Biomedical Engineering and Bioengineering Commons^™

Dna I-Motifs: Biophysical Characterization And Structure-Property Correlation As Foundation For Functional Material Design, Alexander Minasyan

Graduate Research Theses & Dissertations

Over the past decades, nucleic acids have emerged as crucial frameworks with significance in biological systems and functional material engineering. Cytosine-rich deoxyribonucleotide sequences can form quadruplex structures a.k.a. i-motifs. Recently, i-motifs have attracted scientific interest in biological and material design areas.

In this work, we systematically investigate an effect of structured and unstructured modifications such as hairpins, stems, loops and overhangs on the kinetic and thermodynamic properties of DNA i-motifs. We demonstrate that the modifications can influence i-motif’s stability and folding/unfolding rates: thus, double stranded stems and hairpins are the best at stabilizing i-motifs and increasing kinetic rates of folding. …

Evaluation Of Silk Fibroin And Hylauronic Acid As Otic Drug Delivery System Additives; Investigation Of Silk Fibroins Responses To Enviromental Stimulii, Kolton Charles Sandau

Graduate Student Theses, Dissertations, & Professional Papers

The Serban lab has previously developed and reported on a single application drug delivery system for the treatment of otitis externa. Otitis externa also known as outer ear infections is a very common ailment that impacts large portions of both human and domestic animal populations. Typical treatment for otitis externa typically requires an extended dosing regimen over several days that is inconvenient and can lead to poor clinical outcomes due to poor patient compliance. Our delivery system employs a thixotropic gel to deliver a steady dose of medication over the duration of the infection.

Here we evaluated the reproducibility and …

Serious Game-Based Training For Improved Utilization Of A Novel Temporalis Emg Interface For Controlling Powered Wheelchairs, Calvin Macdonald

Honors Undergraduate Theses

Amyotrophic lateral sclerosis (ALS) is a terminal neurodegenerative disease that leads to a lack of independent mobility. One solution uses a unilateral surface EMG (sEMG) interface on the temporalis muscle to provide autonomous control of a powered wheelchair. Limbitless Journey, an EMG-controlled serious game, intends to provide users with a virtual environment to train in before use in a real-world scenario. A recent study analyzed the effect of video game training on the use of sEMG systems on the forearm, showing significant improvement in the usage of the interface but no difference between Free Play and structured play. The study …

De-Risking Pretreatment Of Microalgae To Produce Fuels And Chemical Co-Products, Jacob S. Kruger, Skylar Schutter, Eric P. Knoshaug, Bonnie Panczak, Hannah Alt, Alicia Sowell, Stafanie Van Wychen, Matthew Fowler, Kyoko Hirayama, Anuj Thakkar, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

Conversion of microalgae to renewable fuels and chemical co-products by pretreating and fractionation holds promise as an algal biorefinery concept, but a better understanding of the pretreatment performance as a function of algae strain and composition is necessary to de-risk algae conversion operations. Similarly, there are few examples of algae pretreatment at scales larger than the bench scale. This work aims to de-risk algal biorefinery operations by evaluating the pretreatment performance across nine different microalgae samples and five different pretreatment methods at small (5 mL) scale and further de-risk the operation by scaling pretreatment for one species to the 80 …

Identification And Characterization Of Two Novel Kcnh2 Mutations Contributing To Long Qt Syndrome, Anthony Owusu-Mensah, Jacqueline Treat, Joyce Bernardi, Ryan Pfeiffer, Robert Goodrow, Bright Tsevi, Victoria Lam, Michel Audette, Jonathan M. Cordeiro, Makarand Deo

Electrical & Computer Engineering Faculty Publications

We identified two different inherited mutations in KCNH2 gene, or human ether-a-go-go related gene (hERG), which are linked to Long QT Syndrome. The first mutation was in a 1-day-old infant, whereas the second was in a 14-year-old girl. The two KCNH2 mutations were transiently transfected into either human embryonic kidney (HEK) cells or human induced pluripotent stem-cell derived cardiomyocytes. We performed associated multiscale computer simulations to elucidate the arrhythmogenic potentials of the KCNH2 mutations. Genetic screening of the first and second index patients revealed a heterozygous missense mutation in KCNH2, resulting in an amino acid change (P632L) in the …

