Engineering Commons^™

Resolving The Three-Dimensional Rotational And Translational Dynamics Of Single Molecules Using Radially And Azimuthally Polarized Fluorescence, Oumeng Zhang, Weiyan Zhou, Jin Lu, Tingting Wu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR’s orientational diffusion to be dramatically reduced, but curiously NR’s median lateral displacements drastically increase from 20.8 to …

Advanced Materials For Skin Regeneration, Ingrid Safina

Theses and Dissertations

Massive skin loss, over 20% of the total body surface area, is challenging to heal (Rowan et al. 2015). Ideally, autologous skin grafts have the ability to support complete skin reconstruction. However, skin grafting faces major limitations, such as shortage of donor sites and secondary injury. Alternatively, advanced materials can be used to produce skin constructs that could potentially serve as skin substitutes (Stanton and Billmire 2002). Herein, we used two polymeric materials: graphene and polyurethane (PU) to produce films that support skin cells in their growth and maturation. The surface properties of these materials were modified to enhance their …

Deep Learning-Based Quality Assessment Of Clinical Protocol Adherence In Fetal Ultrasound Dating Scans, Sevim Cengiz, Mohammad Yaqub

Computer Vision Faculty Publications

To assess fetal health during pregnancy, doctors use the gestational age (GA) calculation based on the Crown Rump Length (CRL) measurement in order to check for fetal size and growth trajectory. However, GA estimation based on CRL, requires proper positioning of calipers on the fetal crown and rump view, which is not always an easy plane to find, especially for an inexperienced sonographer. Finding a slightly oblique view from the true CRL view could lead to a different CRL value and therefore incorrect estimation of GA. This study presents an AI-based method for a quality assessment of the CRL view …

Automatic Segmentation Of Head And Neck Tumor: How Powerful Transformers Are?, Ikboljon Sobirov, Otabek Nazarov, Hussain Alasmawi, Mohammad Yaqub

Computer Vision Faculty Publications

Cancer is one of the leading causes of death worldwide, and head and neck (H&N) cancer is amongst the most prevalent types. Positron emission tomography and computed tomography are used to detect and segment the tumor region. Clinically, tumor segmentation is extensively time-consuming and prone to error. Machine learning, and deep learning in particular, can assist to automate this process, yielding results as accurate as the results of a clinician. In this research study, we develop a vision transformers-based method to automatically delineate H&N tumor, and compare its results to leading convolutional neural network (CNN)-based models. We use multi-modal data …

Combined Ibuprofen And Curcumin Delivery Using Mg-Mof-74 As A Single Nanocarrier, Shane Lawson, Ali A. Rownaghi, Fateme Rezaei

Chemical and Biochemical Engineering Faculty Research & Creative Works

Metal-organic frameworks (MOFs) have been extensively used as drug delivery platforms because of their considerable textural properties and physiochemical tunability. However, most medicinal treatments often administer multiple therapeutic pharmaceuticals simultaneously and combined drug delivery over a single MOF carrier has not been extensively developed. As such, in this study we implemented Mg-MOF-74, which is known to have rapid pharmacokinetic properties, for the combined delivery of ibuprofen and curcumin to demonstrate the proof-of-concept for dual-drug delivery over this previously unexplored MOF. To this end, 30 wt % total drug loading of two drugs was impregnated at various ratios (25:5 ibuprofen-curcumin, 20:5 …

Is Contrastive Learning Suitable For Left Ventricular Segmentation In Echocardiographic Images?, Mohamed Saeed, Rand Muhtaseb, Mohammad Yaqub

Computer Vision Faculty Publications

Contrastive learning has proven useful in many applications where access to labelled data is limited. The lack of annotated data is particularly problematic in medical image segmenta-tion as it is difficult to have clinical experts manually annotate large volumes of data. One such task is the segmentation of cardiac structures in ultrasound images of the heart. In this paper, we argue whether or not contrastive pretraining is helpful for the segmentation of the left ventricle in echocardiography images. Furthermore, we study the effect of this on two segmentation networks, DeepLabV3, as well as the commonly used segmentation net-work, UNet. Our …

Is It Possible To Predict Mgmt Promoter Methylation From Brain Tumor Mri Scans Using Deep Learning Models?, Numan Saeed, Shahad Hardan, Kudaibergen Abutalip, Mohammad Yaqub

Computer Vision Faculty Publications

Glioblastoma is a common brain malignancy that tends to occur in older adults and is almost always lethal. The effectiveness of chemotherapy, being the standard treatment for most cancer types, can be improved if a particular genetic sequence in the tumor known as MGMT promoter is methylated. However, to identify the state of the MGMT promoter, the conventional approach is to perform a biopsy for genetic analysis, which is time and effort consuming. A couple of recent publications proposed a connection between the MGMT promoter state and the MRI scans of the tumor and hence suggested the use of deep …

