Biomedical Engineering and Bioengineering Commons^™

Intercellular Mitochondrial Transfer Contributes To Microenvironmental Fate Redirection Of Mammary Cancer Cells, Julie Sofie Bjerring

Biomedical Sciences Theses & Dissertations

The dynamic cellular microenvironment, made up of resident cells and various macromolecules, differs markedly across tissues in the body. The multidirectional signals that cells receive from this microenvironment, along with the signaling they send back, heavily influence their physiology and behavior. Recent important findings have further validated this notion as the mammary microenvironment has been shown to suppress tumor progression by redirecting cancer cells to adopt a normal mammary epithelial progenitor fate in vivo. However, the mechanism(s) driving changes in metabolic reprogramming and cancer fate redirection is understudied. The work presented in this dissertation focuses on exploring the impact of …

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 …

Nanopore Signal Deviations From Pseudouridine Modifications In Rna Are Sequence-Specific: Quantification Requires Dedicated Synthetic Controls, Amr Makhamreh, Sepideh Tavakoli, Ali Fallahi, Xinqi Kang, Howard Gamper, Mohammad Nabizadehmashhadtoroghi, Miten Jain, Ya-Ming Hou, Sara H Rouhanifard, Meni Wanunu

Department of Biochemistry and Molecular Biology Faculty Papers

Chemical modifications to mRNA respond dynamically to environmental cues and are important modulators of gene expression. Nanopore direct RNA sequencing has been applied for assessing the presence of pseudouridine (ψ) modifications through basecalling errors and signal analysis. These approaches strongly depend on the sequence context around the modification, and the occupancies derived from these measurements are not quantitative. In this work, we combine direct RNA sequencing of synthetic RNAs bearing site-specific modifications and supervised machine learning models (ModQuant) to achieve near-analytical, site-specific ψ quantification. Our models demonstrate that the ionic current signal features important for accurate ψ classification are sequence …

A Novel Model Of Autologous Tooth Transplantation For The Study Of Nerve Recruitment, Teresa E. Fowler, Doan T. Bloomquist, Caroline Glessner, Poonam Patel, Jeffrey N. James, Kathryn Bollinger, Lynnette P. Mccluskey, Ryan F. Bloomquist

School of Dentistry Faculty Publications

Background: Limited treatment options exist for damaged nerves and despite impressive advances in tissue engineering, scientists and clinicians have yet to fully replicate nerve development and recruitment. Innervation is a critical feature for normal organ function. While most organs are innervated prior to birth, a rare example of postnatal nerve recruitment occurs in the natural development of secondary teeth during adolescence. Many animals undergo postnatal shedding of deciduous teeth with development and eruption of secondary teeth, a process requiring recruitment of nerve and vasculature to each tooth pulp for viability. Here, the investigators created a novel model for the study …

Amino Acid-Based Protein-Mimic Hydrogel Incorporating Pro-Regenerative Lipid Mediator And Microvascular Fragments Promotes The Healing Of Deep Burn Wounds, Yan Lu, Shanchun Su, Chih Chang Chu, Yuichi Kobayashi, Abdul Razak Masoud, Hongying Peng, Nathan Lien, Mingyu He, Christopher Vuong, Ryan Tran, Song Hong

School of Medicine Faculty Publications

Pro-regenerative lipid mediator 1 (PreM1) is a specialized pro-resolving lipid mediator that promotes wound healing and regenerative functions of mesenchymal stem cells (MSCs), endothelial cells, and macrophages. The healing of third-degree (3°) burns and regenerative functions of MSCs are enhanced by ACgel1, an arginine-and-chitosan-based protein-mimic hybrid hydrogel. Adipose-tissue derived microvascular fragments (MVFs) are native vascularization units and a rich source of MSCs, endothelial cells, and perivascular cells for tissue regeneration. Here we describe an innovative PreM1-MVFs-ACgel1 construct that incorporated PreM1 and MVFs into ACgel1 via optimal design and fabrication. This construct delivered PreM1 to 3°-burn wounds at least up to …

