Engineering Commons^™

A Machine Learning Framework For Identifying Molecular Biomarkers From Transcriptomic Cancer Data, Md Abdullah Al Mamun

FIU Electronic Theses and Dissertations

Cancer is a complex molecular process due to abnormal changes in the genome, such as mutation and copy number variation, and epigenetic aberrations such as dysregulations of long non-coding RNA (lncRNA). These abnormal changes are reflected in transcriptome by turning oncogenes on and tumor suppressor genes off, which are considered cancer biomarkers.

However, transcriptomic data is high dimensional, and finding the best subset of genes (features) related to causing cancer is computationally challenging and expensive. Thus, developing a feature selection framework to discover molecular biomarkers for cancer is critical.

Traditional approaches for biomarker discovery calculate the fold change for each …

Polarimetric Imaging Of The Uterine Cervix, Mariacarla Gonzalez

FIU Electronic Theses and Dissertations

Cervical cancer is the fourth most common cancer in women, with more than half a million women diagnosed each year due to persistent human papillomavirus (HPV) infection and a mortality of 311,000 women. According to the World Cancer Research Fund, developing countries have 84% of the global burden of the disease and 80% of the mortality due to a lack of effective screening programs. Several screening techniques have been developed and implemented to aid in low resource setting cervical screening, however, most require physician interpretation of color images. Other modalities utilize contrast agents to highlight pathological tissue but have small …

Development Of A Plasmonic On-Chip System To Characterize Changes From External Perturbations In Cardiomyocytes, Maedeh Mozneb

FIU Electronic Theses and Dissertations

Today’s heart-on-a-chip devices are hoped to be the state-of-the-art cell and tissue characterizing tool, in clinically applicable regenerative medicine and cardiac tissue engineering. Due to the coupled electromechanical activity of cardiomyocytes (CM), a comprehensive heart-on-a-chip device as a cell characterizing tool must encompass the capability to quantify cellular contractility, conductivity, excitability, and rhythmicity. This dissertation focuses on developing a successful and statistically relevant surface plasmon resonance (SPR) biosensor for simultaneous recording of neonatal rat cardiomyocytes’ electrophysiological profile and mechanical motion under normal and perturbed conditions. The surface plasmon resonance technique can quantify (1) molecular binding onto a metal film, (2) …

Volitional Control Of Lower-Limb Prosthesis With Vision-Assisted Environmental Awareness, S M Shafiul Hasan

FIU Electronic Theses and Dissertations

Early and reliable prediction of user’s intention to change locomotion mode or speed is critical for a smooth and natural lower limb prosthesis. Meanwhile, incorporation of explicit environmental feedback can facilitate context aware intelligent prosthesis which allows seamless operation in a variety of gait demands. This dissertation introduces environmental awareness through computer vision and enables early and accurate prediction of intention to start, stop or change speeds while walking. Electromyography (EMG), Electroencephalography (EEG), Inertial Measurement Unit (IMU), and Ground Reaction Force (GRF) sensors were used to predict intention to start, stop or increase walking speed. Furthermore, it was investigated whether …

Therapeutic Approaches To Alter Mineral Formation And Growth In Vascular Calcification, Amirala Bakhshiannik

FIU Electronic Theses and Dissertations

Cardiovascular diseases represent the global leading cause of morbidity and mortality. Cardiovascular calcification is the most significant predictor of cardiovascular events, but no therapeutic options exist to prevent or treat mineral formation in the vasculature. The presence of bone-like mineral increases cardiac work required to move blood through systemic circulation and can lead to mechanical stress in atherosclerotic plaques, promoting plaque rupture events that cause heart attacks. Clinical trials correlated bisphosphonates (BiPs), common anti-osteoporosis pharmaceuticals, with contradicting cardiovascular outcomes. Here, we demonstrated the importance of treatment timing in BiP-induced mineral disruption or promotion. We showed that BiPs can alter morphological …

Photonic Crystal Hydrogels: Simulation, Fabrication & Biomedical Application, Mehenur Sarwar

FIU Electronic Theses and Dissertations

Photonic crystal (PhC) hydrogels are a unique class of material that has tremendous promise as biomedical sensors. The underlying crystal structure allows for simple analysis of microstructural properties by assessing the diffraction pattern generated following laser illumination. The hydrogel medium provides elasticity, regenerability, and potential functionalization. Combining these two properties, photonic crystal hydrogels have the potential for sensing physical forces and chemical reagents using a low-cost, reusable platform.

