Engineering Commons^™

Nonuniform Sampling-Based Breast Cancer Classification, Santiago Posso

Theses and Dissertations--Electrical and Computer Engineering

The emergence of deep learning models and their success in visual object recognition have fueled the medical imaging community's interest in integrating these algorithms to improve medical diagnosis. However, natural images, which have been the main focus of deep learning models and mammograms, exhibit fundamental differences. First, breast tissue abnormalities are often smaller than salient objects in natural images. Second, breast images have significantly higher resolutions but are generally heavily downsampled to fit these images to deep learning models. Models that handle high-resolution mammograms require many exams and complex architectures. Additionally, spatially resizing mammograms leads to losing discriminative details essential …

Novel Machine Learning And Wearable Sensor Based Solutions For Smart Healthcare Monitoring, Rajdeep Kumar Nath

Theses and Dissertations--Electrical and Computer Engineering

The advent of IoT has enabled the design of connected and integrated smart health monitoring systems. These health monitoring systems can be utilized for monitoring the mental and physical wellbeing of a person. Stress, anxiety, and hypertension are the major elements responsible for the plethora of physical and mental illnesses. In this context, the older population demands special attention because of the several age-related complications that exacerbate the effects of stress, anxiety, and hypertension. Monitoring stress, anxiety, and blood pressure regularly can prevent long-term damage by initiating necessary intervention or clinical treatment beforehand. This will improve the quality of life …

Bamorc: A Software Package For Accurate And Robust 13C Reference Correction Of Protein Nmr Spectra, Xi Chen, Andrey Smelter, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

We describe Bayesian Model Optimized Reference Correction (BaMORC), a software package that performs ¹³C chemical shifts reference correction for either assigned or unassigned peak lists derived from protein NMR spectra. BaMORC provides an intuitive command line interface that allows non-nuclear magnetic resonance (NMR) experts to detect and correct ¹³C chemical shift referencing errors of unassigned peak lists at the very beginning of NMR data analysis, further lowering the bar of expertise required for effective protein NMR analysis. Furthermore, BaMORC provides an application programming interface for integration into sophisticated protein NMR data analysis pipelines, both before and after the …

Novel Applications Of Machine Learning In Bioinformatics, Yi Zhang

Theses and Dissertations--Computer Science

Technological advances in next-generation sequencing and biomedical imaging have led to a rapid increase in biomedical data dimension and acquisition rate, which is challenging the conventional data analysis strategies. Modern machine learning techniques promise to leverage large data sets for finding hidden patterns within them, and for making accurate predictions. This dissertation aims to design novel machine learning-based models to transform biomedical big data into valuable biological insights. The research presented in this dissertation focuses on three bioinformatics domains: splice junction classification, gene regulatory network reconstruction, and lesion detection in mammograms.

A critical step in defining gene structures and mRNA …

Relation Prediction Over Biomedical Knowledge Bases For Drug Repositioning, Mehmet Bakal

Theses and Dissertations--Computer Science

Identifying new potential treatment options for medical conditions that cause human disease burden is a central task of biomedical research. Since all candidate drugs cannot be tested with animal and clinical trials, in vitro approaches are first attempted to identify promising candidates. Likewise, identifying other essential relations (e.g., causation, prevention) between biomedical entities is also critical to understand biomedical processes. Hence, it is crucial to develop automated relation prediction systems that can yield plausible biomedical relations to expedite the discovery process. In this dissertation, we demonstrate three approaches to predict treatment relations between biomedical entities for the drug repositioning task …

X-Search: An Open Access Interface For Cross-Cohort Exploration Of The National Sleep Research Resource, Licong Cui, Ningzhou Zeng, Matthew Kim, Remo Mueller, Emily Ruth Hankosky, Susan Redline, Guo-Qiang Zhang

Computer Science Faculty Publications

Background: The National Sleep Research Resource (NSRR) is a large-scale, openly shared, data repository of de-identified, highly curated clinical sleep data from multiple NIH-funded epidemiological studies. Although many data repositories allow users to browse their content, few support fine-grained, cross-cohort query and exploration at study-subject level. We introduce a cross-cohort query and exploration system, called X-search, to enable researchers to query patient cohort counts across a growing number of completed, NIH-funded studies in NSRR and explore the feasibility or likelihood of reusing the data for research studies.

