Biomedical Engineering and Bioengineering Commons^™

Prediction Of Lncrna-Protein Interactions Based On Deep Learning Model, Natsuda Navamajiti

Chulalongkorn University Theses and Dissertations (Chula ETD)

One main function of long non-coding RNAs (lncRNAs) is to act as a scaffold facilitating multiple proteins to form complexes. Most of available prediction models for protein-RNA interactions, however, were proposed as a binary classifier, which limited on predicting the interaction between the non-coding RNAs and each individual RNA-binding protein (RBP). Hence, to predict if a lncRNA is acting as a scaffold, we consider this problem as a multiclass multilabel classification problem. To solve this problem, the high confident CLIP-seq data were selected from the POSTAR2 database with an augmentation of the data for the RBP classes with a small …

Msg-Fast: Metagenomic Shotgun Data Fast Annotation Using Microbial Gene Catalogs, Stuart M. Brown, Hao Chen, Yuhan Hao, Bobby P. Laungani, Thahmina A. Ali, Changsu Dong, Carlos Lijeron, Baekdoo Kim, Claudia Wultsch, Zhiheng Pei, Konstantinos Krampis

Publications and Research

Background: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.

Results: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this …

The Role Of Kras In Mechanosensing In Non-Small Cell Lung Cancer, Krista M. Powell

Theses and Dissertations

Lung cancer is the number one cause of cancer related death worldwide, with more than 1.6 million fatalities each year. Non-small cell lung cancer (NSCLC) accounts for 80-85% of all lung cancers, with KRAS being one of the most prevalent oncogenic driver mutations. Therapeutic approaches for KRAS-mutated NSCLC have been extensively explored due to the US National Cancer Institute RAS Initiative, but methods of directly targeting KRAS or downstream effectors, such as MEK, still have poor results. Previous reports have shown that KRAS-mutated NSCLC activate distinct receptor tyrosine kinases (RTKs) depending on the epithelial or mesenchymal state. Epithelial-to-mesenchymal transition (EMT) …

A Computational Assessment Of Lisfranc Injuries And Their Surgical Repairs, Michael Perez

Theses and Dissertations

While Lisfranc injuries in the mid foot are less common than other ankle and mid foot injuries, they pose challenges in both properly identifying them and treating them. When Lisfranc injuries are ligamentous and do not include obvious fractures, they are very challenging for clinicians to identify unless weight bearing radiographs are used. The result is that 20%-40% of Lisfranc injuries are missed in the initial evaluation. Even when injuries are correctly identified the outcomes of surgical procedures remain poor. Existing literature has compared the different surgical procedures but has not had a standard approach or procedures across studies. This …

The Role Of The Mechanical Environment On Cd117+ Endothelial Cell Angiogenesis, Patrick Link

Theses and Dissertations

Angiogenesis is a complex process coordinating cell migration, proliferation, and lumen formation. Changes to the microenvironment regulate angiogenesis through mechanotransduction and cytokine signals. In pulmonary hypertension, something in the process becomes abnormal, resulting in changes to the microenvironment and the formation of a glomerulus of dysfunctional capillaries, called a plexiform lesion. Endothelial cells, expressing CD117 (CD117+ EC clones) increase in the plexiform lesions of pulmonary hypertension, independent of pro-angiogenic VEGF signaling. We hypothesize that the mechanical environment and the macromolecular composition of the extracellular matrix, both, contribute to the aberrant angiogenesis. When we changed the mechanical environment, we changed the …

Engineering The Alveolar Gas Exchange Barrier With Extracellular Matrix Coatings For Bioengineered Lungs, Bethany M. Young

Theses and Dissertations

Lower respiratory diseases are currently the third leading cause of death worldwide. For many end-stage patients with these diseases, there is no cure and a shortage of donor organs available for transplant. A promising solution is to design regenerative scaffolds or complete bioengineered lungs, using decellularized lung tissues as a template for regeneration. Recent advances in the field have made significant strides towards developing a transplantable lung. However, the current technology has not produced a functional lung for in vivo transplant due to immature gas exchange barriers. The mechanisms driving alveolar barrier maturation and role that extracellular matrix (ECM) plays …

Eralpha Isoforms Modulate The Tumorigenicity Of 24r,25(Oh)2d3 In Estrogen-Responsive Cancer, Anjali Verma

Theses and Dissertations

Over 200,000 cases of breast cancer are diagnosed every year. Nearly 20% of these patients supplement their diets with some form of vitamin D. This high frequency of vitamin D supplement use may be due in part to research suggesting that cancer patients with higher serum vitamin D₃ levels have better prognoses than patients with low serum vitamin D_3. However, double-blind clinical trials on the efficacy of vitamin D₃ supplementation in breast cancer have been inconclusive. A recent meta-analysis showed evidence of reduced cancer recurrence in patients taking vitamin D₃ supplements who had ‘estrogen receptor positive’ …