The development of biomedical sensors using this material is limited due to the lack of a method to accurately predict the diffraction pattern generated. To overcome this, a computational model was developed …

Correlation Of Acute Radiation Dermatitis To Tissue Oxygenation In Radiation Therapy Treated Breast Cancer Subjects, Edwin Alexander Robledo

FIU Electronic Theses and Dissertations

Over 95% of radiation therapy (RT) treated breast cancer subjects undergo an adverse skin reaction known as radiation dermatitis (RD). Assessment of severity or grading of RD is clinically visual and hence subjective. Our objective is to determine sub-clinical tissue oxygenation (StO₂) changes in response to RT treatment in breast cancer subjects using near-infrared spectroscopic imaging and correlate these changes to RD grading. A WIRB approved 6-8 week longitudinal pilot study was carried out on 10 RT-treated subjects at Miami Cancer Institute. Significant changes (p < 0.05) in StO₂ of irradiated and contralateral chest wall and axilla regions with weeks of …

Understanding The Underlying Mechanism Of Age-Related Underactive Bladder And Proposing A Treatment Option To Mitigate Its Symptoms, Arezoo Gerami Pour

FIU Electronic Theses and Dissertations

The prevalence of underactive bladder (UAB) increases with age, suggesting a link between age-related processes and lower urinary tract (LUT) symptoms; however, the underlying mechanisms of age-related UAB are poorly understood. UAB is characterized by inefficient voiding and bladder overdistension. Due to the unknown etiology, current therapeutic options are insufficient. Thus, a detailed understanding of its mechanism will facilitate the discovery of new treatments.

In Aim 1, we investigated the relationship between age and systems-level function of the LUT reflexes in three age groups of rats, testing the hypothesis that aging causes voiding reflexes to weaken. We systematically investigated the …

Functional And Dysrhythmic Slow Waves In The Stomach - An In Silico Study, Md Ashfaq Ahmed

FIU Electronic Theses and Dissertations

Peristalsis, the coordinated contraction and relaxation of the muscles of the stomach, is important for normal gastric motility and is impaired in motility disorders. Coordinated electrical depolarizations that originate and propagate within a mutually coupled network of interstitial cells of Cajal (ICC) and smooth muscle cells of the stomach wall as a slow-wave, underly peristalsis. Normally, the gastric slow-wave (GSW) oscillates with a single period and uniform rostro-caudal lag, exhibiting network entrainment. Loss of entrainment in the coupled network and the resulting impairment in slow-wave propagation is associated with various gastric motility disorders. Our study provides an enhanced understanding of …

Stimulation Paradigms And Transduction Patterns For Optogenetic Intervention Of Astrocytes, Lakshmini Balachandar

FIU Electronic Theses and Dissertations

Gliosis observed in several neurological disorders is associated with neuroinflammation and enhanced astrocytic Ca2+ levels. The inherent multicellular nature of this neuroinflammation poses challenges in deciphering the exact role of astrocytic Ca2+ signaling and whether it leads to the generation and/or exacerbation of neuroinflammation. These challenges are aggravated by the dearth of systematic characterization of a regulated method for eliciting astrocytic Ca2+ increases.

The primary goal of this dissertation is to address the lack of a characterized method by studying optogenetics for eliciting astrocytic Ca2+ increases. As part of this analysis, we aim to identify light stimulation paradigms resulting in …

Development Of A Real-Time Single-Lead Single-Beat Frequency-Independent Myocardial Infarction Detector, Harold Martin

FIU Electronic Theses and Dissertations

The central aim of this research is the development and deployment of a novel multilayer machine learning design with unique application for the diagnosis of myocardial infarctions (MIs) from individual heartbeats of single-lead electrocardiograms (EKGs) irrespective of their sampling frequencies over a given range. To the best of our knowledge, this design is the first to attempt inter-patient myocardial infarction detection from individual heartbeats of single-lead (lead II) electrocardiograms that achieves high accuracy and near real-time diagnosis. The processing time of 300 milliseconds to a diagnosis is just at the time range in between extremely fast heartbeats of around 300 …

Correlating The Effect Of Dynamic Variability In The Sensor Environment On Sensor Design, Pulak Bhushan

FIU Electronic Theses and Dissertations

This dissertation studies the effect of biofluid dynamics on the electrochemical response of a wearable sensor for monitoring of chronic wounds. The research investigates various dynamic in vivo parameters and correlates them with experimentally measured behavior with wound monitoring as a use case. Wearable electrochemical biosensors suffer from several unaddressed challenges, like stability and sensitivity, that need to be resolved for obtaining accurate data. One of the major challenges in the use of these sensors is continuous variation in biofluid composition. Wound healing is a dynamic process with wound composition changing continuously. This dissertation investigates the effects of several in …