Methods: X-search has been designed as a general framework with two loosely-coupled components: …

Individualized Clinical Practice Guidelines For Pressure Injury Management: Development Of An Integrated Multi-Modal Biomedical Information Resource, Kathie M. Bogie, Guo-Qiang Zhang, Steven K. Roggenkamp, Ningzhou Zeng, Jacinta Seton, Shiqiang Tao, Arielle L. Bloostein, Jiayang Sun

Institute for Biomedical Informatics Faculty Publications

Background: Pressure ulcers (PU) and deep tissue injuries (DTI), collectively known as pressure injuries are serious complications causing staggering costs and human suffering with over 200 reported risk factors from many domains. Primary pressure injury prevention seeks to prevent the first incidence, while secondary PU/DTI prevention aims to decrease chronic recurrence. Clinical practice guidelines (CPG) combine evidence-based practice and expert opinion to aid clinicians in the goal of achieving best practices for primary and secondary prevention. The correction of all risk factors can be both overwhelming and impractical to implement in clinical practice. There is a need to develop practical …

Query-Constraint-Based Mining Of Association Rules For Exploratory Analysis Of Clinical Datasets In The National Sleep Research Resource, Rashmie Abeysinghe, Licong Cui

Computer Science Faculty Publications

Background: Association Rule Mining (ARM) has been widely used by biomedical researchers to perform exploratory data analysis and uncover potential relationships among variables in biomedical datasets. However, when biomedical datasets are high-dimensional, performing ARM on such datasets will yield a large number of rules, many of which may be uninteresting. Especially for imbalanced datasets, performing ARM directly would result in uninteresting rules that are dominated by certain variables that capture general characteristics.

Methods: We introduce a query-constraint-based ARM (QARM) approach for exploratory analysis of multiple, diverse clinical datasets in the National Sleep Research Resource (NSRR). QARM enables rule mining on …

Compact Hardware Implementation Of A Sha-3 Core For Wireless Body Sensor Networks, Yi Yang, Debiao He, Neeraj Kumar, Sherali Zeadally

Information Science Faculty Publications

One of the most important Internet of Things applications is the wireless body sensor network (WBSN), which can provide universal health care, disease prevention, and control. Due to large deployments of small scale smart sensors in WBSNs, security, and privacy guarantees (e.g., security and safety-critical data, sensitive private information) are becoming a challenging issue because these sensor nodes communicate using an open channel, i.e., Internet. We implement data integrity (to resist against malicious tampering) using the secure hash algorithm 3 (SHA-3) when smart sensors in WBSNs communicate with each other using the Internet. Due to the limited resources (i.e., storage, …

Self-Image Multimedia Technologies For Feedforward Observational Learning, Nkiruka M. A. Uzuegbunam

Theses and Dissertations--Electrical and Computer Engineering

This dissertation investigates the development and use of self-images in augmented reality systems for learning and learning-based activities. This work focuses on self- modeling, a particular form of learning, actively employed in various settings for therapy or teaching. In particular, this work aims to develop novel multimedia systems to support the display and rendering of augmented self-images. It aims to use interactivity (via games) as a means of obtaining imagery for use in creating augmented self-images. Two multimedia systems are developed, discussed and analyzed. The proposed systems are validated in terms of their technical innovation and their clinical efficacy in …

Interactive Clinical Event Pattern Mining And Visualization Using Insurance Claims Data, Zhenhui Piao

Theses and Dissertations--Computer Science

With exponential growth on a daily basis, there is potentially valuable information hidden in complex electronic medical records (EMR) systems. In this thesis, several efficient data mining algorithms were explored to discover hidden knowledge in insurance claims data. The first aim was to cluster three levels of information overload(IO) groups among chronic rheumatic disease (CRD) patient groups based on their clinical events extracted from insurance claims data. The second aim was to discover hidden patterns using three renowned pattern mining algorithms: Apriori, frequent pattern growth(FP-Growth), and sequential pattern discovery using equivalence classes(SPADE). The SPADE algorithm was found to be the …

Synthesis And Characterization Of Thermoresponsive Hydrogels Based On N-Isopropylacrylamide Crosslinked With 4,4′-Dihydroxybiphenyl Diacrylate, Shuo Tang, Martha Floy, Rohit Bhandari, Manjula Sunkara, Andrew J. Morris, Thomas D. Dziubla, J. Zach Hilt

Chemical and Materials Engineering Faculty Publications

A novel crosslinker [4,4′-dihydroxybiphenyl diacrylate (44BDA)] was developed, and a series of temperature-responsive hydrogels were synthesized through free radical polymerization of N-isopropylacrylamide (NIPAAm) with 44BDA. The temperature-responsive behavior of the resulting gels was characterized by swelling studies, and the lower critical solution temperature (LCST) of the hydrogels was characterized through differential scanning calorimetry. Increased content of 44BDA led to a decreased swelling ratio and shifted the LCST to lower temperatures. These novel hydrogels also displayed resiliency through multiple swelling–deswelling cycles, and their temperature responsiveness was reversible. The successful synthesis of NIPAAm-based hydrogels crosslinked with 44BDA has led to a …

Properties And Optimization Of Respiratory Navigator Gating For Spiral Cine Dense Cardiac Mri, Sean Michael Hamlet

Theses and Dissertations--Electrical and Computer Engineering

Cardiac magnetic resonance (MR) imaging can non-invasively assess heart function. Displacement encoding with stimulated echoes (DENSE) is an advanced cardiac MR imaging technique that measures tissue displacement and can be used to quantify cardiac mechanics (e.g. strain and torsion). When combined with clinical risk factors, cardiac mechanics have been shown to be better predictors of mortality than traditional measures of heart function.

