Biomedical Engineering and Bioengineering Commons^™

Multi-Modality Breast Mri Segmentation Using Nn-Unet For Preoperative Planning Of Robotic Surgery Navigation, Motaz Alqaoud, John Plemmons Md, Eric Feliberti Md, Facs, Krishnanand Kaipa, Siqin Dong, Gabor Fichtinger, Yimming Xiao, Michel Audette

Modeling, Simulation and Visualization Student Capstone Conference

Segmentation of the chest region and breast tissues is essential for surgery planning and navigation. This paper proposes the foundation for preoperative segmentation based on two cascaded architectures of deep neural networks (DNN) based on the state-of-the-art nnU-Net. Additionally, this study introduces a polyvinyl alcohol cryogel (PVA-C) breast phantom based on the segmentation of the DNN automated approach, enabling the experiments of navigation system for robotic breast surgery. Multi-modality breast MRI datasets of T2W and STIR images were acquired from 10 patients. Segmentation evaluation utilized the Dice Similarity Coefficient (DSC), segmentation accuracy, sensitivity, and specificity. First, a single class labeling …

Fumarate-Based Polymers: Oligo(Poly(Ethylene Glycol) Fumarate) And Poly(Butylene Fumarate) For Tissue Engineering Heart Valve And Bone Tissue, Christian T. Denny

Biomedical Engineering ETDs

Tissue engineering is an emerging field that came from the fields of medicine, materials science, and engineering. The foundation of tissue engineering uses a paradigm that incorporates cells, biomaterials, and exogenous factors to create living tissues for medical, pharmaceutical, and research purposes. Within the last 100 years, biomaterials have been developed to solve many medical and research problems. As biomaterials have developed throughout the years new materials have been developed to have specific properties appropriate for medical applications. Fumarate is a naturally derived molecule in the body and has been found useful for developing polyesters that can be crosslinked into …

A Meshless Approach To Computational Pharmacokinetics, Anthony Matthew Khoury

Doctoral Dissertations and Master's Theses

The meshless method is an incredibly powerful technique for solving a variety of problems with unparalleled accuracy and efficiency. The pharmacokinetic problem of transdermal drug delivery (TDDD) is one such topic and is of significant complexity. The locally collocated meshless method (LCMM) is developed in solution to this topic. First, the meshless method is formulated to model this transport phenomenon and is then validated against an analytical solution of a pharmacokinetic problem set, to demonstrate this accuracy and efficiency. The analytical solution provides a locus by which convergence behavior are evaluated, demonstrating the super convergence of the locally collocated meshless …

Noninvasive In Vivo Optoacoustic Imaging Of Alcohol Use Disorder Using A Mouse Model Of Alcohol Use Disorder, Augustine Meombe Mbolle

USF Tampa Graduate Theses and Dissertations

This research has two parts. The first part focuses on the use of photoacoustic imaging (PAI) to study alcohol-induced effects in the cerebral vasculature of selectively bred alcohol-preferring mice. Part two extends the application of PAI by developing a novel Photoacoustic imaging guided system for repetitive low intensity focused ultrasound (PAI-LIFU) stimulation treatment for alcohol use disorder in crossed high alcohol preferring (cHAP) mice.

Photoacoustic imaging is an emerging hybrid non-invasive optical imaging modality which relies on optical absorption contrast to visualize deep tissue structures and function. It combines the high contrast associated with pure optical imaging and the high …

The Tin Man Needs A Heart: A Proposed Framework For The Regulation Of Bioprinted Organs, Linda Foit

Fordham Law Review

Each day, seventeen people die in the United States while waiting for an organ transplant. At least part of this need could be met by bioprinting, a technology that allows the on-demand production of custom-sized organs from a patient’s own cells. The field of bioprinting is progressing rapidly: the first bioprinted organs have already entered the clinic. Yet, developers of bioprinted organs face significant uncertainty as to how their potentially lifesaving products will be regulated—and by which government agency. Such regulatory uncertainty has the potential to decrease investment and stifle innovation in this promising technological field. This Note examines how …

Bayesian Network-Based Diagnostic Support Tool With Limited Point-Of-Care Ultrasound For Work-Related Elbow Injuries, Cristina Maria Franceschini Sánchez

