Biomedical Engineering and Bioengineering Commons^™

Neural Control Of Stopping And Stabilizing The Arm, Shanie A. L. Jayasinghe, Robert A. Scheidt, Robert L. Sainburg

Biomedical Engineering Faculty Research and Publications

Stopping is a crucial yet under-studied action for planning and producing meaningful and efficient movements. In this review, we discuss classical human psychophysics studies as well as those using engineered systems that aim to develop models of motor control of the upper limb. We present evidence for a hybrid model of motor control, which has an evolutionary advantage due to division of labor between cerebral hemispheres. Stopping is a fundamental aspect of movement that deserves more attention in research than it currently receives. Such research may provide a basis for understanding arm stabilization deficits that can occur following central nervous …

Assessment Of Protection Offered By The Nrf2 Pathway Against Hyperoxia-Induced Acute Lung Injury In Nrf2 Knockout Rats, Said H. Audi, Elizabeth R. Jacobs, Taheri Pardis, Swetha Ganesh, Anne V. Clough

Biomedical Engineering Faculty Research and Publications

Nuclear factor erythroid 2-related factor (Nrf2) is a redox-sensitive transcription factor that responds to oxidative stress by activating expressions of key antioxidant and cytoprotective enzymes via the Nrf2-antioxidant response element (ARE) signaling pathway. Our objective was to characterize hyperoxia-induced acute lung injury (HALI) in Nrf2 knock-out (KO) rats to elucidate the role of this pathway in HALI. Adult Nrf2 wildtype (WT), and KO rats were exposed to room air (normoxia) or >95% O₂ (hyperoxia) for 48 h, after which selected injury and functional endpoints were measured in vivo and ex vivo. Results demonstrate that the Nrf2-ARE signaling pathway …

Integration Of Electrical Impedance Spectroscopy For Multichannel Cell Culture Measurement, Conard Chan

Master's Theses

ELECTROCHEMICAL IMPEDANCE SPECTROSCOPY (EIS) has been widely used to study the electrical properties of biological material due to its non-invasive nature and experimental reliability. However, most of the precision impedance analyzers used in EIS only provide single- or two-channel measurements which are inadequate for larger-scale multiplexed measurements, such as those found in modern microfluidic cell culture experiments. The Biomedical Microsystems Laboratory has developed a 16-channel cell culture platform with integrated electrode arrays for monitoring cell growth and electrical properties (i.e., the so-called “electrical phenotype”). In this paper, a system consisting of a 16-channel solid-state analog multiplexer (MUX)paired with a low-cost, …

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) …

Development Of Custom Wall-Less Cardiovascular Flow Phantoms With Tissue-Mimicking Gel, Megan Laughlin, Sam E. Stephens, Jamie A. Hestekin, Morten O. Jensen

Biomedical Engineering Faculty Publications and Presentations

Purpose

Flow phantoms are used in experimental settings to aid in the simulation of blood flow. Custom geometries are available, but current phantom materials present issues with degradability and/or mimicking the mechanical properties of human tissue. In this study, a method of fabricating custom wall-less flow phantoms from a tissue-mimicking gel using 3D printed inserts is developed.

Methods

A 3D blood vessel geometry example of a bifurcated artery model was 3D printed in polyvinyl alcohol, embedded in tissue-mimicking gel, and subsequently dissolved to create a phantom. Uniaxial compression testing was performed to determine the Young’s moduli of the five gel …

Identification Of A Novel Glucuronyltransferase From Streptomyces Chromofuscus Atcc 49982 For Patural Product Glucuronidation, Jie Ren, Caleb Don Barton, Kathryn Eternity Sorenson, Jixun Zhan

Biological Engineering Faculty Publications

Glycosylation is an effective way to increase the polarity of natural products. UDP-glucuronyltransferases (UGTs) are commonly observed and extensively studied in phase II drug metabolism. However, UGTs in microorganisms are not well studied, which hampered the utilization of this type of enzyme in microbial glucuronidation of natural products. Screening of five actinomycete strains showed that Streptomyces chromofuscus ATCC 49982 can convert diverse plant polyphenols into more polar products, which were characterized as various glucuronides based on their spectral data. Analysis of the genome of this strain revealed a putative glucuronidation gene cluster that contains a UGT gene (gcaC) …

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 …

Alf3-Al2o3 Ald Thin-Film-Coated Li1.2mn0.54co0.13ni0.13o2 Particles For Lithium-Ion Batteries: Long-Term Protection, Han Yu, Xiaoqing He, Xinhua Liang

Chemical and Biochemical Engineering Faculty Research & Creative Works

Improving the performance of existing cathode materials of lithium-ion batteries (LIBs) through surface modification has been proven to be an effective way to improve the performance of LIBs. However, it is a challenge to use a traditional method to prepare an effective coating film, which meets the requirements of uniformity, continuity, electrochemical stability, and strong mechanical properties. In this study, an ultrathin AlF₃-Al₂O₃ film was coated on the surface of Li_1.2Mn_0.54Co_0.13Ni_0.13O₂ (LRNMC) particles by atomic layer deposition (ALD) in a fluidized bed reactor. A cathode electrolyte …

Assistive Technologies For Independent Navigation For People With Blindness, Howard Kaplan

USF Tampa Graduate Theses and Dissertations

The necessity for individuals to navigate from location to location is essential to daily life. The majority of humans use sight as the main source for determining how to move through their environment. However, there is a large population of people who are either blind or living with low vision. Based on a 2017 National Health Survey there are around 27 million adult Americans that have experienced vision loss (National Center for Health Statistics, 2017). According to the Eye Diseases Prevalence Research Group there are 3.4 million Americans 40 years and older that are legally blind or visually impaired (EDPRG, …

Transformers In Medical Imaging: A Survey, Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat, Fahad Shahbaz Khan, Huazhu Fu

Computer Vision Faculty Publications

Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as de facto operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved …

Stabilizing The Interface Of All-Solid-State Electrolytes Against Cathode Electrodes By Atomic Layer Deposition, Ye Jin, Han Yu, Xiaoqing He, Xinhua Liang

Chemical and Biochemical Engineering Faculty Research & Creative Works

In recent years, with the severe safety problems of organic electrolytes, all-solid-state electrolytes (ASSEs) have been considered as an appealing choice to replace organic electrolytes due to their high reliability and safety. However, the uncontrolled interfacial chemical reactions between electrodes and ASSEs would lead to high interfacial resistance, which is detrimental for the battery performance. In this work, LiFePO₄ (LFP) particles were coated with ultra-thin ZrO₂ films by atomic layer deposition (ALD) and the effects of thin film coating on the electrochemical performance of lithium-ion batteries using the NASICON-type Li_1.5Al_0.5Ge_1.5(PO₄) …

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 …