3d Bioactive Thiol-Norbornene Hydrogels For Guiding Stem Cell Mechanosensing And Differentiation, Arielle Gsell

U-RISE Undergraduate Theses

Hydrogels are soft, highly hydrated polymeric networks commonly used as biomaterial scaffolds in tissue engineering. To mimic the extracellular matrix of tissues, hydrogels can be chemically modified to incorporate either bioactive molecules such as peptides, or physically modified with crosslinkers to alter hydrogel stiffness and degradation. Hydrogels with defined characteristics can be synthesized using chemical reaction schemes such as photo-click chemistry, which offers spatial and temporal control over biochemical and physical properties. The goal of this thesis is to leverage thiol-norbornene click chemistry, a subtype of photo-click chemistry, to develop 3D hydrogels with biochemical and biophysical cues that guide mesenchymal …

Development Of A Haptic System For Robot-Assisted Femur Fracture Surgery, Fayez H. Alruwaili

Theses and Dissertations

Robot-assisted surgery has emerged within the field of surgical technology, driven by the need for greater accuracy and speed in the ongoing evolution of healthcare. This advancement has influenced numerous areas requiring enhancements to achieve optimal surgical results. However, surgical robotics tends to lack the surgeon’s connection to the operation, creating a gap in the intuitive skill set required for successful operations. The gap is seen through the lack of sense of touch, which may result in tissue damage and additional injury when the robot interacts with the patient. Furthermore, challenges faced during femur fracture surgery have positioned robot-assisted surgery …

Nanofiber-Hydrogel Composite Scaffold Fabrication Methods For Peripheral Nerve Regeneration, Jacob Lee Carter

Theses and Dissertations

Nerve graft conduits (NGCs) are a rapidly advancing field for treating peripheral nerve injuries that aim to guide the growth of regenerating axons across damaged gaps. A more effective NGC can be manufactured by combining the use of nanofibers to act as guidewires within a 3-D hydrogel that imitates the extracellular matrix of nerve tissue. Several methods have been developed to embed aligned nanofibers in an ordered architecture within a hydrogel matrix. The first method involves layer-by-layer additive manufacturing to create NGCs with rows of polycaprolactone (PCL) nanofibers surrounded by a gelatin methacrylate (GelMe) hydrogel in a 3-D structure. A …

Smart Toys For Sensing And Soothing Distress In Pediatric Patients, Jonathan Daniel Bonilla

Dartmouth College Master’s Theses

This thesis develops and evaluates child-centered technologies to support remote monitoring of pediatric patients, with an emphasis on childhood cancer and pediatric chronic pain. For these and many other health conditions, current therapies tend to focus on treating physical symptoms yet neglect the psycho-emotional aspects of managing the illness. However, such mental states play a major role in recovery. Research has shown that cancer patients with better mental health have better prognoses, higher possibilities of remission, and faster healing processes, while chronic pain patients with better mental health report lower levels of pain. To enable more personalized, continuous, and scalable …

Paper-Recorded Ecg Digitization Method With Automatic Reference Voltage Selection For Telemonitoring And Diagnosis, Liang Hung Wang, Chao Xin Xie, Tao Yang, Hong Xin Tan, Ming Hui Fan, I. Chun Kuo, Zne Jung Lee, Tsung Yi Chen, Pao Cheng Huang, Shih Lun Chen, Patricia Angela R. Abu

Department of Information Systems & Computer Science Faculty Publications

In electrocardiograms (ECGs), multiple forms of encryption and preservation formats create difficulties for data sharing and retrospective disease analysis. Additionally, photography and storage using mobile devices are convenient, but the images acquired contain different noise interferences. To address this problem, a suite of novel methodologies was proposed for converting paper-recorded ECGs into digital data. Firstly, this study ingeniously removed gridlines by utilizing the Hue Saturation Value (HSV) spatial properties of ECGs. Moreover, this study introduced an innovative adaptive local thresholding method with high robustness for foreground–background separation. Subsequently, an algorithm for the automatic recognition of calibration square waves was proposed …