Penta-Modal Imaging Platform With Oct- Guided Dynamic Focusing For Simultaneous Multimodal Imaging, Arash Dadkhah

FIU Electronic Theses and Dissertations

Complex diseases, such as Alzheimer’s disease, are associated with sequences of changes in multiple disease-specific biomarkers. These biomarkers may show dynamic changes at specific stages of disease progression. Thus, testing/monitoring each biomarker may provide insight into specific disease-related processes, which can result in early diagnosis or even development of preventive measures. Obtaining a comprehensive information of biological tissues requires imaging of multiple optical contrasts, which is not typically offered by a single imaging modality. Thus, combining different contrast mechanisms to achieve simultaneous multimodal imaging is desirable. However, this process is highly challenging due to specific optical and hardware requirements for …

Development Of All-Optical Quantitative Ultrasound Imaging System, Mohamed Abdulrahman Almadi

FIU Electronic Theses and Dissertations

Ultrasound (US) is a well-established deep-tissue imaging modality in biomedicine. It distinguishes different tissue types based on their echogenicity, but this approach provides limited diagnostic sensitivity and accuracy. The majority of the US transducers nowadays rely on lead zirconate titanate (PZT) ceramic elements to transmit and receive ultrasound. Unfortunately, significant limitations arise from these transducers due to their frequency characteristics and complex fabrication process. A recently introduced technique, Quantitative Ultrasound (QUS) Measurement, shows a great promise to improve US-based tissue diagnosis, but it requires a transducer with a large spectrum bandwidth, which is a feature not available in PZT transducers. …

Engineering Electromagnetic Systems For Next-Generation Brain-Machine Interface, Brayan Ricardo Navarrete

FIU Electronic Theses and Dissertations

MagnetoElectric Nanoparticles (MENPs) are known to be a powerful tool for a broad range of applications spanning from medicine to energy-efficient electronics. MENPs allow to couple intrinsic electric fields in the nervous system with externally controlled magnetic fields. This thesis exploited MENPs to achieve contactless brain-machine interface (BMIs). Special electromagnetic devices were engineered for controlling the MENPs’ magnetoelectric effect to enable stimulation and recording. The most important engineering breakthroughs of the study are summarized below.

(I) Metastable Physics to Localize Nanoparticles: One of the main challenges is to localize the nanoparticles at any selected site(s) in the brain. The fundamental …

Bioscaffold Valve With And Without Mechanically Conditioned Stem Cells For The Treatment Of Critical Mitral Valve Diseases In The Young, Brittany A. Gonzalez

FIU Electronic Theses and Dissertations

Congenital heart disease, which includes heart valve defects, are the most common type of birth abnormality in the US. Infants with critical congenital valve disease have no established treatment-measure other than compassionate care options, owing to an absence of prosthetic valves in small sizes and their inability to support somatic growth. A regenerable valve would be appealing since these barriers could be overcome; it can potentially provide for growth, self-repair, infection resistance and be a permanent approach for replacing defective heart valves.

Porcine small intestinal submucosa (PSIS) bioscaffold was used to create valvular constructs with the possibility to grow overtime. …

Characterization Of Aortic Valve Interstitial Cells Responsible For Elastogenesis, Sana Nasim

FIU Electronic Theses and Dissertations

The aortic valve (AoV) controls unidirectional blood distribution from the left ventricle of the heart to the aorta for systemic circulation. During the systolic and diastolic phases, AoV leaflets rely on a precise extracellular matrix (ECM) microarchitecture for appropriate biomechanical performance based on the arrangement of collagen, elastin, and glycosaminoglycans. The ECM structure is generated and maintained by valvular interstitial cells (VICs), which reside within the leaflets. VICs are a heterogeneous population of cells that are derived from a mixture of developmental precursors. Mainly, VICs arise from endocardial and neural crest cells that migrate into the cardiac cushions during development. …

A Comprehensive Analysis Of Balance, Symmetry, And Center Of Mass In The Gait Cycle Of Transfemoral Amputees, Kayla T. Etienne

FIU Electronic Theses and Dissertations

The purpose of this thesis is to create a framework that assists in the transfemoral prosthesis fitting process by calculating balance and symmetry to quantify patient comfort with an understanding of bipedal locomotion and human anatomy. Three different software applications were used to compare (1) the body position during gait cycle, (2) the natural and amputee anatomies, (3) the natural and prosthetic legs, and (4) the equilibrium and torque movements of the hip, knee, and ankle joints. Models were created in Maya for analysis in Solidworks and MEL code evaluation with MatLab. The MatLab code tested combinations of joint degrees …

