Bioimaging and Biomedical Optics Commons^™

Ai-Driven Approach For Diagnosis Of Renal Transplant Rejection Based On Biomarkers Identification And Integration., Israa Sharaby

Electronic Theses and Dissertations

They kidney is a vital organ for which humans are fortunate to find a spare through transplantation to sustain critical body functions, offering a hope to those struggling with renal failure. Kidney transplant procedure is the optimal treatment for people who suffer from end-stage renal failure. However, there are posed challenges due to the risk of immune rejection and the limited availability of donors. Early detection of renal rejection can provide timely intervention and accurate diagnosis that are critical to improve the transplant outcomes. This study explores the innovative approaches for addressing the current challenges through biomarkers identification, imaging techniques, …

Hypoxic Incubator: Improving Robustness/Reliability And Demonstrating Physiological Efficacy, Damon Dennis Tan

Master's Theses

The Microphysiological Systems Laboratory aims to develop colorectal cancer tumor models under a hypoxic environment to assess model response to pharmaceutical compounds in vitro. To perform relevant studies, researchers have attempted to use different hypoxic inducing strategies such as a nitrogen pod and hypoxic incubator to recreate in vivo physiological responses to hypoxia. However, studies would be interrupted due to incubator functionality failure. To ensure successful and physiologically relevant studies, I improved and verified the robustness and reliability of a hypoxic incubator previously designed and manufactured in the lab. Through the testing and iterating design processes, I engineered and implemented …

Real-Time Navigation System For Breast Cancer Surgery With Pre- And Intra-Operative Imaging Using Neural Networks, Motaz Alqaoud

Biomedical Engineering Theses & Dissertations

Breast cancer is one of the most frequently diagnosed malignancies in women worldwide, necessitating precise diagnosis and treatment. Breast-conserving surgery (BCS) is the primary treatment for nonpalpable cases, yet current approaches often lack accuracy due to the absence of real-time 3D imaging during surgery. This limitation impairs surgeons’ ability to visualize tumor locations, compromising outcomes and potentially leading to repeat surgeries with higher risks, undesirable cosmetic results, increased costs, and, in some cases, mastectomy. Thus, there is a critical need for a navigation system to facilitate accurate tumor excision in nonpalpable breast cancer through real-time patient-specific 3D tracking.

This study …

Hyperspectral Image Classification Of Bacteria Using A Deep Convolutional Neural Network, Bruce S. Vogelsberg Jr

All Theses

Hyperspectral imaging is a non-invasive imaging method capable of collecting both spatial and spectral information. However, because of the large volume of data collected, much of it is redundant or not useful for classification. Deep learning is a subset of machine learning that uses artificial neurons in a multilayered structure to learn representations from data. One of the main advantages of deep learning is the powerful feature extraction capabilities, which allow the model to learn both high- and low-level features. Convolutional neural networks are a type of deep learning model that have alternating convolutional and pooling layers capable of extracting …

Denoising And Super-Resolution Of In-Vitro 4e Flow Mri In A Stenotic Phantom Model Using Physics-Informed Neural Networks., Shrouk M. Wally

Electronic Theses and Dissertations

In recent years, the use of 4D flow MRI has revolutionized cardiovascular imag- ing by providing comprehensive data on blood flow dynamics over time. However, the limited spatial and temporal resolution of this imaging modality can hinder the accurate assessment of complex hemodynamic phenomena. This thesis explores the application of Physics-Informed Neural Networks (PINNs) to enhance the resolution of 4D flow MRI data, thereby improving its clinical utility. PINNs are a class of neural networks that integrate physical laws into their training process. By embedding these physics equations, PINNs can discover the underlying physics of fluid dynamics to produce more …

Fluid-Solid Coupled Analysis Of Biological Samples In A Flow Chamber Using Optical Coherence Tomography, Reece W. Fratus

All Dissertations

Forces from fluid flow on a tissue or cellular boundary can drive remodeling processes through mechanotransduction pathways. In most cases, the exact mechanisms are not understood, such as in marine biofilm development or vascular remodeling. To gain a better understanding of these interactions, the flow profile at a solid boundary and the mechanical changes of that solid can be coupled together to determine the impact of fluid flow on mechanical remodeling. To achieve this, optical coherence tomography (OCT) is used to image the fluid and solid simultaneously. Fluid seeded with particles can be imaged and run through a particle image …

Contribution Of Collagen Type I To The Mechanical Properties Of Myocardial Tissues At The Micron Level, Adam Baker