Domain Adaptive Federated Learning For Multi-Institution Molecular Mutation Prediction And Bias Identification, W. Farzana, M. A. Witherow, I. Longoria, M. S. Sadique, A. Temtam, K. M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Deep learning models have shown potential in medical image analysis tasks. However, training a generalized deep learning model requires huge amounts of patient data that is usually gathered from multiple institutions which may raise privacy concerns. Federated learning (FL) provides an alternative to sharing data across institutions. Nonetheless, FL is susceptible to a few challenges including inversion attacks on model weights, heterogenous data distributions, and bias. This study addresses heterogeneity and bias issues for multi-institution patient data by proposing domain adaptive FL modeling using several radiomics (volume, fractal, texture) features for O6-methylguanine-DNA methyltransferase (MGMT) classification across multiple institutions. The proposed …

Wavelet-Based Harmonization Of Local And Global Model Shifts In Federated Learning For Histopathological Images, W. Farzana, A. Temtam, K. M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Federated Learning (FL) is a promising machine learning approach for development of data-driven global model using collaborative local models across multiple local institutions. However, the heterogeneity of medical imaging data is one of the challenges within FL. This heterogeneity is caused by the variation in imaging scanner protocols across institutions, which may result in weight shift among local models leading to deterioration in predictive accuracy of global model. The prevailing approaches involve applying different FL averaging techniques to enhance the performance of the global model, ignoring the distinct imaging features of the local domain. In this work, we address both …

Investigation Of The Effect Of Preparation Parameters On The Structural And Mechanical Properties Of Gelatin/Elastin/Sodium Hyaluronate Scaffolds Fabricated By The Combined Foaming And Freeze-Drying Techniques, Mansour Qamash, S. Misagh Imani, Meisam Omidi, Ciara Glancy, Lobat Tayebi

Electrical & Computer Engineering Faculty Publications

This paper aimed to evaluate the effects of different preparation parameters, including agitation speed, agitation time, and chilling temperature, on the structural and mechanical properties of a novel gelatin/elastin/sodium hyaluronate tissue engineering scaffold, recently developed by our research group. Fabricated using a combination of foaming and freeze-drying techniques, the scaffolds were assessed to understand how these parameters influence their morphology, internal microstructure, porosity, mechanical properties, and degradation behavior. The fabrication process used in this study involved preparing a homogeneous aqueous solution containing 8% gelatin, 2% elastin, and 0.5% sodium hyaluronate (w/v), which was then subjected to mechanical agitation at speeds …

Advancing Chronic Kidney Disease Prediction Through Machine Learning And Deep Learning With Feature Analysis, Shiddarth Dey Tusar, S. M. Ahad Ali Chowdhury, Md. Jalal Uddin Chowdhury, Rana M. Pir, H. M. Nur A. Alam, Muhammad Rezaur Rahman, Md. Nural Absar Siddiky, Muhammad Enayetur Rahman

Electrical & Computer Engineering Faculty Publications

Chronic Kidney Diesease (CKD) is a significant health issue, ranking as the fourth leading cause of mortality worldwide. The traditional diagnosis and treatment process, reliant on medical experts, is time-consuming. Therefore, thereis an urgent need for more efficient diagnostic methods to improve patient outcomes and reduce mortality rates. In this study, we employ Machine Learning (ML) and Deep Learning (DL) techniques to predict CKD based on important features. Feature analysis was performed using a correlation matrix and the LASSO algo-rithm to identify the most relevant features for model training. We evaluated several ML and DL classifiers, including Logistic Regression (LR), …

Salmonella Detection In Food Using A Hek-Htlr5 Reported Cell-Based Sensor, Esma Eser, Victoria A. Felton, Rishi Drolia, Arun K. Bhunia

Biological Sciences Faculty Publications

The development of a rapid, sensitive, specific method for detecting foodborne pathogens is paramount for supplying safe food to enhance public health safety. Despite the significant improvement in pathogen detection methods, key issues are still associated with rapid methods, such as distinguishing living cells from dead, the pathogenic potential or health risk of the analyte at the time of consumption, the detection limit, and the sample-to-result. Mammalian cell-based assays analyze pathogens’ interaction with host cells and are responsive only to live pathogens or active toxins. In this study, a human embryonic kidney (HEK293) cell line expressing Toll-Like Receptor 5 (TLR-5) …