3d Architectural Analysis Of Neurons, Astrocytes, Vasculature & Nuclei In The Motor And Somatosensory Murine Cortical Columns, Jared Leichner

FIU Electronic Theses and Dissertations

Characterization of the complex cortical structure of the brain at a cellular level is a fundamental goal of neuroscience which can provide a better understanding of both normal function as well as disease state progression. Many challenges exist however when carrying out this form of analysis. Immunofluorescent staining is a key technique for revealing 3-dimensional structure, but subsequent fluorescence microscopy is limited by the quantity of simultaneous targets that can be labeled and intrinsic lateral and isotropic axial point-spread function (PSF) blurring during the imaging process in a spectral and depth-dependent manner. Even after successful staining, imaging and optical deconvolution, …

Development Of Gaussian Learning Algorithms For Early Detection Of Alzheimer's Disease, Chen Fang

FIU Electronic Theses and Dissertations

Alzheimer’s disease (AD) is the most common form of dementia affecting 10% of the population over the age of 65 and the growing costs in managing AD are estimated to be $259 billion, according to data reported in the 2017 by the Alzheimer's Association. Moreover, with cognitive decline, daily life of the affected persons and their families are severely impacted. Taking advantage of the diagnosis of AD and its prodromal stage of mild cognitive impairment (MCI), an early treatment may help patients preserve the quality of life and slow the progression of the disease, even though the underlying disease cannot …

Enhanced Surface Electrical Neurostimulation (Esens): A Non-Invasive Platform For Peripheral Neuromodulation, Andres Eduardo Pena

FIU Electronic Theses and Dissertations

Electrical stimulation of peripheral afferents has been used to study the sensory neural code and restore lost sensory function after amputation. Recently, implantable neural interfaces have prompted multiple breakthroughs in artificial somatosensory feedback for individuals with amputation, resulting in functional and psychological benefits. Although promising, the invasive nature of these approaches limits wide clinical applications, hindering the development of advanced neuromodulation strategies for intuitive sensory feedback. Transcutaneous (surface) stimulation is a potential non-invasive alternative. However, traditional surface stimulation methods are hampered by inadequate electrode and stimulation parameter fitting, localized discomfort, poor selectivity, and limited percept modulation.

An enhanced surface electrical …

Scalable Profiling And Visualization For Characterizing Microbiomes, Camilo Valdes

FIU Electronic Theses and Dissertations

Metagenomics is the study of the combined genetic material found in microbiome samples, and it serves as an instrument for studying microbial communities, their biodiversities, and the relationships to their host environments. Creating, interpreting, and understanding microbial community profiles produced from microbiome samples is a challenging task as it requires large computational resources along with innovative techniques to process and analyze datasets that can contain terabytes of information.

The community profiles are critical because they provide information about what microorganisms are present in the sample, and in what proportions. This is particularly important as many human diseases and environmental disasters …

Visible Optical Coherence Tomography Based Multimodal Imaging For Quantification Of Retinal Lipofuscin, Zahra Nafar

FIU Electronic Theses and Dissertations

Retinal degeneration is the leading cause of irreversible low vision and blindness in the world, that describes conditions characterized by progressive loss of photoreceptors. Retinal Pigment Epithelium (RPE) is located under photoreceptors’ outer segments and plays an important role in the maintenance of photoreceptors by completing the visual cycle and phagocytosis of shed photoreceptor outer segments. Lipofuscin, a byproduct of the visual cycle, is a nondegradable compound that accumulates in the RPE cells and eventually damages the RPE cells and inevitably causes photoreceptor degeneration. Lipofuscin is the major cause of fundus fluorescence that can be detected by Fundus Autofluorescent (FAF) …

Offset Electrodes For Enhanced Neural Recording In Microchannels, Iian Black

FIU Electronic Theses and Dissertations

Microchannel electrodes have emerged in recent years as promising interfaces for recording signals in peripheral nerves. Unlike many technologies, microchannels maintain stable long-term connections and can record activity in individual or small groups of axons. Unfortunately, a traditional symmetrical mid-channel electrode configuration, designed to reduce noise artifacts, prevents microchannels from being used to distinguish between signals traveling in opposite directions. This is a profound limitation given that most nerves contain a mix of efferent and afferent axons and microchannels were initially conceived and later used as the basic building block in arrays designed to record bi-directional neural traffic in regenerated …

Synergistic Activation Of Inspiratory Muscles By An Adaptive Closed-Loop Controller, Rabeya Zinnat Adury

