Biomedical Engineering and Bioengineering Commons^™

Deutj: An Imagej Plugin For Improved Automatic Masking And Segmentation Of Images From Confocal Microscopy, Sunny Cui

Independent Student Projects and Publications

Due to advances in microscopic imaging, there are a plethora of biological molecules that can now be tagged and subsequentially imaged from almost any cell, organism, or tissue. However, the ability of software to analyze these images remains to be a challenge. ImageJ is open source software that allows for the processing of these images, but faces challenges when dealing with images that show weak contrast between objects of interest and background. DeutJ is an ImageJ plugin that color corrects and brightness corrects gradients that inhibit segmentation in confocal microscopy images. It can analyze hundreds of images from a given …

Session 12: Active Learning To Minimize The Possible Risk From Future Epidemics, Kc Santosh

SDSU Data Science Symposium

In medical imaging informatics, for any future epidemics (e.g., Covid-19), deep learning (DL) models are of no use as they require a large dataset as they take months and even years to collect enough data (with annotations). In such a context, active learning (or human/expert-in-the-loop) is the must, where a machine can learn from the first day with minimum possible labeled data. In unsupervised learning, we propose to build pre-trained DL models that iteratively learn independently over time, where human/expert intervenes only when it makes mistakes and for only a limited data. In our work, deep features are used to …

Electrochemical Sensors And Biosensors Of Biomarkers And Therapeutic Agents Detection, Mahmoud Abdelhakem

Theses and Dissertations

Electrochemical sensing is a pioneering tool amongst all other sensing techniques even though it had been started in the early 20th century. Due to their cost efficacy, accuracy, and real-time measurement, electrochemical sensing has been utilized in a vast of biomedical applications in therapeutic drug monitoring and biomarker detection. This thesis work concerned the monitoring of three therapeutic agents in spiked plasma, urine, dosage form, and interstitial skin fluid with high specificity and accuracy. Two of our sensing platforms utilized nanomaterials for sensing (sensors) of Cilostazol and Velpatasvir utilizing α-MnO2-V2O5 (metal oxide nanorods) and NH2- MIL-53 (Aluminum-based metal organic frameworks), …

Modeling Of The Chest Wall Response To Prolonged Bracing In Pectus Carinatum, Brandon Sargent, Katie Varela, Dennis Eggett, Emily Mckenna, Christina Bates, Rebeccah Brown, Victor Garcia, Larry Howell

Biomedical Engineering Faculty Scholarship

Pectus carinatum is a chest wall deformity that is often treated through the wearing of an external brace. The treatment of the deformity could benefit from a greater understanding of chest wall characteristics under prolonged loading. These characteristics are difficult to model directly but empirical studies can be used to create statistical models. 185 patients from 2018-2020 received bracing treatment. Data on the severity of the deformity, treatment pressures, and time of wear were recorded at the first fitting and all subsequent follow-up visits. This data was analyzed using a statistical mixed effects model to identify significant measures and trends …

Evaluation Of Cold Atmospheric Plasma For The Decontamination Of Flexible Endoscopes, R. C. Hervé, Michael G. Kong, Sudhir Bhatt, Hai-Lan Chen, E. E. Comoy, J-P. Deslys, T. J. Secker, C. W. Keevil

Bioelectrics Publications

Background: Despite adherence to standard protocols, residues including live microorganisms may remain on the various surfaces of reprocessed flexible endoscopes. Prions are infectious proteins notoriously difficult to eliminate.

Aim: We tested the potential of cold atmospheric plasma (CAP) for the decontamination of flexible endoscope various surfaces, measuring total proteins and prion-residual infectivity as an indicator of efficacy.

Methods: New PTFE endoscope channels and metal test surfaces spiked with test soil or prion-infected tissues were treated using different CAP-generating prototypes. Surfaces were then examined for the presence of residues using very sensitive fluorescence epi-microscopy. Prion residual infectivity was determined using the …

An Acute Respiratory Distress Syndrome Drug Development Collaboration Stimulated By The Virginia Drug Discovery Consortium, John S. Lazo, Ruben M.L. Colunga-Biancatelli, Pavel A. Solopov, John D. Catravas

Bioelectrics Publications

The genesis of most older medicinal agents has generally been empirical. During the past one and a half centuries, at least in the Western countries, discovering and developing drugs has been primarily the domain of pharmaceutical companies largely built upon concepts emerging from organic chemistry. Public sector funding for the discovery of new therapeutics has more recently stimulated local, national, and international groups to band together and focus on new human disease targets and novel treatment approaches. This Perspective describes one contemporary example of a newly formed collaboration that was simulated by a regional drug discovery consortium. University of Virginia, …