USF Tampa Graduate Theses and Dissertations

The upper extremity is commonly injured at the workplace, frequently involving the elbow. Currently, there are not many diagnostic support tools for elbow injuries. Developing a clinical decision support tool would allow for narrowing differential diagnoses and guide management steps in a timely and cost-effective manner. In a descriptive retrospective cohort study, 85 non-contrast elbow MRIs were obtained from a large Workers Compensation insurer database. MRIs were either (a) greater than 2 weeks after first clinic visit, or (b) more than 6 weeks after injury, but (c) not more than 3 months after injury. A Bayesian network-based diagnostic support tool …

Optimization Of The Musculoskeletal Simulation In Estimation Of Metabolic Cost, Arash Mohammadzadeh Gonabadi, Philippe Malcolm

UNO Student Research and Creative Activity Fair

Energy from food is supplied to the human body in the form of chemical energy in the muscles. This metabolic energy expenditure is one of the main determinants of the way we walk, and indirect calorimetry measurements are an essential tool for understanding how increases in metabolic cost restrict the mobility of clinical populations. Respiratory oxygen consumption measurements allow recording of the average metabolic cost of walking. However, the time required for these measurements prevents assessing metabolic rate in patients who cannot walk long enough. Musculoskeletal modeling techniques allow to estimate average muscle energy expenditure during locomotion in conjunction with …

How Can Actuation Timing And Magnitude Of A Bilateral Semi-Rigid Hip Exoskeleton Optimize Metabolic Cost, Arash Mohammadzadeh Gonabadi, Prokopios Antonellis, Sara Myers, Iraklis Pipinos, Philippe Malcolm

UNO Student Research and Creative Activity Fair

Semi-rigid exoskeletons could combine some advantages of rigid and soft approaches. The purpose of this study was to investigate the effects of timing and magnitude of assistance from a semi-rigid hip exoskeleton. For ten participants, we tested ten conditions that were combinations of 5 different end-timings, ranging from 21% to 49%, and 2 different moment magnitudes ranging from 0.06 to 0.12 Nm.kg^-1. The participants walked in two reference conditions: a condition without actuation and a condition without the exoskeleton. A semi-rigid hip exoskeleton could alter metabolic rate. However, to produce a net assistive effect, it is necessary to …

Design And Development Of Software With A Graphical User Interface To Display And Convert Multiple Microscopic Histology Images, Sayed Ahmadreza Razian, Majid Jadidi, Alexey Kamenskiy

UNO Student Research and Creative Activity Fair

Histological images are widely used to assess the microscopic anatomy of biological tissues. Recent advancements in image analysis allow the identification of structural features on histological sections that can help advance medical device development, brain and cancer research, drug discovery, vascular mechanobiology, and many other fields. Histological slide scanners create images in SVS and TIFF formats that were designed to archive image blocks and high-resolution textual information. Because these formats were primarily intended for storage, they are often not compatible with conventional image analysis software and require conversion before they can be used in research. We have developed a user-friendly …

Breaks In Longitudinal Elastic Fibers Of Human Femoropopliteal Arteries, Elham Zamani

UNO Student Research and Creative Activity Fair

Breaks in Longitudinal Elastic Fibers of Human Femoropopliteal Arteries

Elham Zamani1, Majid Jadidi1

1 Department of Biomechanics, University of Nebraska Omaha, Omaha, NE

Introduction: Elastin is a major protein in the body with half-life >50 years. It is thought that elastic fibers are formed before the postnatal period. In the femoropopliteal artery (FPA), the main artery in the leg, longitudinal elastic fibers are present in External Elastic Lamina (EEL). Our team has studied more than 1000 cadaveric human FPA and has noticed that there are big breaks in their longitudinal elastic fibers in some subjects. Our goal in this work …

Cbct In Clinical Practice, Tarunjeet Pabla Bds, Dmd, Ms, Dip. Abomr, Hugo C. Campos Dds, Dmd, Mds, Dip. Abomr, Aruna Ramesh Bds, Dmd, Ms, Dip. Abomr

The Journal of the Michigan Dental Association

This feature explores the integration of Cone Beam Computed Tomography (CBCT) into dental practice, offering guidelines for best practices. Introduced in 2001, CBCT revolutionized dental radiography, impacting various clinical areas. The article emphasizes the need for clinicians to comprehend CBCT technology, its benefits, and potential risks. It delves into CBCT imaging considerations, technical parameters (Field of View, Voxel Size, Spatial and Contrast Resolution), image viewing, artifacts, machine calibration, and service. Addressing radiation dose, risks, and protection, the article outlines decision-making for 2D vs. 3D imaging. It underscores the responsibility of interpreting CBCT images, legal considerations, return on investment, and the …

