Biomedical Engineering Research Open House Presentation Schedule

Poster ID: 1

12:00 - 1:00

Alam, Wahidul

BME

Grad

A novel 16-channel upper airway receive coil array for the investigation of accelerated dynamic MRI

Authors: Alam, Mohammad Wahidul

MRI is a highly potential non-invasive tool to assess upper airway dynamics during sleep to evaluate severe sleeping disorders like sleep apnea, which has a wide prevalence worldwide. Current works on MRI have exhibited the magnitude of improvements required in terms of both spatial and temporal resolution. Intending to improve spatiotemporal resolution, our study endeavors at demonstrating the effectiveness of a novel 16-channel upper airway receive coil array. This coil is compared with the existing 16-channel head and neck coil array to investigate the performance of accelerated 3-D dynamic imaging during natural sleep.

Three-Minute Video: https://youtu.be/iTekddz3XV4

Presentationalam_bme_vroh_2020.pdf

 

Poster ID: 2

11:00 - 12:00

Allen, Brittany

BME

Grad

Microstructured Photoreceptor Replacement Scaffolds: Photopolymerization can be used to fabricate photoreceptor replacement scaffolds, from methacrylated gelatin and hyaluronic acid, for the purpose of retinal tissue engineering

Authors: Allen, Brittany; Thompson, Jacob; Wiley, Luke; Tucker, Budd; Kristan, Worthington

Age-related macular degeneration (AMD) results in gradual blindness due to tissue death in the macula. Current treatments for AMD can slow the progression of blindness but cannot reverse vision loss due to a lack of functional photoreceptor cells (rods and cones). Replacing photoreceptors could restore vision to patients, but a scaffold is required to transport viable, correctly oriented, photoreceptor cells. Retina-mimetic scaffolds were fabricated from methacrylated gelatin and hyaluronic acid using photopolymerization. We fabricated photoreceptor-replacement scaffolds and tested their fidelity to our model, mechanical properties, and biocompatibility. These results pave the way for development of effective retinal cell replacement therapies.

Three-Minute Video: https://youtu.be/Xxk1WFIAo_s

Presentation: allen_bme_vroh_2020.pdf

 

Poster ID: 3

10:00 - 11:00

Althof, Zac

BME

Grad

PRM Reveals Prone Vs. Supine Lung Tissue Expansion Differences In An Ovine Model Of ARDS

Authors: Althof, Zachary; Kaczka, David; Musch, Guido; Reinhardt, Joseph

Prone positioning during mechanical ventilation impacts the regional distribution of lung aeration and reduces mortality in patients with the acute respiratory distress syndrome (ARDS). Using parametric response mapping (PRM) between registered computed tomography (CT) scans of the lungs at end-expiration (EE) and end-inspiration (EI), Cereda et. al. recently demonstrated that regions transitioning between high and low voxel density during a breath are at increased risk for atelectrauma and ventilator-induced lung injury. In

this study, we used PRM analysis to examine differences in such ‘at risk’ regions between prone and supine positioning in an ovine model of ARDS.

Three-Minute Video: https://youtu.be/RA6zE-q73KQ

Presentation: althof_bme_vroh_2020.pdf

 

Poster ID: 4

2:00 - 3:00

Chaudhary, Muhammad Faizyab Ali

BME

Grad

CT texture and biomechanical measures for assessing COPD progression

Authors: Chaudhary, Muhammad F. A.; Pan, Yue; Wang, Di; Bodduluri, Sandeep; Bhatt, Surya P.; Comellas, Alejandro P.; Hoffman, Eric A.; Christensen, Gary E.; Reinhardt, Joseph M.

Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous collection of airways disease and parenchymal tissue damage. Computed tomography (CT) has become a principal tool for evaluating disease phenotypes. One approach for using CT imaging to assess COPD relies on image registration to match inspiratory and expiratory images to extract biomarkers reflective of local tissue biomechanics. In this study, we propose to evaluate the effectiveness of pulmonary biomechanical features to explain several clinical parameters across four state-of-the-art image registration algorithms. The features would also be used to predict COPD status, severity and exacerbations. Moreover, we propose to evaluate the ability of these feature sets to explain various pulmonary function parameters.

Three-Minute Video: https://youtu.be/IncnumJaLUI

Presentation: chaudhary_bme_vroh_2020.pdf

 

Poster ID: 5

9:00 - 10:00

Cole, Erik

BME

Grad

Predicting COPD severity from airway structure in CT images

Authors: Cole, Erik

Chronic obstructive pulmonary disease (COPD) is a progressive disease affecting millions of people in America. COPD treatment currently relies on clinical measurements and does not account for patient specific biomechanical features. In this work, we investigate patient specific lung features from CT images. We analyze the airway features to extract commonalities and trends.  Airway volume and missing airway segments are two examples of features being compared across both the right and left lungs. Within the common features and trends we attempt to classify these groups to identify disease phenotypes. These phenotypes will  allow for more complete information being used to generate patient tailored treatment plans.