Receptor-Targeted Next-Generation Probiotics Ameliorate Mammalian Colitis, Nicholas L. F. Gallina, Vignesh Nathan, Akshay Krishnakumar, Dongqi Liu, Rishi Drolia, Nicole Irrizary Tardi, Yang Fu, Manalee Samadar, Shivendra Tenguria, Alvin Cai, Ruth Eunice Centeno-Martinez, Timothy A. Johnson, Abigail Cox, Lavanya Reddivari, Bruce Applegate, Xingjian Bai, Luping Xu, Deepti Tanjore, Ramesh Vemulapalli, Rahim Rahimi, Arun K. Bhunia

Biological Sciences Faculty Publications

Introduction: a loss of intestinal barrier function, inflammation, and an elevated expression of epithelial heat shock protein 60 (Hsp60) are features of an inflamed bowel. Probiotics have been used to alleviate colitis-induced pathologies, but offer poor adhesion and adaptation to the diseased gut. We hypothesize that enhancing probiotic adhesion in the inflamed bowel may ameliorate such pathologies. Listeria adhesion protein (LAP; 94-kDa acetaldehyde alcohol dehydrogenase) aids Listeria attachment to the epithelial cells by interacting with the mammalian receptor Hsp60. Bioengineered Lactobacillus casei probiotics (BLPs) expressing LAP showed strong interaction with epithelial Hsp60, a high immunomodulatory response, and sustained epithelial barrier …

การพัฒนาแผ่นปิดแผลที่มีโปรตีนกาวไหมและสารสกัดจากอบเชยสำหรับแผลติดเชื้อ, สิริพร ปิยะพันธ์

Chulalongkorn University Theses and Dissertations (Chula ETD)

โปรตีนกาวไหม (Silk sericin) เป็นโปรตีนจากธรรมชาติ ซึ่งเป็นวัสดุเหลือทิ้งจากการสกัดรังไหมเอาเส้นใยไหม (Silk fibroin) ไปใช้ โปรตีนกาวไหมถูกนำมาใช้ประโยชน์อย่างแพร่หลายในงานทางการแพทย์ ไม่ว่าจะเป็นงานด้านการนำส่งยา สเต็มเซลล์ การสร้างเนื่อเยื่อใหม่ แผ่นปิดแผล ในรูปแบบของ แผ่นฟิล์ม (film) ไฮโดรเจล (hydrogel) โครงเลี้ยงเซลล์ (scaffold) หรืออนุภาคระดับไมโคร/นาโน เป็นต้น ในงานวิจัยชิ้นนี้ผู้วิจัยมีความสนใจที่นำโปรตีนกาวไหมมาขึ้นรูปเป็นแผ่นปิดแผล ร่วมกับการใช้พอลิไวนิลแอลกอฮอล์และกลีเซอรีน ด้วยการเชื่อมขวาง 2 รูปแบบ คือ การเชื่อมขวางทางกายภาพโดยกระบวนการ freeze-thaw และการเชื่อมขวางทางเคมีด้วยสารเชื่อมขวางกลูตาราลดีไฮด์ (glutaraldehyde) และทำการศึกษาคุณสมบัติต่างๆ จากการศึกษา พบว่า แผ่นปิดแผลที่ขึ้นรูปได้ทั้ง 2 แบบ มีรูพรุนกระจายอยู่ทั่วทั้งแผ่น โครงสร้างภายในจับกันเป็นโครงข่ายได้เป็นอย่างดี ผลการวิเคราะห์หมู่ฟังก์ชัน ปรากฎว่า พบหมู่ amide I ที่ 1618-1640 cm-1 (C=O stretching) หมู่ amide II ที่ 1518-1638 cm-1 (N-H bending and C-N stretching) และ หมู่ amide III ที่ 1238 cm-1 (C-N and C=O stretching) จากแผ่นปิดแผลทุกชนิด โดยในแผ่นปิดแผลที่ใช้สารเชื่อมขวางกลูตาราลดีไฮด์จะพบ peak ที่2830 -3000 cm-1 ซึ่งแสดงถึงพันธะ C-H ของหมู่อัลดีไฮด์กับหมู่แอลคิล การทดสอบสมบัติเชิงกล (mechanical property) แสดงให้เห็นว่า การเชื่อมขวางทั้ง 2 วิธี ทำให้ค่ามอดูลัสของยัง (Young’s modulus) เพิ่มขึ้น แผ่นปิดแผลสามารถทนต่อการเปลี่ยนแปลงรูปร่างได้มากขึ้น และการเชื่อมขวางทางกายภาพยังทำให้ระยะยืดที่จุดขาด (elongation at break) ของแผ่นปิดแผลสูงขึ้น แต่ในขณะเดียวระยะยืดที่จุดขาด (elongation …