All Dissertations

Collagen is a critical component of the organization and one of the key factors contributing to the mechanical stability of the myocardium. Where cardiomyocytes actuate to contract the heart and deliver blood to the lungs and the entire body, the local collagen network must be able to support the mechanical needs of the heart by enhancing rigidity, reducing the mechanical responsibility of cells, and increasing compliance to add loading capacity during diastole. At an organ-wide level, this has been measured and modeled in many ways. At the tissue level, the mechanical properties have been evaluated using techniques such as bi-axial …

Segmentation And Classification Of Left Ventricular Abnormalities In Cardiac Mri Using Initial Point Prediction Based Deformable Model, Md. Asadur Rahman, Md. Al Noman, A. B. M. Aowlad Hossain

Future Computing and Informatics Journal

The shape of the left ventricle (LV) of a cardiac magnetic resonance image (CMRI) helps physicians to diagnose different cardiac abnormalities. The similarity of pixel intensity and shape of LV with neighbor tissues, the imprecision of boundaries, and the presence of noise are the challenges to accurate segmentation of LV. This paper contributes to the successful implementation of an automatic edge contouring method to segment LV area from CMRI and detect whether the ventricle belongs to abnormalities. This method proposes the regression-based artificial neural network to predict the possible initial position of the deformable edge-based active contour model for precise …

Preclinical Examination Of A Nerve Specific Fluorophore Using Ex Vivo Human Tissues, Logan Michael Bateman

Dartmouth College Master’s Theses

Fluorescence-guided surgery (FGS) is a nascent field which seeks to improve patient safety and surgical outcomes using fluorescent agents known as fluorophores. Fluorophores are molecules which upon excitation with a specific wavelength of light emit a photon of a specific wavelength which can be detected using a modified camera system. Creation and translation of a fluorophore for clinical use is a costly, laborious, and time intensive process. Only a handful of fluorophores have received FDA approval and they required multiple years of tightly regulated clinical trials. Prior to these first-in-human studies these agents are subject to a litany of preclinical …

Single-Molecule Orientation Imaging Reveals The Nano-Architecture Of Amyloid Fibrils Undergoing Growth And Decay, Brian Sun, Tianben Ding, Weiyan Zhou, Tara S. Porter, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer’s disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational “wobble” of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order …

Development Of A Two-Photon Imaging System, Jesseca Hollenbaugh

University Honors Theses

The objective of this project was to convert a Sarastro 2000 confocal laser scanning microscope (CLSM) into a system capable of far-field two-photon excitation (TPE) imaging for the use of the PSU Biology department. TPE microscopy operates on the ability of fluorophores to accept two photons each with half the energy of a desired transition in a single quantum event via a virtual energy state and then emit a higher energy photon upon relaxation. This is preferable to single-photon excitation (SPE) imaging due to lower photon imaging, causing less damage to delicate biological samples, as well as the inherent localization …

Data-Driven Insights Into Spatial Patterns And Disease Etiologies Of White Matter Hyperintensities, Sugandha Roy

McKelvey School of Engineering Graduate Student Theses & Dissertations

In this thesis, we have applied Orthogonal Projective Non-Negative Matrix Factorization (opNMF) to identify spatial patterns of white matter hyperintensities (WMH) within UK Biobank's imaging data. Our selection criteria excluded subjects with a history of neurological, mental, and specific cerebrovascular conditions, allowing us to focus on WMH patterns in a healthy aging population. We have interrogated the association of location-specific WMHs with a variety of demographic, clinical, and genetic factors. Our multivariable regression analysis evaluates the strength and nature of the associations between these factors and WMH distribution. The analysis integrates variables such as age, sex, smoking habits, medication usage …

An Attention Lstm U-Net Model For Drosophila Melanogaster Heart Tube Segmentation, Xiangping Ouyang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Machine learning is commonly used in biomedical image analysis, as it allows automated image segmentation and identification that minimizes the need for tedious human involvement. Drosophila melanogaster is often used as a cardiac disease model, where optical coherence microscopy (OCM) is used to image and analyze its beating dynamics. As OCM often generates a large volume of images, automated image segmentation is necessary to quantify the heart beating efficiently. Our most recent heart segmentation model, FlyNet 2.0+, is a fully convolutional LSTM U-Net model. However, the performance of the model diminishes in the presence of artifacts, such as image reflection …

Calcium Analysis Of Intercellular Communications Between Alpha Cells And Delta Cells Across The Pancreatic Islet, Shichao Gao