Three-Minute Video: https://youtu.be/8Aju0LwCpRI

Presentation: cole_bme_vroh_2020.pdf

 

Poster ID: 6

10:00 - 11:00

Corrigan, Rae

BME

Grad

Current Status of Polarizable Implicit Solvents for the AMOEBA Force Field: Development of an implicit solvent model to facilitate accurate and efficient in silico simulation of biomolecules

Authors: Corrigan, Rae

Solvation plays a key role in the accurate representation of molecular processes in vivo and in vitro. Interactions with water in particular govern biomolecular folding, recognition, and binding. For these reasons, solvation effects have to be considered for computational folding and design applications. Often, explicitly representing solvent ( i.e. having hundreds to thousands of water molecules in a simulation) can be too computationally expensive to be useful when working with macromolecules. Here, an implicit treatment of solvent is preferred. To address this issue, implicit solvent models are currently being developed for use with the AMOEBA polarizable multipole force field - the models consists of a novel non-polar estimator along with one of three continuum treatments of electrostatics and have been tested for a range of small, organic molecules. Overall, the development of accurate implicit solvent models will help improve the efficiency of computational biomolecular folding and design.

Three-Minute Video: https://youtu.be/iMkcQ77OzDM

Presentation: corrigan_bme_vroh_2020.pdf

 

Poster ID: 7

11:00 - 12:00

El-Hattab, Mariam

BME

Grad

Adipocyte Secreted Factors Influence Fibroblast Activity In-Vitro: fibroblasts convert to highly synthetic and contractile myofibroblasts when exposed to adipocyte conditioned medium

Authors: El-Hattab, Mariam Y.; Nagumo, Yoshiaki; Gourronc, Francoise A.; Klingelhutz, Aloysius J.; Ankrum, James A.; Sander, Edward A.

An emerging treatment strategy of wound healing is the use of fat or adipose tissue, which has shown some success in treatment of burn patients and patients post-surgery. While using adipose tissue is a promising treatment for healing wounds, the details behind its success are underexplored, especially on the cellular level. To bridge this gap, our group investigates the factors that adipocytes (fat cells) produce and their influence on skin cells (fibroblasts). We have found that adipocyte secreted factors increased fibroblasts migration speed, contractility, collagen production, and conversion to myofibroblasts (mature fibroblasts integral to wound healing).

Three-Minute Video: https://youtu.be/LNujeu4tuQA

Presentation: el-hattab_bme_vroh_2020.pdf

 

Poster ID: 8

9:00 - 10:00

Erattakulangara, Subin

BME

Grad

Upper Airway segmentation using deep learning

Authors: SUBIN ERATTAKULANGARA

Speech production involves a complex and intricate coordination of several articulators such as the lips, tongue, velum, pharyngeal wall, glottis, and epiglottis. As these articulators move, the vocal tract airway geometry deforms and undertakes specific poses for specific sounds. Segmenting the vocal tract airway geometry, therefore, forms a crucial step in characterizing the underlying vocal tract airspace. Current segmentation algorithms in speech MRI range from segmenting the articulators themselves , segmenting the air-tissue interfaces, or segmenting the vocal tract air-space. In my research, we try to develop  a novel fully automatic rapid vocal air-space segmentation algorithm based on the U-NET architecture.

Three-Minute Video: https://youtu.be/qaawp8Al0zg

Presentation: erattakulangara_bme_vroh_2020.pdf

 

Poster ID: 9

11:00 - 12:00

Galloy, Adam

BME

Grad

Understanding Lobar Sliding's Impact on Breathing Mechanics: A Finite Element Analysis of the Lungs with and without Lobar Sliding

Authors: Galloy, Adam; Reinhardt, Joseph; Raghavan, Madhavan

Studying the mechanics of lung motion can help identify the causes of lung diseases. Throughout lung motion, the lobes of the lung slide along the lobar fissures. However, some people have missing or incomplete lobar fissures which can limit or prevent lobar sliding. Lobar sliding (or the lack thereof) is often neglected in biomechanical analyses of the lungs and little is known about how this motion impacts lung physiology. Our goal is to learn more about the mechanics of lobar sliding by comparing finite element models of the lungs that allow lobar sliding to models that restrict lobar sliding.