การพัฒนาเท้าเทียมที่สามารถปรับ Roll-Over Shape สำหรับผู้พิการที่มีกิจวัตรประจำวันระดับต่ำถึงปานกลาง, ณิชนันทน์ ปิดทอง

Chulalongkorn University Theses and Dissertations (Chula ETD)

งานวิจัยนี้เสนอการออกแบบเท้าเทียมแบบใหม่ที่สามารถปรับ Roll-over shape ได้สำหรับผู้พิการที่มีระดับกิจกรรมต่ำถึงปานกลาง เนื่องจากเท้าเทียมสำหรับผู้พิการที่ได้รับสิทธิเบิกจ่ายจากรัฐบาลจะเป็นเท้าเทียม SACH ซึ่งมีข้อจำกัดคือลักษณะฝ่าเท้าที่มีความแข็งและไม่สามารถงอข้อเท้าได้ จึงเป็นเหตุให้ผู้พิการมีลักษณะการเดินที่ไม่สมมาตร โดยเท้าเทียมวิจัยนี้จะสามารถปรับ Roll-over shape ตามความสูงของแต่ละบุคคล เพื่อพัฒนาความสมมาตรในการเดินให้ดีขึ้น การออกแบบเท้าเทียมจะคำนึงถึงปัจจัยต่างๆ เช่น ความยาวเท้า น้ำหนัก และส่วนสูง ซึ่งส่วนสูงเป็นปัจจัยสำคัญที่ส่งผลต่อ Roll-over shape ดังนั้นเท้าเทียมจึงได้รับการพัฒนาให้สามารถปรับ Roll-over shape ได้เพื่อรองรับผู้พิการที่มีส่วนสูงที่แตกต่างกัน การทดสอบความแข็งแรงและ Roll-over radius ทำโดยวิธีการวิเคราะห์ไฟไนต์เอลิเมนต์ด้วยโปรแกรม ANSYS 2021R2 และมีการทดสอบการเดินกับผู้พิการจริงแบบ Single Pilot Study เพื่อทดสอบประสิทธิภาพของเท้าเทียมวิจัยกับความสมมาตรของการเดิน เท้าเทียมวิจัยนี้ถูกออกแบบให้สามารถปรับ Roll-over radius ได้ 289 297 และ 323 มม. ตามลำดับ และจากการทดสอบการเดินกับผู้พิการพบว่าดัชนีสมมาตรจะเพิ่มขึ้นเมื่อปรับเท้าเทียมให้มี Roll-over radius ที่มากขึ้น โดยมีค่าดัชนีความสมมาตรของ Roll-over radius 289 297 323 มม. และเท้า SACH คือ 0.03%, -0.77%, -7.12% และ -11.62% ตามลำดับ และค่าดัชนีความสมมาตรของ Step time สำหรับเท้าเทียมที่มี Roll-over radius 289 297 และ 323 มม. และเท้า SACH คือ -4.14%, -11.07%, -18.19% และ -21.30% ตามลำดับ และจากการทดสอบกับผู้พิการจริงพบว่าดัชนีความสมมาตรของเท้าเทียมที่มี Roll-over radius 289 มม. ดีกว่าเท้า SACH ในแง่ของ Roll-over radius และ Step time 99.7% …

Reevaluating The Paradox: Does Low-Dose Radiation From A-Bombs Affect Lifespan And Cancer Mortality?, Razieh Rashidfar, Zeynab Seyedi Sarhad, Seyed Mohammad Javad Mortazavi, Lembit Sihver

Informatics and Engineering Systems Faculty Publications

No abstract provided.