FIU Electronic Theses and Dissertations

During diaphragmatic pacing reverse recruitment of muscle fibers causes muscle fatigue. Current diaphragmatic pacing paradigms also do not permit sigh-like behavior. In spontaneously breathing anesthetized rats, studies were carried out to determine if synergized pacing of external intercostal muscles and the diaphragm would increase the efficiency of diaphragm stimulation and thus a) achieve the desired ventilatory breath volume profile with reduced diaphragm muscle fatigue, and/or b) be able to elicit sigh-like behavior by periodically increasing stimulation. Under combined inspiratory muscle stimulation, a fatigue index calculated for the diaphragm muscle (n=6 rats) was significantly lower (p<0.05) than in the …

Measuring Collagen Arrangement And Its Relationship With Preterm Birth Using Mueller Matrix Polarimetry, Joseph James Chue-Sang

FIU Electronic Theses and Dissertations

Preterm birth (PTB) is defined as delivery prior to 37 weeks of gestation. It is the leading cause of infant death worldwide, responsible for infant neurological disorders, long-term cognitive impairment, as well as chronic health issues involving the auditory, visual, digestive, and respiratory systems. In expectant mothers, causes for PTB can include infection, inflammation, vascular disease, short intervals between pregnancies, multiple gestations and genetic factors. In the U.S., PTB occurs in over 11% of births and at an elevated 18.1% in Miami-Dade County, FL; while in the developing world the incidence of PB is over 15%. Early identification of at-risk …

Adaptive Closed-Loop Neuromorphic Controller For Use In Respiratory Pacing, Ricardo Siu

FIU Electronic Theses and Dissertations

Respiratory pacing can treat ventilatory insufficiency through electrical stimulation of the respiratory muscles, or the respective innervating nerves, to induce ventilation. It avoids some of the adverse effects associated with mechanical ventilation such as risk of diaphragm atrophy and lung damage. However, current respiratory pacing systems provide stimulation in an open-loop manner. This often requires users to undergo frequent tuning sessions with trained clinicians if the specified stimulation parameters are unable to induce sufficient ventilation in the presence of time-varying changes in muscle properties, chest biomechanics, and metabolic demand. Lack of adaptation to these changes may lead to complications arising …

The Neural Recruitment Of Executive Function In Monolingual Versus Bilingual Preterm-Born Children: An Fnirs Study, Caitlyn F. Myland

FIU Electronic Theses and Dissertations

Premature-birth is defined by the World Health Organization as birth less than 37 weeks. These children are particularly susceptible deficiencies in executive functioning (EF) as compared to term-born children. It has yet to be explored whether bilingualism might also give an edge to preterm-born-children (PBC) in EF. The present study aims to fill this gap by examining the EF of bilingual versus monolingual preterm-born children in Miami-Dade County. All 16 children were right-handed, ages 6-7, and born before 35 weeks. Results showed that both groups performed about the same on the Dimensional Change Card Sort (DCCS) and Go/No Go (GNG) …

Multiscale Model Of Cerebral Blood Flow Control: Application To Small Vessel Disease And Cortical Spreading Depression, Arash Moshkforoush

FIU Electronic Theses and Dissertations

An in-time delivery of oxygen-rich blood into areas of high metabolic demand is pivotal in proper functioning of the brain and neuronal health. This highly precise communication between neuronal activity and cerebral blood flow (CBF) is termed as neurovascular coupling (NVC) or functional hyperemia. NVC is disrupted in major pathological conditions including Alzheimer’s disease, dementia, small vessel pathologies (SVD) and cortical spreading depression. Despite the utmost importance of NVC, its underlying mechanisms are not fully understood. This dissertation presents a multiscale mathematical modeling framework for studying unresolved mechanisms of NVC with major focus on K⁺ ions as a mediator …

The Effect Of Proteome And Lipidome On The Behavior Of Membrane Bound Systems In Thermally-Assisted Acoustophoresis, Elnaz Mirtaheri

FIU Electronic Theses and Dissertations

Changes in the biomechanical properties of cells accompanying the development of various pathological conditions have been increasingly reported as biomarkers for various diseases, including cancers. In cancer cells, the membrane properties have been altered compared to their healthy counterparts primarily due to proteomic and lipidomic dysregulations conferred by the underlying pathology. The separation and selective recovery of these cells or extracellular vesicles secreted from such cells is of high diagnostic and prognostic value.

In this dissertation, the research builds on thermally-assisted acoustophoresis technique which was developed in our laboratory for the separation of vesicles of the same size, charge and …