End-expiratory breath-holds are typically used to minimize respiratory motion artifacts. Unfortunately, requiring subjects to breath-hold introduces limitations with the duration of image acquisition and quality of data acquired, especially in patients with limited ability to hold their breath. …

Detection Of Electrical Alternans In Ventricular Depolarization Phase Of Human Electrocardiogram, David R. Wasemiller

Theses and Dissertations--Biomedical Engineering

T-wave Alternans (TWA) in an electrocardiogram (ECG) has received considerable interest as a potential predictor of sudden cardiac death (SCD). However, large clinical trials have shown that while TWA has a very high negative predictive value, its positive predictive value is poor. Results of previous studies suggest that arrhythmia onset can be affected by the phase relationship of alternans of the depolarization and repolarization phase of the action potentials of the ventricles. To assess this relationship, one would first need to establish that depolarization alternans can be detected and then develop methods to determine its relationship with repolarization alternans, which …

Design Of Highly Stable Low-Density Self-Assembled Monolayers Using Thiol-Yne Click Reaction For The Study Of Protein-Surface Interactions, Leila Safazadeh Haghighi

Theses and Dissertations--Chemical and Materials Engineering

Protein adsorption on solid surfaces is a common yet complicated phenomenon that is not fully understood. Self-assembled monolayers have been utilized in many studies, as well-defined model systems for studying protein-surface interactions in the atomic level. Various strategies, including the use of single component SAMs[1, 2], combinations of long and short alkanethiolates with methyl- and hydroxyl- terminal groups[3, 4], and using mixtures of alkanethiolates with similar chain length and varying terminal functional group [5] have been used to effectively control the surface wettability and determine the effect of surface composition and wettability on protein adsorption. In this dissertation we report …

Nuclei/Cell Detection In Microscopic Skeletal Muscle Fiber Images And Histopathological Brain Tumor Images Using Sparse Optimizations, Hai Su

Theses and Dissertations--Computer Science

Nuclei/Cell detection is usually a prerequisite procedure in many computer-aided biomedical image analysis tasks. In this thesis we propose two automatic nuclei/cell detection frameworks. One is for nuclei detection in skeletal muscle fiber images and the other is for brain tumor histopathological images.

For skeletal muscle fiber images, the major challenges include: i) shape and size variations of the nuclei, ii) overlapping nuclear clumps, and iii) a series of z-stack images with out-of-focus regions. We propose a novel automatic detection algorithm consisting of the following components: 1) The original z-stack images are first converted into one all-in-focus image. 2) A …

Reference Compensation For Localized Surface-Plasmon Resonance Sensors, Neha Nehru

Theses and Dissertations--Electrical and Computer Engineering

Noble metal nanoparticles supporting localized surface plasmon resonances (LSPR) have been extensively investigated for label free detection of various biological and chemical interactions. When compared to other optical sensing techniques, LSPR sensors offer label-free detection of biomolecular interactions in localized sensing volume solutions. However, these sensors also suffer from a major disadvantage – LSPR sensors remain highly susceptible to interference because they respond to both solution refractive index change and non-specific binding as well as specific binding of the target analyte. These interactions can severely compromise the measurement of the target analyte in a complex unknown media and hence limit …

Multi-Mode Self-Referencing Surface Plasmon Resonance Sensors, Jing Guo

Theses and Dissertations--Electrical and Computer Engineering

Surface-plasmon-resonance (SPR) sensors are widely used in biological, chemical, medical, and environmental sensing. This dissertation describes the design and development of dual-mode, self-referencing SPR sensors supporting two surface-plasmon modes (long- and short-range) which can differentiate surface binding interactions from bulk index changes at a single sensing location. Dual-mode SPR sensors have been optimized for surface limit of detection (LOD). In a wavelength interrogated optical setup, both surface plasmons are simultaneously excited at the same location and incident angle but at different wavelengths. To improve the sensor performance, a new approach to dual-mode SPR sensing is presented that offers improved differentiation …

Pathologyxgrid Implementation For The Interproscan Bioinformatics Software, Cody K. Bumgardner

Cody Bumgardner

SoftwareInterProScan is an essential step in the Epichloëfestucae genome project’s pipeline. Complete determination of the genome sequence for Epichloëfestucae, requires substantial programmatic and computing efforts. Due to the running time requirements the computational volume of some of its subtasks exceed the power of a traditional single processor computation and high performance approaches, such as grid computing, are needed.

The Personal Digital Assistant (Pda) As A Tool For Telementoring Endoscopic Procedures., Cody K. Bumgardner

Cody Bumgardner

Abstract: The telementoring of surgical procedures is currently achieved via a wired infrastructure that usually requires sophisticated videoconference systems. This project represents the first step in assessing the potential for using handheld computers as a mobile alternative to current telementoring systems. Specifically, this project compares a handheld computer to a standard CRT monitor regarding their capability to accurately display video images from an endoscopic procedure. Video images from two previously recorded endoscopic procedures were transmitted from a standard VCR to: 1) a handheld computer (iPAQ 3670 running Pocket PC) via a wireless LAN and 2) a standard CRT monitor via …