Use Of Bioheat Modeling To Characterize And Optimize Implantable Medical Devices And Neuromodulation Technologies, Adantchede Louis Zannou

Dissertations and Theses

Medical device development includes prototyping, benchtop characterization, preclinical studies, and clinical trials. Understanding the limitations and potential adverse effects of medical devices prior to their administration in humans is a crucial first step. Optimizing medical devices is essential to employing technology and improving patients care. Computational modeling is widely adopted as a powerful tool to predict stimulation/recording parameter optimization, rapid electrode/device prototyping, investigating novel mechanism of action, and testing working principles of any medical devices. Many implantable neuromodulation technologies including Spinal Cord Stimulation (SCS), which provide substantial therapeutic benefit for patient population with lower back pain, produces heat via the …

Brain Activity Associated With Taste Stimulation: A Mechanism For Neuroplastic Change?, Angela M. Dietsch, Ross M. Westemeyer, Douglas H. Schultz

Department of Special Education and Communication Disorders: Faculty Publications

Purpose: Neuroplasticity may be enhanced by increasing brain activation and bloodflow in neural regions relevant to the target behavior.We administered precisely formulated and dosed taste stimuli to determine whether the associated brain activity patterns included areas that underlie swallowing control.

Methods: Five taste stimuli (unflavored, sour, sweet-sour, lemon, and orange suspensions) were administered in timing-regulated and temperature-controlled 3 mL doses via a customized pump/tubing system to 21 healthy adults during functional magnetic resonance imaging (fMRI). Whole-brain analyses of fMRI data assessed main effects of taste stimulation as well as differential effects of taste profile.

Results: Differences in …

Infrastructure Development For Personalized Risk Prediction To Reduce Cardiovascular Disease In Childhood Cancer Survivors, Suman Shrestha

Dissertations and Theses (Open Access)

Although childhood cancer survivors have lengthy life expectancies, they run the risk of experiencing long-term health issues as a result of their treatment. The most frequent non-cancerous cause of morbidity and mortality for these survivors is cardiac disease. Radiation therapy (RT) has been linked in numerous cohort studies to a higher chance of developing a late cardiac disease in these survivors, and this risk rises with higher mean heart doses and increased RT exposure to larger cardiac volumes. Since, the heart is a heterogeneous organ made up of several distinct substructures, RT dose received by the entire heart does not …

Seeing The Big Picture: System Architecture Trends In Endoscopy And Led-Based Hyperspectral Subsystem Intergration, Craig M. Browning

Graduate Theses and Dissertations (2019 - present)

Early-stage colorectal lesions remain difficult to detect. Early development of neoplasia tends to be small (less than 10 mm) and flat and difficult to distinguish from surrounding mucosa. Additionally, optical diagnosis of neoplasia as benign or malignant is problematic. Low rates of detection of these lesions allow for continued growth in the colorectum and increased risk of cancer formation. Therefore, it is crucial to detect neoplasia and other non-neoplastic lesions to determine risk and guide future treatment. Technology for detection needs to enhance contrast of subtle tissue differences in the colorectum and track multiple biomarkers simultaneously. This work implements one …

Machine Learning And Scalable Informatics Methods To Predict Disease Status From Multimodal Biomedical Data, Hossein Mohammadian Foroushani

McKelvey School of Engineering Graduate Student Theses & Dissertations

Biological understanding of complex diseases such as stroke and obesity is critical for the advancement of medicine. Further knowledge discovery can provide effective biomarkers to improve disease diagnosis and prognosis, identify driver mutations, predict individual genetic susceptibility for early prevention and effective disease management, and facilitate development of personalized drugs. Stroke is the second leading cause of death and long-term disability in the world. Thus, stroke management is a time-sensitive emergency. The initial hours after stroke onset map the trajectory of subsequent neurologic complications. Cerebral edema develops hours to days after acute ischemic stroke and may result in midline shift …

Evaluation And Clinical Implementation Of A Dual-Energy Ct Stopping-Power Ratio Mapping Technique For Proton-Therapy Treatment Planning, Maria Jose Medrano Matamoros