Three-Minute Video: https://www.youtube.com/watch?v=2brCGd6I3p0

Presentation: galloy_bme_vroh_2020.pdf

 

Poster ID: 10

9:00 - 10:00

Ganesh, Venkateswaran

BME

Grad

Improving post-traumatic elbow function using Blebbistatin loaded PLGA pellets

Authors: Ganesh, Venkateswaran; Sander, Edward;

The human elbow joint is one of the fundamental articulating joints of the upper extremity, and preserving its function is vital for various activities of daily living. In addition to direct trauma, burns, strokes, and head injuries can cause damage to the soft tissue architecture of the elbow joint. Post-injury, due to a lack of harmony between the different stages of tissue repair, the ideal wound healing is lost, leading to scar tissue formation. The scarring of soft tissue at the joint affects its functions, and blebbistatin is a potential candidate that can prevent scarring and promote ideal wound healing.

Three-Minute Video: https://youtu.be/tg2m3fOwztE

Presentation: ganesh_bme_vroh_2020.pdf

 

Poster ID: 11

9:00 - 10:00

Gochee, Chad

BME

Undergrad

Investigating the Role of the ULK1 Gene in Insulin Resistance and Diabetes

Authors: Gochee, Chad

Currently, Type 2 Diabetes is affecting over 30 million Americans.  The cause of the disease is not fully understood, and better treatment is needed.  Through genetic engineering and selective breeding, three different groups of mice models will be obtained: one lacking a functional ULK1 gene, one with regular ULK1 levels, and one with overexpressed ULK1.  We will then subject them all to an identical diet and compare the resultant responses with the hopes of better understanding the role of the ULK1 gene as it relates to metabolism, diabetes, and insulin resistance.

Three-Minute Video: https://youtu.be/PNgdnzVijZg

Presentation: gochee_bme_vroh_2020.pdf

 

Poster ID: 12

9:00 - 10:00

Jensen, Jordan

BME

Grad

Improving Joint Health after Arthroscopic Procedures

Authors: Jensen, Jordan; Sander, Edward

Annually, around 750,000 knee arthroscopic surgeries are performed in the United States. This minimally invasive procedure could have unanticipated consequences to joint health as reported by various studies. The saline solution commonly used for the joint irrigation has adverse effects on cells that produce lubricin, a joint lubrication protein. Additionally, the amount of lubricin may be compromised by the shear flow of saline over the articulating surface. This increases friction during motion, leading to irreversible damage to the cartilage.  Characterizing the relationship between shear fluid flow and the loss of lubricin can improve the joint health after an arthroscopic procedure.

Three-Minute Video: https://youtu.be/j2-7yDHEdFw

Presentation: jensen_bme_vroh_2020.pdf

 

Poster ID: 13

11:00 - 12:00

Kettelkamp, Joseph

BME

Undergrad

Estimating Pharmaco-kinetic Maps from Undersampled kt-space

Authors: Joseph Kettelkamp

Traditional structural imaging struggles to identify common neurological diseases in the early stages (e.g., glioblastomas).  However, all these diseases have a significant Microvascular (MV) component.  Dynamic contrast-enhanced MRI (DCE-MRI) aims to quantify the Blood-Brain Barrier leakage (Microvascular) by fitting it to a Pharmaco-kinetic model.  Pharmaco-kinetic parameters like K_trans (forward flux across the endothelium) can be used to identify neurological diseases in their early stages.  However, current methods produce low-resolution parameters. We propose a scheme to estimate high spatial and temporal resolution data. We found that by using the theory of variable splitting. Pharmaco-kinetic parameters could be estimated from undersampled kt-space.

Three-Minute Video: https://www.youtube.com/watch?v=ufiz6W8I1uA

Presentation: kettelkamp_bme_vroh_2020.pdf

 

Poster ID: 14

2:00 - 3:00

Kim, Joseph

BME

Grad

Objective Yield Point Identification From Tensile Testing of Soft Tissues

Authors: Kim, Joseph; Raghavan, M.L.

Cardiovascular aneurysms occur when the walls of a blood vessel weaken and bulge out. Eventually, they can expand like a balloon and burst, which can be quite fatal. My research utilizes machine learning to identify the yield point, a useful indicator of soft tissue's susceptibility to failure or permanent damage.

Three-Minute Video: https://youtu.be/PH7cu1b0cbI

Presentation: kim_bme_vroh_2020.pdf

 

Poster ID: 15

11:00 - 12:00

Knoernschild, Kevin

BME

Grad

Data Acquisition and Preprocessing for Characterization of a Minipig Model of Batten Disease

Authors: Knoernschild, Kevin;

Batten disease is a rare neurodegenerative disease occurring in children, for which magnetic resonance imaging (MRI) is used for clinical evaluation. However, research studies in children are difficult. Hence a large animal model of Battens can be beneficial for understanding early changes in the brain. We have established a methodology for systematic MRI brain evaluation of Battens minipigs at pre- and post-symptomatic timepoints, including whole-cohort image orientation and alignment standardization. The long-term study objective is automated brain structure segmentation for quantifying post symptomatic changes in this model.