Challenges In Covid-19 Chest X-Ray Classification: Problematic Data Or Ineffective Approaches?, Muhammad Ridzuan, Ameera Ali Bawazir, Ivo Gollini Navarrete, Ibrahim Almakky, Mohammad Yaqub

Computer Vision Faculty Publications

The value of quick, accurate, and confident diagnoses cannot be undermined to mitigate the effects of COVID-19 infection, particularly for severe cases. Enormous effort has been put towards developing deep learning methods to classify and detect COVID-19 infections from chest radiography images. However, recently some questions have been raised surrounding the clinical viability and effectiveness of such methods. In this work, we carry out extensive experiments on a large COVID-19 chest X-ray dataset to investigate the challenges faced with creating reliable solutions from both the data and machine learning perspectives. Accordingly, we offer an in-depth discussion into the challenges faced …

Contact‐Free Remote Manipulation Of Hydrogel Properties Using Light‐Triggerable Nanoparticles: A Materials Science Perspective For Biomedical Applications, Cho-E Choi, Aishik Chakraborty, Ali Coyle, Yasmeen Shamiya, Arghya Paul

Chemical and Biochemical Engineering Publications

Considerable progress has been made in synthesizing “intelligent”, biodegradable hydrogels that undergo rapid changes in physicochemical properties once exposed to external stimuli. These advantageous properties of stimulus-triggered materials make them highly appealing to diverse biomedical applications. Of late, research on the incorporation of light-triggered nanoparticles (NPs) into polymeric hydrogel networks has gained momentum due to their ability to remotely tune hydrogel properties using facile, contact-free approaches, such as adjustment of wavelength and intensity of light source. These multi-functional NPs, in combination with tissue-mimicking hydrogels, are increasingly being used for on-demand drug release, preparing diagnostic kits, and fabricating smart scaffolds. Here, …

Assessing Leachable Cytotoxicity Of 3d-Printed Polymers And Facile Detoxification Methods, Venkatakrishnan Rengarajan, Angela Clyde, Jefferson Pontsler, Jonathan Valiente, Adreann Peel, Yu Huang

Biological Engineering Faculty Publications

Additive manufacturing of polymers is gaining momentum in health care industries by providing rapid 3D printing of customizable designs. Yet, little is explored about the cytotoxicity of leachable toxins that the 3D printing process introduced into the final product. We studied three printable materials, which have various mechanical properties and are widely used in stereolithography 3D printing. We evaluated the cytotoxicity of these materials through exposing two fibroblast cell lines (human and mouse derived) to the 3D-printed parts, using overlay indirect contact assays. All the 3D-printed parts were measured toxic to the cells in a leachable manner, with flexible materials …

Graphene Oxide Functionalized Biosensor For Detection Of Stress-Related Biomarkers, Erican Santiago, Shailu Shree Poudyal, Sung Y. Shin, Hyeun Joong Yoon

Michigan Tech Publications, Part 1

A graphene oxide (GO)-based cortisol biosensor was developed to accurately detect corti-sol concentrations from sweat samples at point-of-care (POC) sites. A reference electrode, counter electrode, and working electrode make up the biosensor, and the working electrode was functional-ized using multiple layers consisting of GO and antibodies, including Protein A, IgG, and anti-Cab. Sweat samples contact the anti-Cab antibodies to transport electrons to the electrode, resulting in an electrochemical current response. The sensor was tested at each additional functionalization layer and at cortisol concentrations between 0.1 and 150 ng/mL to determine how the current response differed. A potentiostat galvanostat device was …

Transcranial Direct Current Stimulation On Parkinson’S Disease: Systematic Review And Meta-Analysis, Paloma Cristina Alves De Oliveira, Thiago Anderson Brito De Araújo, Daniel Gomes Da Silva Machado, Abner Cardoso Rodrigues, Marom Bikson, Suellen Marinho Andrade, Alexandre Hideki Okano, Hougelle Simplicio, Rodrigo Pegado, Edgard Morya

Publications and Research

Background: Clinical impact of transcranial direct current stimulation (tDCS) alone for Parkinson’s disease (PD) is still a challenge. Thus, there is a need to synthesize available results, analyze methodologically and statistically, and provide evidence to guide tDCS in PD.

Objective: Investigate isolated tDCS effect in different brain areas and number of stimulated targets on PD motor symptoms.