McKelvey School of Engineering Graduate Student Theses & Dissertations

Proton radiotherapy has the potential to treat tumors with better conformal dose distribution than competing modalities when the rapid dose falloff at the end of the proton-beam range is correctly aligned to the edge of the clinical target volume (CTV). However, its clinical potential is dependent on the accurate localization of the Bragg-peak position from predicted stopping-power ratio maps. The method that is most commonly used in today’s clinical practice for predicting stopping-power ratio (SPR) consists of a stoichiometric calibrationtechnique based on single-energy CT (SECT) for direct estimation of patient-specific SPR distribution from vendor-reconstructed Hounsfield Unit (HU) images. Unfortunately, this …

Advancing The Portability, Field Of View, And Spatiotemporal Resolution Of Multi-Parametric Photoacoustic Microscopy, Fenghe Zhong

McKelvey School of Engineering Graduate Student Theses & Dissertations

Capable of structural, functional, molecular, and metabolic imaging with high spatial resolution in vivo, photoacoustic microscopy (PAM) is an emerging tool in biomedical research. Further, recent advances in multi-parametric acquisition and analysis make PAM uniquely capable of simultaneously mapping the total concentration of hemoglobin (CHb), oxygen saturation of hemoglobin (sO2), and blood flow speed. However, there are multiple major limitations, including, the large footprint, low imaging speed, limited imaging contrast, and insufficient axial resolution, which impedance its applications in basic and translational research. In this dissertation, I presented potential solutions to overcome the limitations above.In the first part of this …

Multicolor Fluorescence Guided Surgery For Head And Neck Cancer, Dani Szafran-Reeder

University Honors Theses

This project aims to take a novel, NIR nerve-specific fluorophore LGW05-75⁴ and test its compatibility with a tumor-targeting affibody molecule, ABY-029⁶ that has been labeled with IRDye800CW. The overall goal is to show that these two molecules can be co-administered to show the nerves and tumor cells in real-time to better assist surgeons in a full resection while avoiding iatrogenic nerve damage.

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 …

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 …

Theta Burst Brain Stimulation In Painful Diabetic Neuropathy Patients: Investigating Neural Mechanisms, Bhushan Thakkar

Theses and Dissertations

Chronic pain (CP) is a significant contributor to disability and disease burden globally. In 2019, approximately 50.2 million adults (20.4% of the US population) experienced chronic pain, contributing to $560-635 billion in direct medical costs. In addition, the worldwide prevalence of diabetes mellitus has reached epidemic proportions and is set to increase to 629 million by 2045. Almost 50% of patients with diabetes present with diabetic neuropathy (DN), and one in five patients with diabetes presents with painful DN (pDN) which is the most common cause of neuropathic pain (NP) in the US. Symptomatic treatment is the mainstay of management …

Modeling Of Patient-Specific Periaortic Mechanics And Pulmonary Artery Hemodynamics Based On Phase-Contrast Magnetic Resonance Imaging Sequences., Johane H. Bracamonte

Theses and Dissertations

Inverse modeling in cardiovascular medicine is a collection of methodologies that can provide non-invasive patient-specific estimations of clinical risk factors using medical imaging as inputs. Its incorporation into clinical practice has the potential to improve diagnosis and treatment planning with low associated risks and costs.

Herein, three different phase contrast magnetic resonance imaging (MRI) modalities were implemented as input data, displacement encoding with stimulated echoes (DENSE MRI) applied, and time-resolved velocity encoding phase-contrast MRI, in 1D and 3D, applied to pulmonary artery (PA) hemodynamics.

A model to account for the effect of periaortic interactions due to static and dynamic structures …

Neuromotor Changes In Participants With A Concussion History Can Be Detected With A Custom Smartphone App, Christopher K. Rhea, Masahiro Yamada, Nikita A. Kuznetsov, Jason T. Jakiela, Chanel T. Lojacono, Scott E. Ross, F. J. Haran, Jason M. Bailie, W. Geoffrey Wright

Rehabilitation Sciences Faculty Publications

Neuromotor dysfunction after a concussion is common, but balance tests used to assess neuromotor dysfunction are typically subjective. Current objective balance tests are either cost- or space-prohibitive, or utilize a static balance protocol, which may mask neuromotor dysfunction due to the simplicity of the task. To address this gap, our team developed an Android-based smartphone app (portable and cost-effective) that uses the sensors in the device (objective) to record movement profiles during a stepping-in-place task (dynamic movement). The purpose of this study was to examine the extent to which our custom smartphone app and protocol could discriminate neuromotor behavior between …

