Faculty Research and Publications

The goal of this study was to evaluate the influence of wrist tendon vibration on a multijoint elbow/shoulder tracking task. We hypothesized that tendon vibration applied at the wrist musculature would improve upper arm tracking performance in chronic stroke survivors through increased, Ia-afferent feedback to the central nervous system (CNS). To test this hypothesis, 10 chronic stroke and 5 neurologically intact subjects grasped the handle of a planar robot as they tracked a target through a horizontal figure-8 pattern. A total of 36 trials were completed by each subject. During the middle trials, 70-Hz tendon vibration was applied at the …

Improved Manufacturing Methods Of Bovine Femur Samples For Ultrasonic Testing And Assessment Of Materials Through Contract Angle Measurement, Kevin Mathew Lopez Galang

Biomedical Engineering

At California Polytechnic State University of San Luis Obispo (Cal Poly), the Biomedical Engineering department (BMED) requires its students to take the course listed as “BMED 420: Principles of Biomaterial Designs.” BMED 420 has a required laboratory section every week throughout the duration of the course that is meant to be a supplemental tool for learning. During the lab sections, students perform experiments and exercises that are currently being implemented in the industry. Despite accuracy of the methods and experiments relative to their use in the industry, there is always room for improvement. The objective of this project will illustrate …

Impaired Resistance Artery Reactivity Following Arteriogenesis, Michael (Mike) Machado

Biomedical Engineering

No abstract provided.

Robust Cns Regeneration After Complete Spinal Cord Transection Using Aligned Poly-L-Lactic Acid Microfibers, Andres Hurtado, Jared M. Cregg, Han B. Wang, Dane F. Wendell, Martin Oudega, Ryan J. Gilbert, John W. Mcdonald

Chemical and Biochemical Engineering Faculty Research & Creative Works

Following spinal cord injury, axons fail to regenerate without exogenous intervention. In this study we report that aligned microfiber-based grafts foster robust regeneration of vascularized CNS tissue. Film, random, and aligned microfiber-based conduits were grafted into a 3 mm thoracic rat spinal cord gap created by complete transection. Over the course of 4 weeks, microtopography presented by aligned or random poly- l-lactic acid microfibers facilitated infiltration of host tissue, and the initial 3 mm gap was closed by endogenous cell populations. This bulk tissue response was composed of regenerating axons accompanied by morphologically aligned astrocytes. Aligned fibers promoted long distance …

The Impact Of Dynamic And Passive Standing On Bone Mineral Density And Appositional Growth In Immobilized Children, Megan Diane Damcott

Dissertations

The first discovery of the potential role that mechanical loading has on determining the strength of bone occurred in 1892. However, for almost a century after this discovery, the specific mechanisms influenced by mechanical loading remained locked in a mysterious 'black box'. Then in the 1960s, the 'black box' was opened and continued work has now unlocked the basic mechanisms involved in mechanical loading and whole-bone strength. This increased knowledge has spurred clinicians and researchers to investigate the impact of weight-bearing interventions on individuals with an increased risk of osteoporosis. The most common weight-bearing clinical intervention used in non-ambulant populations …

Influence Of Rear Wheel Tire Type On Wheelchair Propulsion Biomechanics, Mathew Yarossi

Theses

The objective of this study was to determine how rear wheel tire type affects wheelchair propulsion mechanics. Four persons with paraplegia and four persons with tetraplegia propelled their own wheelchairs on a roller system at self-selected speed using five different pairs of tires. Upper limb and trunk kinematics, perceived exertion, stroke pattern and the temporal characteristics of propulsion were measured. When using pneumatic (air filled) tires, with lower rolling resistance, participants had lower push frequency (p < .05), higher self selected speed (p < .05), less perceived exertion, less shoulder internal rotation, and a longer push stroke than when using solid, high rolling resistance tires. As rolling resistance increased, participants experienced negative changes in propulsion characteristic that contradicted current clinical practice guidelines for upper limb preservation following spinal cord injury. In addition, kinematics with solid, high rolling resistance tires were similar to those described during uphill or over carpet propulsion. In order to avoid unnecessary strain on the upper limbs and unwanted changes in propulsion biomechanics, wheelchair users, clinicians, and researchers should consider the use of lower rolling resistance, pneumatic rear tires.

Use Of Fluorescent Micropsheres To Measure Coronary Flow Reserve In Rat Animal Model, Riddhi Harsh Shah

Theses

Heart attacks result from reduced or blocked blood flow through major coronary arteries, resulting in permanent damage to heart muscle. Coronary blood flow (CBF) is thus important to measure in experimental animal models of heart disease. A standard method to measure CBF uses tracer microspheres (Ø = 15 µm) injected into the left ventricle that flow through coronary arteries but cannot pass through capillaries and so become trapped in heart muscle. Previously, radioactive or colored microspheres have quantified the number of tracers trapped in the muscle. Fluorescent microspheres offer a more recent and more sensitive measurement mode. However, fluorescent microspheres …

Left Ventricular Assist Devices: Engineering Design Considerations, Marwan A. Simaan, Eduardo Divo, George Faragallah, Yu Wang

Publications

Patients with end-stage congestive heart failure awaiting heart transplantation often wait long periods of time (300 days or more on the average) before a suitable donor heart becomes available. The medical community has placed increased emphasis on the use of Left Ventricular Assist Devices or LVADs that can substitute for, or enhance, the function of the natural heart while the patient is waiting for the heart transplant (Poirier, 1997; Frazier & Myers, 1999). Essentially, a rotary LVAD is a pump that operates continuously directing blood from the left ventricle into the aorta by avoiding the aortic valve. Generally speaking, the …

An Objective Assessment Of Fetal Neurological Maturation Based On The Co-Variation Of Brain And Heart Rate Patterns, Srinivasan Vairavan

Theses and Dissertations

An in-utero neurological assessment would aid clinicians in an early detection of fetal neurological distress. However, accessing the fetal brain signal has remained a major challenge. With the advent of Superconducting Quantum Interference Device (SQUID) technology, magnetoencephalogram (MEG), is now an established technique for recording human brain activity. This technique is non-invasive and records the magnetic fields corresponding to electric currents generated by the neurons in the brain. Based on MEG technology, a first-of-a-kind device, named SARA (SQUID Array for Reproductive Assessment), was specifically designed and installed in the Department of Obstetrics and Gynecology, University of Arkansas for Medical Sciences, …

Effect Of Prostaglandin E2 On Mechanical Stresses Applied By Mc3t3-E1 Osteoblast-Like Cells On A Soft Hydrogel Substrate, Abhijit Deb Roy

Master's Theses

Osteoblasts are sensitive to mechanical stimuli and release Prostaglandin E2 (PGE2) when exposed to a fluid shear stress. The exact mechanism by which these cells sense mechanical stress is not well established. A study of the stresses applied by the osteoblasts, under the influence of PGE2, on a hydrogel provided information regarding intercellular-communication via changes in the substrate surface pattern.

A digital image correlation program was developed using the Levenberg-Marquardt optimization algorithm to analyze images and compare the deformations between pairs of images. Comparisons of images before and after the addition of PE2 to the media showed differences in the …