Resting-State Eeg Microstate Features For Major Depressive Disorder Classification, George M. V. Quinn

Dissertations, Theses, and Capstone Projects

Neuroimaging studies have revealed consistent abnormalities in functional connectivity within specific neural networks that may serve as biomarkers for major depressive disorder (MDD). It is important to find inexpensive, non-invasive techniques that target these biomarkers to make diagnosis easier and more objective. EEG microstates are quasi-stable potential topographies that are thought to reflect the quasi-stable network activity of the underlying neural generators. MDD has been shown to alter features of the four canonical EEG microstates (A, B, C, D) with some conflicting results. The most consistent network abnormalities in MDD are found in the anterior default mode network, and this …

Precision Medicine For Apical Lesions And Peri-Endo Combined Lesions Based On Transfer Learning Using Periapical Radiographs, Pei Yi Wu, Yi Cheng Mao, Yuan Jin Lin, Xin Hua Li, Li Tzu Ku, Kuo Chen Li, Chiung An Chen, Tsung Yi Chen, Shih Lun Chen, Wei Chen Tu, Patricia Angela R. Abu

Ateneo Laboratory for Intelligent Visual Environments

An apical lesion is caused by bacteria invading the tooth apex through caries. Periodontal disease is caused by plaque accumulation. Peri-endo combined lesions include both diseases and significantly affect dental prognosis. The lack of clear symptoms in the early stages of onset makes diagnosis challenging, and delayed treatment can lead to the spread of symptoms. Early infection detection is crucial for preventing complications. PAs used as the database were provided by Chang Gung Memorial Medical Center, Taoyuan, Taiwan, with permission from the Institutional Review Board (IRB): 02002030B0. The tooth apex image enhancement method is a new technology in PA detection. …

In Silico Modelling And Docking Simulation Of Egfr-Targeted Diphtheria Toxin Chimera With Various Targeting Moieties, Muhammad Afif Naufal Bmed, Benedictus Ansell Susanto Bmed, Talitha Dinda Gunawan Bmed, Azhar Ridha Lukman Bmed, Alifa Rahma Rizqina Bmed, Muhammad Misbahul Fuad Bmed

Indonesian Journal of Medical Chemistry and Bioinformatics

Introduction: Cancer is a major etiology of death worldwide due to high mortality and suboptimal medicine. However, an emerging field, targeted therapy enabled a more selective and effective therapeutic action. This article aims to analyze in-silico the hypothetical targeted therapy agent that is combinations of conjugate consisting of EGFR targeting moieties and diphtheria toxin (DT-390).

Method: Our novel peptide is a conjugate of a novel EGFR targeting peptide and DT-390, forming a chimera. The tertiary structure was predicted using AlphaFold 2.0. The best IDDT scoring and stereochemistry profiles were utilized. The HADDOCK2.4 webserver modelled the docking between our …

The Prospect Of Indonesian Herbal As An Alternative Treatment For Covid-19 Patient: A Literature-Based Study, Hadi Sunaryo, Wahyu Hidayati

Indonesian Journal of Medical Chemistry and Bioinformatics

Coronavirus disease 2019 (COVID-19) is a new disease caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The disease has several symptoms from mild to severe and could lead to death for comorbidities and the elderly. Therefore, the infections and mortality cases keep growing day by day, moreover many authorities are trying to suppress it by applying several health protocols, including medicines. Several studies were conducted on drug discovery from plants to cure the disease. The article aimed to do a narrative review about the prospect of JAMU becoming an alternative medicine to cure COVID-19 by mapping …

Metabolite Biomarker Discovery For Lung Cancer Using Machine Learning, Ariski Fajarido, Linda Erlina, Aryo Tedjo, Fadilah Fadilah, Wawaimuli Arozal