Deep Learning Approach To Improved Image Quality For Medical Diagnostics, Olivia Loesch, Katie Leyba, Halyley Chan, Craig Goergen

Discovery Undergraduate Interdisciplinary Research Internship

The United Nation’s health-related Sustainable Development Goals are difficult to achieve in low- and middle-income countries due to workforce shortages and inadequate health surveillance systems. However, with the growth of artificial intelligence (AI) and computer algorithms, it is possible to apply AI to healthcare technologies to improve progress towards these UN standards. This project aims at using and improving computer algorithms and deep learning to aid in the extraction of important structural and functional information from murine carotid artery ultrasound and photoacoustic images. First, we created a large database of simulated photoacoustic images to optimize the algorithms. These images were …

3-In-1 Medical Lancet, Jonathan J. Panella, Gage Vogtlin, Marissa Koski, Benjamin Neyland

Mechanical Engineering

First responders need a quick, sterile, and convenient way to sample blood for glucose testing because glucose levels are a vital metric in assessing time-critical emergency situations. The blood sampling process consists of pre-sterilizing the sample site on the skin with an alcohol pad, pricking the skin with a lancet, and lastly, after sampling, putting a bandage over the prick site. The scope of this project is to design a device which integrates and streamlines the use of the three sub-processes (sterilization, lancing, and bandaging) while upholding the necessary requirements of a single-use medical device and considering other factors which …

Creating Reel Designs: Reflecting On Arthrogryposis Multiplex Congenita In The Community, Iris Layadi

Purdue Journal of Service-Learning and International Engagement

Because of its extreme rarity, the genetic disease arthrogryposis multiplex congenita (AMC) and the needs of individuals with the diagnosis are often overlooked. AMC refers to the development of nonprogressive contractures in disparate areas of the body and is characterized by decreased flexibility in joints, muscle atrophy, and developmental delays. Colton Darst, a seven-year-old boy from Indianapolis, Indiana, was born with the disorder, and since then, he has undergone numerous surgical interventions and continues to receive orthopedic therapy to reduce his physical limitations. His parents, Michael and Amber Darst, have hopes for him to regain his limbic motion and are …

Development Of Quantitative Molecular Photoacoustic Imaging For Noninvasive Cancer Diagnostics, Cayla Zandbergen

Dissertations and Theses (Open Access)

Traditional diagnostic imaging provides clinicians with anatomical information that guides both diagnosis and treatment planning; however, once a tumor has progressed enough to be visible, it has often reached an advanced stage. Molecular imaging techniques allow for real-time visualization of chemical and biological processes via imaging of specific biomarkers, which can facilitate detection of malignancies before they become visible. One biomarker of interest is blood oxygen saturation (SO₂) due to its correlation with hypoxia, which is associated with increased tumor malignancy; some studies have also established SO₂ as an independent biomarker of disease progression. Additionally, because cancerous …

Detection Methods And Clinical Applications Of Circulating Tumor Cells In Breast Cancer, Hongyi Zhang, Xiaoyan Lin, Yuan Huang, Minghong Wang, Chunmei Cen, Shasha Tang, Marcia R. Dique, Lu Cai, Manuel A. Luis, Jillian Smollar, Yuan Wan, Fengfeng Cai

Publications and Research

Circulating Tumor Cells (CTCs) are cancer cells that split away from the primary tumor and appear in the circulatory system as singular units or clusters, which was first reported by Dr. Thomas Ashworth in 1869. CTCs migrate and implantation occurs at a new site, in a process commonly known as tumor metastasis. In the case of breast cancer, the tumor cells often migrate into locations such as the lungs, brain, and bones, even during the early stages, and this is a notable characteristic of breast cancer. Survival rates have increased significantly over the past few decades because of progress made …

Optimal Analytical Methods For High Accuracy Cardiac Disease Classification And Treatment Based On Ecg Data, Jianwei Zheng

Computational and Data Sciences (PhD) Dissertations

This work constitutes six projects. In the first project, a newly inaugurated research database for 12-lead electrocardiogram signals was created under the auspices of Chapman University and Shaoxing People's Hospital (Shaoxing Hospital Zhejiang University School of Medicine). This database aims to enable the scientific community in conducting new studies on arrhythmia and other cardiovascular conditions. In the second project, we created a new 12-lead ECG database under the auspices of Chapman University and Ningbo First Hospital of Zhejiang University that aims to provide high quality data enabling detection of the distinctions between idiopathic ventricular arrhythmia from right ventricular outflow tract …