McKelvey School of Engineering Graduate Student Theses & Dissertations

The intricate communication between different cell types within pancreatic islets plays a crucial role in regulating glucose homeostasis. Among these cellular interactions, the interplay between α cells (responsible for glucagon secretion) and δ cells (secreting somatostatin) is particularly intriguing due to the inhibitory effects of somatostatin on glucagon release. Understanding the intercellular interactions between α and δ cells may provide insights into the mechanisms underlying the coordinated regulation of blood glucose levels. In this study, we employed a multi-modal approach combining confocal imaging, image analysis, and correlation network analysis to investigate the spatial relationships and potential functional connections between α …

Structured Light Radial-View Endoscope Imaging Development For Evaluation Of Human Tissue, Xiyan Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

In this thesis, we improved an existing structured light methodology to more accurately estimate tissue optical properties imaged in a single snapshot. The developed approach is a major enhancement of the traditional three-phase spatial frequency domain imaging system: It greatly simplifies the operational procedure while also maintaining high accuracy in optical property measurements .

Leveraging this improved approach, we have developed a low-cost, compact, and radial-view endoscope prototype. This prototype combines affordability with high functionality and a user-friendly design. To assess the performance and reliability of our endoscope, we conducted comprehensive evaluations involving tissue-mimicking phantoms, as well as ex vivo …

Evaluating Neuroimaging Modalities In The A/T/N Framework: Single And Combined Fdg-Pet And T1-Weighted Mri For Alzheimer’S Diagnosis, Peiwang Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

With the escalating prevalence of dementia, particularly Alzheimer's Disease (AD), the need for early and precise diagnostic techniques is rising. This study delves into the comparative efficacy of Fluorodeoxyglucose Positron Emission Tomography (FDG-PET) and T1-weighted Magnetic Resonance Imaging (MRI) in diagnosing AD, where the integration of multimodal models is becoming a trend. Leveraging data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), we employed linear Support Vector Machines (SVM) to assess the diagnostic potential of these modalities, both individually and in combination, within the AD continuum. Our analysis, under the A/T/N framework's 'N' category, reveals that FDG-PET consistently outperforms T1w-MRI across …

Utilizing Spatial Transcriptomics To Compare Gene Expression In Volumetric Muscle Loss Injury Recovery, Colton Gattis

Biomedical Engineering Undergraduate Honors Theses

Volumetric Muscle Loss (VML) injuries are known to disrupt the normal regenerative process via fibrosis leading to an extensive permanent loss of muscle function. The specific causation of this disruption remains to be defined; however, with new developments in transcriptomics, genetic trends can be identified across regions of tissue over time. This study follows VML injuries within the tibialis anterior of a mouse model for fifteen days after initial injury to attempt to identify expected transitions in healing. Genetic presence began to become more diversified as recovery progressed from four to fifteen days post injury with spatial clusters becoming globalized …

Advancements Of A Breast Tissue Marker And Localization System, Azrin Jamison

All Theses

Breast cancer has become the most prominent cancer worldwide in women. Annual mammograms are encouraged for women of high risk to increase early detection allowing for lumpectomies rather than mastectomies to occur. Prior to a lumpectomy, a biopsy must be taken to determine if the tissue is cancerous, and a breast cancer biopsy marker (BBM) is left in the region of possible cancerous tissue. Wire localization has been the gold standard for localizing these BBMs. However, due to the reported patient discomfort and logistical inefficiencies faced by healthcare providers (HCP), non-wire localization solutions have been recently developed. This study aims …

Microwave Imaging Technique For Breast Cancer Detection, Nure Alam Chowdhury

Theses and Dissertations

Breast cancer is a global problem, and it is inevitable to detect cancerous cells at early stages. In recent years, microwave imaging technology has been widely applied in biomedical applications for its non-ionizing radiation. In this study, we design a micro-strip patch antenna with an inverted T-type notch in the partial ground to detect tumor cells inside the human breast. The size of the current antenna is small enough (18 mm × 21 mm × 1.6 mm) to distribute around the breast phantom. The operating frequency has been observed from 6–14 GHz with a minimum return loss of −61.18 dB …

Secured Blockchain And Fractional Discrete Cosine Transform-Based Framework For Medical Images, Abhay Kumar Yadav, Virendra P. Vishwakarma

Makara Journal of Technology

Images can store large amounts of data and are useful for transmitting large amounts of information across different geographical locations using different cloud services. This data sharing increases the chances of cyber-attacks on digital images. Blockchain has properties that enable it to work as a solution to this problem, providing enhanced security and unchangeable storage. However, image size poses a challenge in image storage, as it increases the related storage cost. Compressing images using fractional discrete cosine transform (fctDCT) reduces the amount of data required to express an image securely. This paper presents a novel framework for securely storing and …