Advancing Ubiquitous Collaboration For Telehealth - A Framework To Evaluate Technology-Mediated Collaborative Workflow For Telehealth, Hypertension Exam Workflow Study, Christopher Bondy Ph.D., Linlin Chen Ph.D, Pamela Grover Md, Pengcheng Shi Ph.D

Articles

Healthcare systems are under siege globally regarding technology adoption; the recent pandemic has only magnified the issues. Providers and patients alike look to new enabling technologies to establish real-time connectivity and capability for a growing range of remote telehealth solutions. The migration to new technology is not as seamless as clinicians and patients would like since the new workflows pose new responsibilities and barriers to adoption across the telehealth ecosystem. Technology-mediated workflows (integrated software and personal medical devices) are increasingly important in patient-centered healthcare; software-intense systems will become integral in prescribed treatment plans [1]. My research explored the path to …

An Ensemble Approach For Patient Prognosis Of Head And Neck Tumor Using Multimodal Data, Numan Saeed, Roba Al Majzoub, Ikboljon Sobirov, Mohammad Yaqub

Computer Vision Faculty Publications

Accurate prognosis of a tumor can help doctors provide a proper course of treatment and, therefore, save the lives of many. Tradi-tional machine learning algorithms have been eminently useful in crafting prognostic models in the last few decades. Recently, deep learning algorithms have shown significant improvement when developing diag-nosis and prognosis solutions to different healthcare problems. However, most of these solutions rely solely on either imaging or clinical data. Utilizing patient tabular data such as demographics and patient med-ical history alongside imaging data in a multimodal approach to solve a prognosis task has started to gain more interest recently and …

The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi

Plant Pathology Faculty Publications

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG …

Bladder Tumor In A Young Leukemic Patient Cured By Chemotherapy: A Case Report, Mohamed Tebaa, Mamoutou Dit Mody, Sylla Mahamadou, Mohamed Amine Lakmichi

Health Sciences

Adult bladder tumor is estimated to be the 10th most common tumor worldwide. However, its incidence is much less common in children. It is a disease of the elderly that peaks in the sixth decade of life. Nevertheless, bladder tumors could also affect children, adolescents, and young adults with a prevalence of

Subomiembed: Self-Supervised Representation Learning Of Multi-Omics Data For Cancer Type Classification, Sayed Hashim, Muhammad Ali, Karthik Nandakumar, Mohammad Yaqub

Computer Vision Faculty Publications

For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of omics data show various aspects of samples. Integration and analysis of multi-omics data give us a broad view of tumours, which can improve clinical decision making. Omics data, mainly DNA methylation and gene expression profiles are usually high dimensional data with a lot of molecular features. In recent years, variational autoencoders (VAE) [13] have been extensively used in embedding image and text data into …

Anesthetics Affect Peripheral Venous Pressure Waveforms And The Cross-Talk With Arterial Pressure, Ali Z. Al-Alawi, Kaylee R. Henry, Lauren D. Crimmins, Patrick C. Bonasso, Md Abul Hayat, Melvin S. Dassinger, Jeffrey M. Burford, Hanna K. Jensen, Joseph Sanford, Jingxian Wu, Kevin W. Sexton, Morten O. Jensen

Biomedical Engineering Faculty Publications and Presentations

Analysis of peripheral venous pressure (PVP) waveforms is a novel method of monitoring intravascular volume. Two pediatric cohorts were studied to test the effect of anesthetic agents on the PVP waveform and cross-talk between peripheral veins and arteries: (1) dehydration setting in a pyloromyotomy using the infused anesthetic propofol and (2) hemorrhage setting during elective surgery for craniosynostosis with the inhaled anesthetic isoflurane. PVP waveforms were collected from 39 patients that received propofol and 9 that received isoflurane. A multiple analysis of variance test determined if anesthetics influence the PVP waveform. A prediction system was built using k-nearest neighbor (k-NN) …

Hyperparameter Optimization For Covid-19 Chest X-Ray Classification, Ibraheem Hamdi, Muhammad Ridzuan, Mohammad Yaqub

Computer Vision Faculty Publications

Despite the introduction of vaccines, Coronavirus disease (COVID-19) remains a worldwide dilemma, continuously developing new variants such as Delta and the recent Omicron. The current standard for testing is through polymerase chain reaction (PCR). However, PCRs can be expensive, slow, and/or inaccessible to many people. X-rays on the other hand have been readily used since the early 20th century and are relatively cheaper, quicker to obtain, and typically covered by health insurance. With a careful selection of model, hyperparameters, and augmentations, we show that it is possible to develop models with 83% accuracy in binary classification and 64% in multi-class …