Zein And Lignin-Based Nanoparticles As Delivery Systems: Pesticide Release And Nanoparticle Health Impact On Soybean Plants, Fallon Polette Salinas Gonzalez

LSU Doctoral Dissertations

This research examined the effect of biodegradable, polymeric, lignin-based nanoparticles (LNPs, 113.8±3.4, negatively charged) and zein nanoparticles (ZNP, 141.6±3.9, positively charged) on soybean plant health. The LNPs were synthesized from lignin, covalently linked to poly(lactic-co-glycolic) acid by emulsion evaporation. ZNPs were synthesized by nanoprecipitation. Soybeans grown hydroponically were treated with three concentrations (0.02, 0.2, and 2 mg/ml) of NPs at 28 days after germination. The effect of ZNPs and LNPs on plant health was determined through analysis of root and stem length, chlorophyll concentration, dry biomass of roots and stem, as well as carbon, nitrogen, and micronutrient absorption after 1, …

Focused Ultrasound-Mediated Drug Delivery To The Brainstem, Dezhuang Ye

McKelvey School of Engineering Graduate Student Theses & Dissertations

Brainstem gliomas are tumors that occur in the brainstem, the brain region that connects the brain to the spinal cord and controls vital body functions. The critical anatomic location of the brainstem precludes surgical intervention and limits the use of invasive therapeutic techniques. Moreover, the frequently intact blood-brain barrier (BBB) of most brainstem gliomas prevents therapeutic agents from reaching the diseased site. The currently available techniques for brain drug delivery are either invasive (e.g., convection-enhanced delivery) or lack targeting to the diseased site (e.g., intranasal brain drug delivery). Novel techniques that can noninvasively overcome the BBB are critically needed for …

Ecg Monitoring In Athletes, Jalal Jwayyed, Kelly Purgason, Joseph Linder, Annamarie Alfery, Silvia Furman

Williams Honors College, Honors Research Projects

Athletes and medical personnel need reliable methods to monitor vital signs and detect potentially life-threatening issues before they occur. Electrocardiograph (ECG) monitors are currently the best method of detecting heart-related health issues. Current ECG monitors worn by athletes are difficult to use and lack the ability to track ECGs in real time. Through research and interviews with various clinicians, further problems have been identified that include poor electrode adhesion, and a lack of compatibility with the equipment worn by athletes. Our team proposes to develop solutions that will improve performance and comfort associated with ECG monitors for athletic applications. This …

Nebulizer-Based Systems To Improve Pharmaceutical Aerosol Delivery To The Lungs, Benjamin M. Spence

Theses and Dissertations

Combining vibrating mesh nebulizers with additional new technologies leads to substantial improvements in pharmaceutical aerosol delivery to the lungs across therapeutic administration methods. In this dissertation, streamlined components, aerosol administration synchronization, and/or Excipient Enhanced Growth (EEG) technologies were utilized to develop and test several novel devices and aerosol delivery systems. The first focus of this work was to improve the poor delivery efficiency, e.g., 3.6% of nominal dose (Dugernier et al. 2017), of aerosolized medication administration to adult human subjects concurrent with high flow nasal cannula (HFNC) therapy, a form of continuous-flow non-invasive ventilation (NIV). The developed Low-Volume Mixer-Heater (LVMH) …

A Deblurring/Denoising Corrected Scintigraphic Planar Image Reconstruction Model For Targeted Alpha Theory, Charles Ross Schmidtlein, Matthew Maroun, Andrzej Krol, Howard Gifford, Lisa Bodei, Joseph O'Donoghue, Ida Häggström, Yuesheng Xu, Si Li

Mathematics & Statistics Faculty Publications

Scintigraphy is a common nuclear medicine method to image molecular target’s bio-distribution and pharmacokinetics through the use of radiotracers and gamma cameras. The patient’s images are obtained by using a pair of opposing large flat gamma ray detectors equipped with parallel-hole lead or tungsten collimators that preferentially detect gamma-rays that are emitted perpendicular to the plane of the detector. The resulting images form an anterior/posterior (A/P) planar image pairs. The obtained images are contaminated by noise and contain artifacts caused by gamma-ray attenuation, collimator penetration, scatter and other detrimental factors. Post-filtering of the images can reduce the noise, but at …