Resolving The Nanoscale Structure Of Β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation–Localization Microscopy, Weiyan Zhou, Conor L. O'Neill, Tianben Ding, Oumeng Zhang, Jai S. Rudra, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8^L and KFE8^D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) …

6d Single-Fluorogen Orientation-Localization Microscopy For Elucidating The Architecture Of Beta-Sheet Assemblies And Biomolecular Condensates, Tingting Wu, Weiyan Zhou, Jai S. Rudra, Rohit V. Pappu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We develop six-dimensional single-molecule orientation-localization microscopy (SMOLM) to measure the 3D positions and 3D orientations simultaneously of single fluorophores. We show how careful optimization of phase and polarization modulation components can encode phase, polarization, and angular spectrum information from each fluorescence photon into a microscope’s dipole-spread function. We used the transient binding and blinking of Nile red (NR) to characterize the helical structure of fibrils formed by designed amphipathic peptides, KFE8^L and KFE8^D, and the pathological amyloid-beta peptide Aβ42. We also deployed merocyanine 540 to uncover the interfacial architectures of biomolecular condensates.

Comparison Of Scanning Electron Microscopy And Confocal Laser Microscopy For Tissue Surface Roughness Characterization, Tarnvir Dhaliwal

Master's Theses

It was found that the measurements captured by confocal microscopy and scanning electron microscopy had a statistically significant difference for bovine tissue. There was not a statistically significant for porcine and poultry tissue.

The intent of the study is to perform a comparative study to examine efficacy of two distinct technologies for a singular purpose: tissue surface roughness characterization. The two technologies compared are a confocal reflectance microscope and a scanning electron microscope. The comparison was made by comparing two surface roughness parameters [Ra and Rq] within ImageJ.

The study examined three different animal species [porcine, bovine, and poultry] to …

Development Of An In Vitro 3-Dimensional Co-Culture Human Colorectal Cancer Model In Microfluidic Devices, Abby Jens

Master's Theses

Colorectal cancer is the second most common cause of cancer-related deaths in the United States, with the relative 5-year survival rate for distant stage cancer being only 14%. The most common treatment for colorectal cancer is with chemotherapeutic drugs; however, the discovery of these drugs is costly, time-consuming, and often requires the use of animal models that do not yield results that translate to clinical trials. Due to these shortcomings, researchers seek to develop physiologically relevant in vitro tumor models that more accurately mimic the tumor microenvironment for cheaper and faster high-throughput drug screening. The aim of this research was …

Nanoparticles For Applications In Specific Diagnostics And Precision Medicine, Naxhije Berisha

Dissertations, Theses, and Capstone Projects

Heterogeneity is common in the expression of cancer and treatment response. Precision medicine enables healthcare providers to tailor medical care to an individual's distinct genetic and environmental makeup. This customization has the potential to result in more efficient treatments while minimizing side effects. We believe that by studying the interface of nanotechnology and cancer medicine we can elucidate innovative solutions that address the challenges of disease heterogeneity. This includes advancements in drug delivery, formulations development, and diagnostic sensing. We highlight three studies that use nanotechnology for applications in precision medicine. In Chapter 2, we highlight design optimization of drug formulations …

Algorithm Development For Analysis Of Optical Time-Series Data Generated By Biomodal Optical-Electrical Nanopore Sensor, Yu-Shiuan Huang

Bioengineering Theses - Archive

Nanopore biosensors have played an essential role in the scientific investigation of DNA, RNA, proteins, and other bio-analytes. Traditional nanopore biosensors detect variations in electrical current conductance caused by the analyte blocking the current passing transiently through a nano-sized aperture, i.e., the nanopore. This electrical data provides information about the amount of current blockage when the analyte is inside the nanopore and the time it takes for analytes to travel through the nanopore (translocation time). The translocation time of analytes in standard nanopore measurements is typically very short, usually tens of microseconds, limiting the accuracy of measuring the analytes’ characteristics. …

Computational And Experimental Analysis Of Silica Nanoparticles Under Dc And Ac Electric Fields Using A Self-Induced Back Action Actuated Nanopore Electrophoresis (Sane) Sensor, Homayoun Asadzadeh, Scott Renkes, George Alexandrakis, Minjun Kim, Scott Turpin