Methods: A systematic review was carried out up to February 2021, in databases: Cochrane Library, EMBASE, PubMed/MEDLINE, Scopus, and Web of science. Full text articles evaluating effect of active tDCS (anodic or cathodic) vs. sham or control on motor symptoms of PD were …

Magnetic Nanoparticles Enhanced Surface Plasmon Resonance Biosensor For Rapid Detection Of Salmonella Typhimurium In Romaine Lettuce, Devendra Bhandari, Fur-Chi Chen, Roger C. Bridgman

Human Sciences Faculty Research

Salmonella is one of the major foodborne pathogens responsible for many cases of illnesses, hospitalizations and deaths worldwide. Although different methods are available to timely detect Salmonella in foods, surface plasmon resonance (SPR) has the benefit of real-time detection with a high sensitivity and specificity. The purpose of this study was to develop an SPR method in conjunction with magnetic nanoparticles (MNPs) for the rapid detection of Salmonella Typhimurium. The assay utilizes a pair of well-characterized, flagellin-specific monoclonal antibodies; one is immobilized on the sensor surface and the other is coupled to the MNPs. Samples of romaine lettuce contaminated with …

Role Of Inflammatory Niche And Adult Cardiomyocyte Coculture On Differentiation, Matrix Synthesis, And Secretome Release By Human Bone Marrow Mesenchymal Stem Cells, Jyotsna Joshi, Chandrasekhar R. Kothapalli

Chemical & Biomedical Engineering Faculty Publications

Myocardial infarction (MI) causes cardiomyocyte death, provokes innate immune response, and initiates tissue remodeling. The intrinsic healing process is insufficient to replace the lost cells, or regenerate and restore the functional features of the native myocardium. Autologous bone marrow-derived mesenchymal stem cell (BM-MSC) transplantation is being explored to offer therapeutic potential after MI. Here, we cultured human BM-MSC spheroids in three-dimensional collagenous gels for 28 days under exposure to tumor necrosis factor-alpha (+ TNFα), and coculture with adult human cardiomyocytes, or with conditioned media (CM) pooled from TNFα-stimulated adult cardiomyocytes. MSC differentiation marker (CD90, GATA4, cTnI, cTnT, Cx43, MHC, α-actin) …

Glycocalyx Mechanotransduction Mechanisms Are Involved In Renal Cancer Metastasis, Heriberto Moran, Limary M. Cancel, Peigen Huang, Sylvie Roberge, Tuoye Xu, John M. Tarbell, Lance L. Munn

Publications and Research

Mammalian cells, including cancer cells, are covered by a surface layer containing cell bound proteoglycans, glycoproteins, associated glycosaminoglycans and bound proteins that is commonly referred to as the glycocalyx. Solid tumors also have a dynamic fluid microenvironment with elevated interstitial flow. In the present work we further investigate the hypothesis that interstitial flow is sensed by the tumor glycocalyx leading to activation of cell motility and metastasis. Using a highly metastatic renal carcinoma cell line (SN12L1) and its low metastatic counterpart (SN12C) we demonstrate in vitro that the small molecule Suberoylanilide Hydroxamic Acid (SAHA) inhibits the heparan sulfate synthesis enzyme …

In Vitro Mitral Valve Model With Unrestricted Ventricular Access: Using Vacuum To Close The Valve And Enable Static Trans-Mitral Pressure, Sam E. Stephens, Alexander J. Kammien, Jacob C. Paris, Alexis P. Applequist, Neil B. Ingels, Hanna K. Jensen, Drew E. Rodgers, Charles R. Cole, Jonathan F. Wenk, Morten O. Jensen

Biomedical Engineering Faculty Publications and Presentations

Current in vitro models of the left heart establish the pressure difference required to close the mitral valve by sealing and pressurizing the ventricular side of the valve, limiting important access to the subvalvular apparatus. This paper describes and evaluates a system that establishes physiological pressure differences across the valve using vacuum on the atrial side. The subvalvular apparatus is open to atmospheric pressure and accessible by tools and sensors, establishing a novel technique for experimentation on atrioventricular valves. Porcine mitral valves were excised and closed by vacuum within the atrial chamber. Images were used to document and analyze closure …

Optimizing Biomedical Discoveries As An Engine Of Culture Change In An Academic Medical Center, Anne K. Dechant, Stephen Fening, Michael Haag, William Harte, Mark R. Chance