Three-Minute Video: https://youtu.be/oHSvKFfQ8RY

Presentation: knoernschild_bme_vroh_2020.pdf

 

Poster ID: 16

1:00 - 2:00

Li, Frank

BME

Grad

Latent Traits of Lung Tissue Patterns in Former Smokers derived by Dual Channel Deep Learning in Computed Tomography Images

Authors: Li, Frank

Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease and the traditional variables extracted from computed tomography images may not be sufficient to describe all the topological features of lung tissues in COPD patients. We employed an unsupervised three-dimensional convolutional autoencoder (CAE)-feature constructor (FC) deep learning network to learn from CT data and derive tissue pattern-clusters jointly. We then applied exploratory factor analysis (EFA) to discover the unobserved latent traits (factors) among pattern-clusters. Two factors were found to be discriminants of patients across all severity stages. Our findings suggest the potential of developing factor-based surrogate markers for new COPD phenotypes.

Three-Minute Video: https://youtu.be/DCVfjBK6FOw

Presentation: li_bme_vroh_2020.pdf

 

Poster ID: 17

10:00 - 11:00

Mhatre, Pareen

BME

Undergrad

Designing a Connector for a Face Shield and Baseball Cap

Authors: Mhatre, Pareen; Nino, Marco; Gossiho, Didier; Wellington, Melanie; Raghavan, Suresh

In order for athletes to train and play safely during the pandemic, the use of PPE is crucial, so we designed a clasp to connect a face shield to a standard baseball cap. After 3D modeling several iterations in Creo Parametric and conducting field tests with various prototypes, we settled on a design that is universal to most caps, provides appropriate face coverage, is cleanable and is durable. In the future, we plan to explore design modifications that would lend itself to mass production, as 3D printing currently is time consuming.

Three-Minute Video: https://youtu.be/UOkUzd7yT8A

Presentation: mhatre_bme_vroh_2020.pdf

 

Poster ID: 18

10:00 - 11:00

Mueller, Marissa

BME

Undergrad

Accelerometer Analysis Options Impact Physical Activity Measurements

Authors: Mueller, Marissa; Chimenti, Ruth; Merkle, Shannon; Frey-Law, Laura

Accelerometers are commonly used to objectively measure physical activity, and require many equations and data filters to interpret motion. However, the cumulative effects of these algorithms are not well understood. We conducted a secondary analysis on wrist-worn accelerometer data to determine how different analysis methods impact physical activity measurements. We found that estimates differed with variable but frequently large effect sizes with equation choice (p<0.05, d=0.08–1.88), the wrist correction (p<0.05, d=0.00–3.04), and the low-frequency-extension (p<0.05, d = 1.44 for steps). Physical activity measurements are highly dependent on analysis specifications, which emphasizes a need for standardization across clinical applications.

Three-Minute Video: https://youtu.be/QChZNFuAJKU

Presentation: mueller_bme_vroh_2020.pdf

 

Poster ID: 19

10:00 - 11:00

Mullan, Sean

BME

Grad

Using Transparent Deep Learning for Error Detection in Medical Imaging Segmentation

Authors: Mullan, Sean; Sonka, Milan

Deep learning models have shown remarkable accuracy in many medical image related tasks, but the high cost of failure requires manual checking of automated results. We report a novel machine-learning approach that uses transparent deep learning methods to detect regions of uncertainty in lung segmentations of pulmonary CT volumes. The automatic identification and quantification of these regions can allow for a manual reviewer to quickly identify and correct any potential areas of concern.

Three-Minute Video: https://youtu.be/bChIZNYHBV8

Presentation: mullan_bme_vroh_2020.pdf

 

Poster ID: 20

11:00 - 12:00

Nastruz, Madison

BME

Undergrad

Motorized Laparoscopy: The importance of motorizing a laparoscopic surgery

Authors: Nastruz, Madison; Vessey, Kai; Lamuta, Caterina

Laparoscopic surgeries are often done with two surgeons.  One holds the camera, and the other does the surgery.  This causes multiple issues around communication, stability, and control throughout the surgery.  Using Creo, we then developed a motorized arm to hold a laparoscope, allowing it to be steady, and have it be controlled by the feet of the surgeon performing the operation.  When it is completed, there will only need to be one surgeon, and they will be less frustrated by the quality of the camera view.