Bioengineering Dissertations - Archive

In this dissertation I have studied a novel single-molecule nanosensor that integrates a Solid-State Nanopore (SSNP), milled in silicon nitride with a Double Nanohole (DNH) nanoaperture, milled in gold. This device leverages Self-Induced Back-Action (SIBA) for optical trapping with ssNP electrical sensing and is called the SIBA-Actuated Nanopore Electrophoresis (SANE) sensor. My lab has previously shown that simultaneous acquisition of bimodal optical and direct current (DC) electrical signatures enables more detailed characterization of nanoscopic analytes compared to using electrical data alone, which are typically collected by ssNP sensors. In this work I have first studied by COMSOL Multiphysics simulations the …

Unlv Title Iii Aanapisi & Mcnair Scholars Institute Research Journal 2024, Jesica Godinez-Paredes, Kian Hassankhan, Apia Hickman, Robin Ruth Kee, Kevin Ayala Pineda, Briana Melendez, Kalli Ramos, Saturn L. Reyes, Fabian Leija, Selena Pepe, Silva Topchyan, Celeste Ainsley, Mayra Arzate, Jessica Balistreri, Zantana Ephrem, Mirella Jasso, Karl Panou, Nichole Pelaez, Miklo Alcala, Akshay Dave, Mey Mey Heng, Michael Finkle, Janessa Montenegro, Reynafe Naol Aniga, Victor Mejia, Angelica G. Diaz, Anayeli Flores-Garibay, Kari Lee Joe Goold, Samantha Hernandez, Lianelys Cabrera Martinez, Caitlin Reynolds, Kimberly N. Usbeck, Abdulrahman Alahdal, Angelica Diaz, Willaine Mae Kahano, Raquel Jackson, Cecia Ruiz-Hernandez, Kers Ung-Watson, Yessenia Henriquez, Vanessa Marie Booth, Alexia Brown, Darlyn Magana, Bianca Navarro, Nicholas Pereira, Gia Renemae Calip, Lucky Heng, Ralph Sagun, Lucas Abreu, Alexandra Maria Acosta, Tristan Benally, Cosset Hernandez Pena, Adrian Montenegro, Cierra Paaaina-Daquioag, Nicole Torosian, Tracy Fuentes, Julissa Martinez, Medina Mcallister, Michal Newhouse-Van Vlerin, Tiria Carr, Nima Abkenar, Isabella Aceituno, Yuhan Bi, Victoria Campos, Melika Cummings, Zachary J. Johnigan, Alexis Sotolongo-Marin

McNair Journal

Journal articles based on research conducted by undergraduate students in the AANAPISI, LSAMP, and McNair Scholars Program.

Table of Contents

About AANAPISI

Dr. Chris Heavey, Interim President

Dr. Keith Rogers, Vice President for Student Affairs

Ms. Zhanna Aronov, Associate Vice President for Retention & Outreach

Plasma Protein Signatures Of Adult Asthma, Gordon J. Smilnak, Yura Lee, Abhijnan Chattopadhyay, Annah B. Wyss, Julie D. White, Sinjini Sikdar, Jianping Jin, Andrew J. Grant, Alison A. Motsinger-Reif, Jian-Liang Li, Mikyeong Lee, Bing Yu, Stephanie J. London

Mathematics & Statistics Faculty Publications

Background: Adult asthma is complex and incompletely understood. Plasma proteomics is an evolving technique that can both generate biomarkers and provide insights into disease mechanisms. We aimed to identify plasma proteomic signatures of adult asthma.

Methods: Protein abundance in plasma was measured in individuals from the Agricultural Lung Health Study (ALHS) (761 asthma, 1095 non-case) and the Atherosclerosis Risk in Communities study (470 asthma, 10,669 non-case) using the SOMAScan 5K array. Associations with asthma were estimated using covariate adjusted logistic regression and meta-analyzed using inverse-variance weighting. Additionally, in ALHS, we examined phenotypes based on both asthma and seroatopy (asthma with …

An In-Vitro Model For Visualizing Intraocular Lens And Lens Capsule Interaction In Posterior Capsule Opacification, Amjad Chatila

Bioengineering Dissertations - Archive

Posterior Capsule Opacification (PCO) is a common complication post cataract surgery. It is believed that Intraocular Lens (IOL) physical and chemical properties would affect their PCO potential. The tight binding between IOL and posterior lens capsule (PLC) is believed to have a negative impact on PCO formation, as suggested in the “No space, no cell, no PCO” hypothesis. To test the hypothesis, we have recently developed an in vitro 3D system to simulate IOL and PLC physical interaction. To expand the function and capability of this system, one objective of my work was to develop the next generation adhesion force …