Indonesian Journal of Medical Chemistry and Bioinformatics

Lung cancer is the leading cause of cancer death worldwide. About 2.1 million lung cancer patients were diagnosed in 2018, accounting for about 11.6% of all newly diagnosed cancer cases. For lung cancer, blood is the first choice as a source of screening biomarker candidates. Blood biomarkers provide a snapshot of the patient's entire body, including the primary tumor, metastatic disease, immune response, and peritumoral stroma. However, sputum sampling, bronchial lavage or aspiration, exhaled breath (EB), and airway epithelial sampling represent unique samples for lung cancer and other airway cancers as potential sources for alternative biomarkers. Metabolites are products of …

In-House Polydimethylsiloxane Microfluidic Device On Single Cell Trapping And Culturing Of Leukemia Cell Line: Comparison Between Conventional And Conventional With Centrifugal Methods, Alongkorn Pimpin, Sudchaya Bhanpattanakul, Tepparit Wongpakham, Chomkwan Tawatcharaporn, Thanawit Siha-Umphai, Mookdapa Sinsiriphan, Atikan Chalermchuang, Tewan Tongmanee, Attawut Thanomsridetchai, Thammawit Suwannaphan, Witsaroot Sripumkhaie, Pattaraluck Pattamang, Mayuree Chanasakulniyom, Praprudee Piyaviriyakul, Wutthinun Jeamsaksiri, Achariya Sailasuta, Theerawat Tharasanit, Theerayuth Kaewamatawong

The Thai Journal of Veterinary Medicine

To develop a suitable model to study biological and characterization of Cancer stem cells (CSCs), single cell trapping and culturing using microfluidic techniques have become a high-through put system that can manage and control microenvironment and practical intracellular analysis. The aim of this study was to develop and validate a microfluidic device for single cell trapping and culturing using the leukemia cell line as a cell model. Comparison between conventional and conventional with centrifugal methods was also analyzed. To compare trapping efficacy between these 2 methods, leukemia cell concentration of 1.5×106 cells/ml was loaded with a flow rate of 0.25 …

Sustainable Waste-To-Bioproducts Engineering Center Laboratory Safety Project, Claudine Mock

All Graduate Reports and Creative Projects, Fall 2023 to Present

Laboratory accidents are common in teaching and research labs; these accidents can be injurious or even fatal. The consequences of each type of laboratory accident are different based on the activities performed and the hazardous materials used in each facility. However, the most common issue related to laboratory accidents is the lack of proper safety measures (e.g., poor handling of hazardous materials, not reporting incidents immediately, etc.). This project aimed to establish and strengthen best practices and procedures to ensure laboratory safety at the Utah State University Sustainable Waste-to-Bioproducts Engineering Center. To achieve this goal, different practices and measures were …

The Role Of Kinases Signaling In Organogenesis, Fatemeh Nasehi

All Dissertations

Kinases are crucial regulators of organ development and differentiation. This thesis investi- gates the roles of TAK1, TGFbeta-Activate Kinase 1 (TAK1/Map3K7), and Akt3 kinases in skeletal, cardiac muscle, and cartilage. TAK1 is pivotal for the differentiation of various organ systems, including sinoatrial node and cartilage, and is responsible for phosphorylat- ing a diverse array of downstream kinases. We identified several novel proteins, including phospho-Akts, that are upregulated in response to TAK1 activation. We discovered severe Dilated Cardiomyopathy (DCM) and cartilage defects in Akt3 mutant mice. Although this mouse mutant has been studied for over two decades, we are the first …

Epidural Stimulation For Urogenital Dysfunction In The Spinal Cord Injured Rat., Natasha Lorraine Wilkins