Faculty Scholarship

Academic discovery in biomedicine is a growing enterprise with tens of billions of dollars in research funding available to universities and hospitals. Protecting and optimizing the resultant intellectual property is required in order for the discoveries to have an impact on society. To achieve that, institutions must create a multidisciplinary, collaborative system of review and support, and utilize connections to industry partners. In this study, we outline the efforts of Case Western Reserve University, coordinated through its Clinical and Translational Science Collaborative (CTSC), to promote entrepreneurial culture, and achieve goals of product development and startup formation for biomedical and population …

Toward A Multimodal Computer-Aided Diagnostic Tool For Alzheimer’S Disease Conversion, Danilo Pena, Jessika Suescun, Mya Schiess, Timothy M. Ellmore, Luca Giancardo, Alzheimer’S Disease Neuroimaging Initiative

Publications and Research

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder. It is one of the leading sources of morbidity and mortality in the aging population AD cardinal symptoms include memory and executive function impairment that profoundly alters a patient’s ability to perform activities of daily living. People with mild cognitive impairment (MCI) exhibit many of the early clinical symptoms of patients with AD and have a high chance of converting to AD in their lifetime. Diagnostic criteria rely on clinical assessment and brain magnetic resonance imaging (MRI). Many groups are working to help automate this process to improve the clinical workflow. Current …

Stress Corrosion Analysis And Direct Cell Viability Of Biodegradable Zn-Fe-Ca Alloy In In-Vitro Conditions, Orit Avior, Noa Ben Ghedalia-Peled, Tomer Ron, Jeremy Goldman, Razi Vago, Eli Aghion

Michigan Tech Publications, Part 1

Due to the excellent biocompatibility of Zn and Zn-based alloys, researchers have shown great interest in developing biodegradable implants based on zinc. Furthermore, zinc is an essential component of many enzymes and proteins. The human body requires ~15 mg of Zn per day, and there is minimal concern for systemic toxicity from a small zinc-based cardiovascular implant, such as an arterial stent. However, biodegradable Zn-based implants have been shown to provoke local fibrous encapsulation reactions that may isolate the implant from its surrounding environment and interfere with implant function. The development of biodegradable implants made from Zn-Fe-Ca alloy was designed …

Genome Structure And Evolutionary History Of Frankincense Producing Boswellia Sacra, Abdul Latif Khan, Ahmed Al-Harrasi, Jin-Peng Wang, Sajjad Asaf, Jean-Jack Riethoven, Tariq Shehzad, Chia-Sin Liew, Xiao-Ming Song, Daniel P. Schachtman, Chao Liu, Ji-Gao Yu, Zhi-Kang Zhang, Fan-Bo Meng, Jia-Qing Yuan, Chen-Dan Wei, He Guo, Xuewen Wang, Ahmed Al-Rawahi, In-Jung Lee, Jeffrey L. Bennetzen, Xi-Yin Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Boswellia sacra Flueck (family Burseraceae) tree is wounded to produce frankincense. We report its de novo assembled genome (667.8 Mb) comprising 18,564 high-confidence protein-encoding genes. Comparing conserved single-copy genes across eudicots suggest >97% gene space assembly of B. sacra genome. Evolutionary history shows B. sacra gene-duplications derived from recent paralogous events and retained from ancient hexaploidy shared with other eudicots. The genome indicated a major expansion of Gypsy retroelements in last 2 million years. The B. sacra genetic diversity showed four clades intermixed with a primary genotype—dominating most resin-productive trees. Further, the stemtranscriptome revealed that wounding concurrently activates phytohormones signaling, …

Characterizing Isoform Switching Events In Esophageal Adenocarcinoma, Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty

Nebraska Center for Biotechnology: Faculty and Staff Publications

Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment- naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification …

Evaluation Of Cell-Matrix Interactions In K14+ Leader Cells On Caf-Modulated Matrix, Trey P. Redman, Jessanne Y. Lichtenberg, Priscilla Y. Hwang

Summer REU Program

No abstract provided.

Engineering Instruction, Inclusion, And Comics: Reflections From A Student Illustrator And An Instructor, Addison Totman, Sreyoshi Bhaduri, Krishna Pakala, Cherie D. Edwards, Michelle Soledad

Mechanical and Biomedical Engineering Faculty Publications and Presentations

This paper presents the opportunity gap for comics in engineering education, through reflections from a team redesigning a mechanical engineering syllabi using illustrations. To increase a sense of belonging among diverse students, the authors of this paper propose a graphic narrative focused on the curriculum of the mechanical engineering department at a large public university in Western United States. We hope that this paper addresses the underutilized and largely missed opportunity to add engagement, better conceptual understanding, and improve inclusion in engineering classrooms through incorporating visual illustrations.