Therapeutic Treatment With The Anti-Inflammatory Drug Candidate Mw151 May Partially Reduce Memory Impairment And Normalizes Hippocampal Metabolic Markers In A Mouse Model Of Comorbid Amyloid And Vascular Pathology, David J. Braun, David K. Powell, Christopher J. Mclouth, Saktimayee M. Roy, D. Martin Watterson, Linda J. Van Eldik

Neuroscience Faculty Publications

Alzheimer's disease (AD) is the leading cause of dementia in the elderly, but therapeutic options are lacking. Despite long being able to effectively treat the ill-effects of pathology present in various rodent models of AD, translation of these strategies to the clinic has so far been disappointing. One potential contributor to this situation is the fact that the vast majority of AD patients have other dementia-contributing comorbid pathologies, the most common of which are vascular in nature. This situation is modeled relatively infrequently in basic AD research, and almost never in preclinical studies. As part of our efforts to develop …

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 …

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 …

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 …

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 …

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 …

The Applications And Challenges Of The Development Of In Vitro Tumor Microenvironment Chips, Annika Johnson, Samuel Reimer, Ryan Childres, Grace Cupp, Tia C L Kohs, Owen J T Mccarty, Youngbok (Abraham) Kang

Faculty Publications - Biomedical, Mechanical, and Civil Engineering

The tumor microenvironment (TME) plays a critical, yet mechanistically elusive role in tumor development and progression, as well as drug resistance. To better understand the pathophysiology of the complex TME, a reductionist approach has been employed to create in vitro microfluidic models called “tumor chips”. Herein, we review the fabrication processes, applications, and limitations of the tumor chips currently under development for use in cancer research. Tumor chips afford capabilities for real-time observation, precise control of microenvironment factors (e.g. stromal and cellular components), and application of physiologically relevant fluid shear stresses and perturbations. Applications for tumor chips include drug screening …

Biomedical Applications Of Lanthanide Nanomaterials, For Imaging, Sensing And Therapy, Qize Zhang, Stephen O'Brien, Jan Grimm

Publications and Research

The application of nanomaterials made of rare earth elements within biomedical sciences continues to make significant progress. The rare earth elements, also called the lanthanides, play an essential role in modern life through materials and electronics. As we learn more about their utility, function, and underlying physics, we can contemplate extending their applications to biomedicine. This particularly applies to diagnosis and radiation therapy due to their relatively unique features, such as an ultra-wide Stokes shift in the luminescence, variable magnetism and potentially tunable properties, due to the library of lanthanides available and their multivalent oxidation state chemistry. The ability to …

A Highly Conductive, Flexible, And 3d-Printable Carbon Nanotube-Elastomer Ink For Additive Bio-Manufacturing, Andy Shar, Phillip Glass, Daeha Joung Ph.D.

UROP Posters

The synthesis of a highly conductive, flexible, 3D-printable, and biocompatible ink has been of great interest in the field of bio-based additive manufacturing. Various applications include ultra-sensitive, microscale tactile sensors, patient-customizable scaffolds for cardiac and nerve tissue regeneration, and flexible electrocardiogram (ECG) electrodes. Here, a novel elastomeric carbon nanocomposite is presented consisting of amino-functionalized carbon nanotubes (CNT-NH₂) homogenously dispersed in a one-part room-temperature vulcanizing (RTV) silicone matrix. The use of acetone as a swelling solvent aids in electrical percolation through the elastomer matrix. CNT-NH₂ ratios can be tuned to fit various needs; higher tensile strength is favored …

In Vivo Metabolic Analysis Of The Anticancer Effects Of Plasma-Activated Saline In Three Tumor Animal Models, Miao Qi, Dehui Xu, Shuai Wang, Bing Li, Sansan Peng, Qiaosong Li, Hao Zhang, Runze Fan, Hai-Lan Chen, Michael G. Kong

Bioelectrics Publications

In recent years, the emerging technology of cold atmospheric pressure plasma (CAP) has grown rapidly along with the many medical applications of cold plasma (e.g., cancer, skin disease, tissue repair, etc.). Plasma-activated liquids (e.g., culture media, water, or normal saline, previously exposed to plasma) are being studied as cancer treatments, and due to their advantages, many researchers prefer plasma-activated liquids as an alternative to CAP in the treatment of cancer. In this study, we showed that plasma-activated-saline (PAS) treatment significantly inhibited tumor growth, as compared with saline, in melanoma, and a low-pH environment had little effect on tumor growth in …