Electronic Theses and Dissertations

Spinal cord injury (SCI) is a devastating, life changing event that greatly impacts quality of life. SCI can have body-wide, multi-system consequences including dysfunction within the urogenital system. Challenges with the urinary system include urinary incontinence, urine retention, and detrusor-sphincter dyssynergia all of which require maintenance through the regular use of catheters. Sexual dysfunction in men, who comprise nearly 80% of the SCI population, includes erectile dysfunction, anejaculation, retrograde ejaculation, poor expulsive force during ejaculation, and poor sperm quality. The treatment for sexual function in SCI men is focused more on fertility through the collection of sperm for insemination procedures …

Evaluation Of The Alveolar Crest And Cemento-Enamel Junction In Periodontitis Using Object Detection On Periapical Radiographs, Tai Jung Lin, Yi Cheng Mao, Yuan Jin Lin, Chin Hao Liang, Yi Qing He, Yun Chen Hsu, Shih Lun Chen, Tsung Yi Chen, Chiung An Chen, Kuo Chen Li, Patricia Angela R. Abu

Ateneo Laboratory for Intelligent Visual Environments

The severity of periodontitis can be analyzed by calculating the loss of alveolar crest (ALC) level and the level of bone loss between the tooth’s bone and the cemento-enamel junction (CEJ). However, dentists need to manually mark symptoms on periapical radiographs (PAs) to assess bone loss, a process that is both time-consuming and prone to errors. This study proposes the following new method that contributes to the evaluation of disease and reduces errors. Firstly, innovative periodontitis image enhancement methods are employed to improve PA image quality. Subsequently, single teeth can be accurately extracted from PA images by object detection with …

Medial Patellofemoral Ligament Augmented With A Reinforced Bioinductive Implant Is Biomechanically Similar To The Native Medial Patellofemoral Ligament At Time Zero In A Cadaveric Model, Sean Mcmillan, Seth Sherman, Zachary Brown, Erik Brewer, Elizabeth Ford

Rowan-Virtua School of Translational Biomedical Engineering & Sciences Departmental Research

Purpose: To biomechanically compare primary medial patellofemoral ligament (MPFL) repair (MPFLr) augmented with a reinforced bioinductive implant (RBI) to the native MPFL ligament and a semitendinosus (semi-T) MPFL reconstruction (MPFLR) at time zero. Methods: Four fresh-frozen matched pair cadavers (8 knees) were used to biomechanically compare the native MPFL to augmented MPFLr (n = 4) and semi-T MPFLR (n = 4). The native MPFL (n = 8) was isolated, preserving the femoral and patellar attachments, and pulled to failure. The semi-T was harvested from 1 of the matched pairs and whipstitched, as was a 250-mm × 5-mm RBI. A standard …

Auxiliary Diagnosis Of Dental Calculus Based On Deep Learning And Image Enhancement By Bitewing Radiographs, Tai Jung Lin, Yen Ting Lin, Yuan Jin Lin, Ai Yun Tseng, Chien Yu Lin, Li Ting Lo, Tsung Yi Chen, Shih Lun Chen, Chiung An Chen, Kuo Chen Li, Patricia Angela R. Abu

Ateneo Laboratory for Intelligent Visual Environments

In the field of dentistry, the presence of dental calculus is a commonly encountered issue. If not addressed promptly, it has the potential to lead to gum inflammation and eventual tooth loss. Bitewing (BW) images play a crucial role by providing a comprehensive visual representation of the tooth structure, allowing dentists to examine hard-to-reach areas with precision during clinical assessments. This visual aid significantly aids in the early detection of calculus, facilitating timely interventions and improving overall outcomes for patients. This study introduces a system designed for the detection of dental calculus in BW images, leveraging the power of YOLOv8 …

Chemotherapy Drug Release From Hollow Core Polyethyleneimine Nanoparticles, Brian Boyle