Three-Minute Video: https://youtu.be/som5F3AoNH8

Presentation: nastruz_bme_vroh.pdf

 

Poster ID: 21

10:00 - 11:00

Rusho, Rushdi Zahid

BME

Grad

Dynamic Upper Airway MRI: A potential real-time imaging tool

Authors: Rusho, Rushdi Zahid

Upper airway is the region from nose to neck. The complex coordination of soft tissue structures in the upper airway is responsible for some vital functions, such as breathing, swallowing, and speaking. To understand these functions, effective imaging tools are needed. The rapid biomechanics of these tissues can be captured by a safe imaging modality known as dynamic magnetic resonance imaging (dMRI). However, dMRI is restricted by its slow capturing speed. My research focuses on overcoming these limitations by coming up with techniques that can accurately capture rapid soft tissue motion.

Three-Minute Video: https://youtu.be/PzYnW0E5wb4

Presentation: rusho_bme_vroh_2020.pdf

 

Poster ID: 22

1:00 - 2:00

Shaeffer, Elias

BME

Undergrad

Novel Variant Discovery with Matched Neuroendocrine Tumor and Normal Samples

Authors: Shaeffer, Elias; Brown, Bartley; Braun, Terry; Howe, James

Cancer research and treatment remains difficult because tumors and variants are patient specific. To help alleviate this, we are working to discover disease-causing variants. In this work we used sequencing data from 21 peripheral blood mononuclear cell and matched tumor samples. GATK, Strelka, VEP, and bcftools were used to perform variant calling, and filtering strategies devised to help with assessment. Variants are evaluated on minor allele frequency (MAF), concordance between variant callers, and pathogenicity prediction scores to determine variants associated with cancer.

Three-Minute Video: https://youtu.be/1vanH8K3468

Presentation: shaeffer_bme_vroh_2020.pdf

 

Poster ID: 23

11:00 - 12:00

Wang, Qi

BME

Grad

A photopolymerized and resorbable biomaterial composite for oral mucosal surgical wound repair post cleft palate surgery

Authors: Qi Wang, Dr. Deborah Kacmarynski, Dr. Kristan Worthington

With an incidence of 1 in 690 live births, oral clefts occur frequently worldwide. Cleft palate surgeries are limited by tissue availability, resulting in the denuded bone at the periphery of the hard palate. Unassisted healing results in fistula formation, extensive scarring which disrupts dento-maxillary development and requires additional surgical corrections. Thus, there is a need to develop an affordable and accessible biomaterial that is easily incorporated into standard surgical procedures to improve the outcome of cleft palate repair surgeries. A mixture of gelatin, chitosan, and other potential materials that can be light-cured has the ability to mitigate surgical complications.

Presentation: wang_bme_vroh_2020.pdf

 

Poster ID: 24

9:00 - 10:00

Wendland, Rion

BME

Grad

The effect of retinal scaffold modulus on performance during surgical handling

Authors: Wendland, Rion; Allen, Brittany; Jiao, Chunhua; Sohn, Elliott; Worthington, Kristan

Retinal degenerative diseases result in currently irreversible vision loss, due to the death of photoreceptor cells in the retina. One proposed treatment involves replacing the lost photoreceptor cells with new ones. This retinal replacement therapy uses supportive cell scaffolds to grow, protect, and accurately transplant the new cells into the retina. However, how the mechanical properties of these scaffolds effect the surgical procedure has yet to be characterized. Here, we quantitatively investigated how the stiffness of the cell scaffolds effects performance during surgical handling, and we identified a lower stiffness limit below which the scaffolds were too fragile to be used.

Presentation: wendland_bme_vroh_2020.pdf

 

Poster ID: 25

10:00 - 11:00

Wiley, Madison

BME

Undergrad

Development of a Pediatric Soft Tissue Model: An Iterative Design and Refinement of a Soft Tissue Covering for a Pediatric Distal Humerus Fracture Fixation Simulator

Authors: Wiley, Madison

A pediatric elbow fracture surgical simulator has been developed by a group at the University of Iowa to train surgeons on how to place surgical wires in the pinning of a fractured humerus. The soft tissue model of the simulator was not representative of true surgical conditions. An iterative design process was employed to better resemble the surgery. This process included testing of materials used for the soft tissue, how the materials withstand multiple wire placements, and increased variation of wire placement. The resulting model allows for accurate tactile representation of the surgery and increased variation of wire placement compared to the previous model.

Three-Minute Video: https://youtu.be/cYHwM7l-Nq0

Presentation: wiley_bme_vroh_2020.pdf