Mechanochemical Regulation Of Epithelial Tissue Remodeling: A Multiscale Computational Model Of The Epithelial-Mesenchymal Transition Program, Lewis Scott

Theses and Dissertations

Epithelial-mesenchymal transition (EMT) regulates the cellular processes of migration, growth, and proliferation - as well as the collective cellular process of tissue remodeling - in response to mechanical and chemical stimuli in the cellular microenvironment. Cells of the epithelium form cell-cell junctions with adjacent cells to function as a barrier between the body and its environment. By distributing localized stress throughout the tissue, this mechanical coupling between cells maintains tensional homeostasis in epithelial tissue structures and provides positional information for regulating cellular processes. Whereas in vitro and in vivo models fail to capture the complex interconnectedness of EMT-associated signaling networks, …

Development Of An Eye Movement Based Predictive Model For Discrimination Of Parkinson's Disease From Other Parkinsonisms And Controls, Mary Anisa Kannan

Theses and Dissertations

Purpose: Due to the neurological aspects of Parkinson’s Disease (PD) and the sensitivity of eye movements to neurological issues, eye tracking has the potential to be an objective biomarker with higher accuracy in diagnosis than current clinical standards. Currently when PD is diagnosed clinically, there is an accuracy of 74% when diagnosed by a general practitioner and 82% when diagnosed by a movement disorder specialist. This study was designed to: 1. Assess eye movements as a potential biomarker for Parkinson’s Disease. 2. Determine if eye movements can distinguish between Parkinson’s Disease and commonly confounded movement disorders with parkinsonian symptoms. 3. …

Assessment Of Access Methods For Mobile Maps For Individuals Who Are Blind Or Visually Impaired, David Parker

Theses and Dissertations

When people go to a mall, museums, or other such locations they tend to rely on maps to find their way around. However, for people who are blind or visually impaired (BVI) maps are not easily accessible and they depend on other means, such as a guide, to get around. Research has only just begun to investigate providing maps for people who are BVI on touch screen devices. Many different types of feedback have been used: audio (sound), tactile (touch), audio-tactile, and multitouch. Some research has been conducted on the benefit of using multiple fingers (multitouch) and has found conflicting …

A Survey Of Attention Deficit Hyperactivity Disorder Identification Using Psychophysiological Data, S. De Silva, S. Dayarathna, G. Ariyarathne, D. Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Attention Deficit Hyperactivity Disorder (ADHD) is one of the most common neurological disorders among children, that affects different areas in the brain that allows executing certain functionalities. This may lead to a variety of impairments such as difficulties in paying attention or focusing, controlling impulsive behaviours and overreacting. The continuous symptoms may have a severe impact in the long-term. This paper explores the ADHD identification studies using eye movement data and functional Magnetic Resonance Imaging (fMRI). This study discusses different machine learning techniques, existing models and analyses the existing literature. We have identified the current challenges and possible future directions …

Assessing Endothelial Dysfunction Estimating The Differences Between 3 Minute And 5 Minute Reactive Hyperemia, Tamiko K. Saldin

Master's Theses

The purpose of this study was to define a lower standard cuff occlusion time to induce reactive hyperemia in assessing endothelial dysfunction. In this study, strong evidence was found by a novel technique that used oscillometric methods, which supported that 3 minute reactive hyperemia was sufficient to elicit a significant difference in arterial compliance from baseline. Twenty healthy Cal Poly students were assessed, (n=12 female, n=8 male) aged 22 years old with a standard deviation of 2.04 years. Arterial compliance was estimated by measuring the peak-to-peak oscillations for baseline, 3 minute reactive hyperemia, and 5 minute reactive hyperemia tests, with …

Ct Automated Exposure Control Using A Generalized Detectability Index, P. Khobragade, Franco Rupcich, Jiahua Fan, Dominic J. Crotty, Naveen M. Kulkarni, Stacy D. O'Connor, W. Dennis Foley, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Purpose

Identifying an appropriate tube current setting can be challenging when using iterative reconstruction due to the varying relationship between spatial resolution, contrast, noise, and dose across different algorithms. This study developed and investigated the application of a generalized detectability index (d'_gen) to determine the noise parameter to input to existing automated exposure control (AEC) systems to provide consistent image quality (IQ) across different reconstruction approaches.