Work-In-Progress: Mobile Assisted Gains Through Innovative Curriculum For Students In The Thermal-Fluids Science Course, Maeve Bakic, Krishna Pakala, Diana Bairaktarova, Devshikha Bose

Mechanical and Biomedical Engineering Faculty Publications and Presentations

A learner-centered higher education ecosystem is essential to effective educational outcomes and societal advancement. Mobile devices such as smartphones, tablets, and tablet computers enable learning anytime and from any location, blurring the boundaries between formal and informal learning. When paired with effective pedagogy, mobile technologies can positively impact the teaching and learning experience for students in high-demand science, technology, engineering and mathematics (STEM) disciplines, increasing the flexibility and ease with which they are able to pursue their education while developing their professional identities as engineers. Student retention remains a problem in STEM programs. In engineering, many students do not even …

Human Interaction With Fake News, Autumn Woodson, Sampath Jayarathna (Mentor)

Computer & Information Science: Research Experiences for Undergraduates in Disinformation Detection and Analytics

No abstract provided.

Development Of Gene Regulatory Elements For Biosensing Applications, Mallory N. Bates

Browse all Theses and Dissertations

21% of U.S adults experienced mental illnesses in 2020. Nearly 1 in 4 active- duty military personnel showed signs of mental health conditions in 2014 [89]. Mental health can be identified in the body by different biomarkers. These biomarkers potentially could be controlled by riboswitches, which could help mental illnesses and regulate diseases. Riboswitches are desirable in these cases due to responding without affecting vital functions. Riboswitches are located in mRNA and switch “ON” or “OFF” depending on the concentration of a biomarker [13]. In this research, riboswitches were re-engineered to take a known riboswitch and control its response in …

Novel Hybrid Solar Nanophotonic Distillation Membrane With Photovoltaic Module For Co-Production Of Electricity And Water, Alejandro Espejo Sanchez, Nipun Goel, Todd Otanicar

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Solar energy utilization and desalination are both critical needs for large portions of the world facing energy and water challenges. Direct contact membrane distillation is an attractive thermally driven desalination technique that can easily be integrated with solar energy. Here we propose and experimentally demonstrate for the first time a hybrid direct contact membrane desalination plus photovoltaic device. The system utilizes partially transparent photovoltaic cells to produce electricity and pass thermal energy to the nanoparticle doped membrane to produce thermal energy at the membrane surface. A custom lab-scale direct contact membrane distillation setup characterizes the membranes fabricated off-sun and on-sun. …

In-Flow Dynamics Of An Area-Difference-Energy Spring-Particle Red Blood Cell Model On Non-Uniform Grids, Brendan Walsh, Fergal Boyle

Articles

In this paper the area-difference-energy spring-particle (ADE-SP) red blood cell (RBC) structural model developed by Chen and Boyle is coupled with a lattice Boltzmann flux solver to simulate RBC dynamics. The novel ADE-SP model accounts for bending resistance due to the membrane area difference of RBCs while the lattice Boltzmann flux solver offers reduced computational runtimes through GPU parallelisation and enabling the employment of non-uniform meshes. This coupled model is used to simulate RBC dynamics and predictions are compared with existing experimental measurements. The simulations successfully predict tumbling, tank-treading, swinging and intermittent behaviour of an RBC in shear flow, and …

Vision And Radar Steering Reduces Agricultural Sprayer Operator Stress Without Compromising Steering Performance, Travis A. Burgers, Kelly J. Vanderwerff

Mechanical Engineering Faculty Publications

Self-propelled agricultural sprayer operators work an average of 15 h d^-1 in peak season, and steering is the task that causes the operator the most stress because of the large number of stimuli involved. Automatic guidance systems help reduce stress and fatigue for operators by allowing them to focus on tasks other than steering. Physiological signals like skin conductance (electrodermal activity, EDA) change with stress and can be used to identify stressful events. The objective of this study was to determine if using a commercially available vision and radar guidance system (VSN®, Raven Industries) reduces agricultural sprayer operators’ stress …

Improving Quantification Of Mitral Regurgitation Through Computational Fluid Dynamics And Ex Vivo Testing, Alexandra Flowers

Electronic Theses and Dissertations

Mitral regurgitation (MR) is a prominent cardiac disease affecting more than two million people in the United States alone. In order for patients to receive proper therapy, regurgitant volume must first be quantified. As there are an array of methods to do so, the proximal isovelocity surface area (PISA) method continues to be the most accurate and clinically used method. However, there are some difficulties obtaining the necessary measurements need for this when performing transthoracic echocardiography. This study aims to evaluate and present techniques that may be used to more accurately quantify regurgitation through ex vivo testing and computational fluid …