Enhanced Skin Cancer Diagnosis Through Grid Search Algorithm-Optimized Deep Learning Models For Skin Lesion Analysis, Rudresh Pillai, Neha Sharma, Sheifali Gupta, Deepali Gupta, Sapna Juneja, Saurav Malik, Hong Qin, Mohammed S. Alqahtani, Amel Ksibi

Computer Science Faculty Publications

Skin cancer is a widespread and perilous disease that necessitates prompt and precise detection for successful treatment. This research introduces a thorough method for identifying skin lesions by utilizing sophisticated deep learning (DL) techniques. The study utilizes three convolutional neural networks (CNNs)-CNN1, CNN2, and CNN3-each assigned to a distinct categorization job. Task 1 involves binary classification to determine whether skin lesions are present or absent. Task 2 involves distinguishing between benign and malignant lesions. Task 3 involves multiclass classification of skin lesion images to identify the precise type of skin lesion from a set of seven categories. The most optimal …

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …

In Vivo Measurement Of Nadh Fluorescence Lifetime In Skeletal Muscle Via Fiber-Coupled Time-Correlated Single Photon Counting, Kathryn M. Priest, Jacob V. Schluns, Nathania Nischal, Colton L. Gattis, Jeffery C. Wolchok, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Nicotinamide adenine dinucleotide (NADH) is a cofactor that serves to shuttle electrons during metabolic processes such as glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation (OXPHOS). NADH is autofluorescent, and its fluorescence lifetime can be used to infer metabolic dynamics in living cells. Fiber-coupled time-correlated single photon counting (TCSPC) equipped with an implantable needle probe can be used to measure NADH lifetime in vivo, enabling investigation of changing metabolic demand during muscle contraction or tissue regeneration. This study illustrates a proof of concept for point-based, minimally-invasive NADH fluorescence lifetime measurement in vivo. Volumetric muscle loss (VML) injuries were …

Designing A Use-Error Robust Machine Learning Model For Quantitative Analysis Of Diffuse Reflectance Spectra, Allison Scarbrough, Keke Chen, Bing Yu

Biomedical Engineering Faculty Research and Publications

Significance

Machine learning (ML)-enabled diffuse reflectance spectroscopy (DRS) is increasingly used as an alternative to the computation-intensive inverse Monte Carlo (MCI) simulation to predict tissue’s optical properties, including the absorption coefficient,μaand reduced scattering coefficient, μs′.

Aim

We aim to develop a use-error-robust ML algorithm for optical property prediction from DRS spectra.

Approach

We developed a wavelength-independent regressor (WIR) to predict optical properties from DRS data. For validation, we generated 1520 simulated DRS spectra with the forward Monte Carlo model, where μa=0.44 to 2.45cm−1, and μs′=6.53 to 9.58cm−1. We introduced common use-errors, such as wavelength miscalibrations and intensity fluctuations. Finally, we …

Integrating Therapy Into Play: Stand-On Ride-On For A Child With Cerebral Palsy, Kira Flanagan

UNF Graduate Theses and Dissertations

This study focuses on the development of an adaptive ride-on toy specifically designed for a 2.5-year-old child with spastic diplegic cerebral palsy. As a feasibility study, the primary objective of this innovative device is to enhance motor function, foster autonomy, and improve the overall quality of life for the child. The Power Mobility Device (PMD) integrates actuation and steering modifications, and a harness mechanism tailored to meet the child's unique needs. Comprehensive assessments of the child's spatiotemporal gait characteristics were conducted before and after a three-month usage period. The results reveal significant improvements in the child's ability to control dynamic …

Transparent And Conductive Gallium Oxide Electrode For Simultaneous Recording And Optogenetic Stimulation, Christopher Patrick Carey

Graduate Theses, Dissertations, and Problem Reports (ETD)

Neural electrode technology has been around for centuries since the times of Galvani. In early electrophysiology experiments metal wires were used to induce contractions in dissected animals. The metal wire electrode has since been a standard tool to both stimulate and record neural activity. In the past two decades, a new strategy for neural stimulation has been formulated based on the emergent field of optogenetics. Optogenetics refers to the use of light-sensitive proteins genetically imbedded in the membrane of a neuron to elicit neural activity. This technique offers more selectivity in the stimulation of neurons. Typical optogenetic neural electrodes, or …