Methods

This study proposes a task‐based automated exposure control (AEC) method using a generalized detectability index (d'_gen). The proposed method leverages existing AEC methods that are based on a prescribed …

Spatial And Temporal Influences On Discrimination Of Vibrotactile Stimuli On The Arm, Valay Shah, Maura Casadio, Robert A. Scheidt, Leigh A. Mrotek

Biomedical Engineering Faculty Research and Publications

Body–machine interfaces (BMIs) provide a non-invasive way to control devices. Vibrotactile stimulation has been used by BMIs to provide performance feedback to the user, thereby reducing visual demands. To advance the goal of developing a compact, multivariate vibrotactile display for BMIs, we performed two psychophysical experiments to determine the acuity of vibrotactile perception across the arm. The first experiment assessed vibration intensity discrimination of sequentially presented stimuli within four dermatomes of the arm (C5, C7, C8, and T1) and on the ulnar head. The second experiment compared vibration intensity discrimination when pairs of vibrotactile stimuli were presented simultaneously vs. sequentially …

Computational Characterization Of The Cellular Origins Of Electroencephalography, Shane Hesprich, Scott A. Beardsley

Biomedical Engineering Faculty Research and Publications

Despite the widespread use of Electroecephalography (EEG) as an imaging modality, neural generators of current dipoles measured by EEG at the scalp are not fully understood. Here, we use two morphologically accurate multicompartments neuron models (layer IV pyramidal cell and layer V spiny stellate cell) to characterize how spiking neurons generate current dipoles in response to synaptic input. The simulations indicate that the dipole generated by synaptic inputs required to drive a pyramidal cell to threshold is smaller than the dipole associated the action potential itself. These results suggest a greater role of spiking neural activity toward EEG signals measured …

Exploring The Role And Impact Of Microscale Phenomena On Electrode, Microdevice, And Cellular Function, Sanaz Habibi

Dissertations, Master's Theses and Master's Reports

Microfluidic technologies enable the development of portable devices to perform multiple high-resolution unit operations with small sample and reagent volumes, low fabrication cost, facile operation, and quick response times. Microfluidic platforms are expected to effectively interpret both wanted and unwanted phenomena; however, a comprehensive evaluation of the unwanted phenomena has not been appropriately investigated in the literature. This work explored an attenuative evaluation of unwanted phenomena, also called here as secondary phenomena, in a unique approach.

Upon electric field utilization within microfluidic devices, electrode miniaturization improves device sensitivity. However, electrodes in contact with medium solution can yield byproducts that can …

Optical Vortex And Poincaré Analysis For Biophysical Dynamics, Anindya Majumdar

Dissertations, Master's Theses and Master's Reports

Coherent light - such as that from a laser - on interaction with biological tissues, undergoes scattering. This scattered light undergoes interference and the resultant field has randomly added phases and amplitudes. This random interference pattern is known as speckles, and has been the subject of multiple applications, including imaging techniques. These speckle fields inherently contain optical vortices, or phase singularities. These are locations where the intensity (or amplitude) of the interference pattern is zero, and the phase is undefined.

In the research presented in this dissertation, dynamic speckle patterns were obtained through computer simulations as well as laboratory setups …

Estimation Of Multi-Directional Ankle Impedance As A Function Of Lower Extremity Muscle Activation, Lauren Knop

Dissertations, Master's Theses and Master's Reports

The purpose of this research is to investigate the relationship between the mechanical impedance of the human ankle and the corresponding lower extremity muscle activity. Three experimental studies were performed to measure the ankle impedance about multiple degrees of freedom (DOF), while the ankle was subjected to different loading conditions and different levels of muscle activity. The first study determined the non-loaded ankle impedance in the sagittal, frontal, and transverse anatomical planes while the ankle was suspended above the ground. The subjects actively co-contracted their agonist and antagonistic muscles to various levels, measured using electromyography (EMG). An Artificial Neural Network …

A Smart Implantable Bone Fixation Plate Providing Actuation And Load Monitoring For Orthopedic Fracture Healing, Brad Nelson

Dissertations, Master's Theses and Master's Reports

Fracture non-union occurs in roughly 5-10% of all fracture cases, and current interventions are both time-consuming and costly. There is therefore significant incentive to develop new tools to improve fracture healing outcomes. Several studies have shown that low-magnitude, high-frequency (LMHF) mechanical loading can promote faster healing and reduce the risk of refracture in critical-size long bone fractures. This is typically done using whole-body vibration, which may result in undesirable systemic effects on the rest of the body. This work discusses an implantable piezoelectric fixation plate that can both apply LMHF loading directly to the fracture site using flexible scheduling and …

3d Printing In Low Resource Healthcare Settings: Analysis Of Potential Implementations, Alenna Beroza

Dissertations, Master's Theses and Master's Reports

3D printing has gained significant momentum in the past ten years, and its unique advantages make it especially ideal for use in low resource healthcare settings, where many designs have already been successfully implemented. Yet, little has been studied on how 3D printing can be sustainably and functionally implemented in low resource healthcare systems as a manufacturing practice. In this report, three business models are proposed for this implementation: In-House Operator, Independent Operator, and Print Farm. These models were then tested over four months in Kisumu county, Kenya, at two workshops and seven public hospitals. I worked with local medical …