Theses and Dissertations

Novel anticancer delivery vehicles are arising from engineered nanostructured materials. This work involved the synthesis, characterization, and release of novel hollow core polymeric nanoparticles (HCPNPs) for controlled drug delivery. Polyethyleneimine (PEI) was bound to AuNPs, forming polymer-shell nanoparticles with dissolution of the gold core via iodine forming HCPNPs with drug intercalated DNA bound to the surface. A high density (85 molecules/particle) of DNA intercalated with daunorubicin was conjugated. Particles were spherical with an average diameter of 105.7 ± 17.3 nm and zeta potential of 20.4 ± 3.54 mV. We hypothesize the DNA backbone electrostatically condensed to the primary amines on …

The Role Of Spontaneous Activity In Maturation Of The Calyx Of Held Nerve Terminal And Its Synaptic Target In The Medial Nucleus Of The Trapezoid Body, Daniel Tatsuo Heller

USF Tampa Graduate Theses and Dissertations

Neural circuit formation is a complex process involving synergistic roles between neurons and glial cells regulated by coordinated genetic and molecular cues and activity-dependent mechanisms. The canonical pathway for synapse formation begins with neurogenesis and migration followed by axonal outgrowth and dendritic arborization allowing for the capture and formation of nascent synapses. These initial synaptic contacts are exuberant in nature ensuring proper neural connectivity and undergo a period of pruning of superfluous inputs followed by maturation and strengthening of the remaining contacts. This maturation includes pre- and postsynaptic specialization of the active zone, localization and clustering of ion channels, and …

Aging-Related Changes In The Mechanical Properties Of Single Cells, Amarnath Singam, Chandrabali Bhattacharya, Seungman Park

Mechanical Engineering Faculty Research

Mechanical properties, along with biochemical and molecular properties, play crucial roles in governing cellular function and homeostasis. Cellular mechanics are influenced by various factors, including physiological and pathological states, making them potential biomarkers for diseases and aging. While several methods such as AFM, particle-tracking microrheology, optical tweezers/stretching, magnetic tweezers/twisting cytometry, microfluidics, and micropipette aspiration have been widely utilized to measure the mechanical properties of single cells, our understanding of how aging affects these properties remains limited. To fill this knowledge gap, we provide a brief overview of the commonly used methods to measure single-cell mechanical properties. We then delve into …

Noninvasive Technique For Measuring Cardiac Output, Grace E. Kolar, Rachel Simonton, Eli Strohecker

Williams Honors College, Honors Research Projects

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Evaluating Visual Dependence In Postural Stability Using Smartphone And Stroboscopic Glasses, Brent A. Harper, Michael Shiraishi, Rahul Soangra

Physical Therapy Faculty Articles and Research

This study explores the efficacy of integrating stroboscopic glasses with smartphone-based applications to evaluate postural control, offering a cost-effective alternative to traditional forceplate technology. Athletes, particularly those with visual and visuo-oculomotor enhancements due to sports, often suffer from injuries that necessitate reliance on visual inputs for balance—conditions that can be simulated and studied using visual perturbation methods such as stroboscopic glasses. These glasses intermittently occlude vision, mimicking visual impairments that are crucial in assessing dependency on visual information for postural stability. Participants performed these tasks under three visual conditions: full vision, partial vision occlusion via stroboscopic glasses, and no vision …

Development Of An Advanced Step Counting Algorithm With Integrated Activity Detection For Free Living Environments, Paige M. Dolan

Master's Theses

Physical activity plays a crucial role in maintaining overall health and reducing the risk of various chronic diseases. Step counting has emerged as a popular method for assessing physical activity levels, given its simplicity and ease of use. However, accurately measuring step counts in free-living environments presents significant challenges, with most activity trackers exhibiting a percent error above 20%. This study aims to address these challenges by creating a machine learning algorithm that leverages activity labels to improve step count accuracy in real-world conditions. Two approaches to balancing data were used: one employed a simpler oversampling technique, while the other …

Naturify 2300, Yarina Yiwei Dai

Masters Theses

In my art practice, I explore the interplay between human desires to manipulate and anthropomorphize nature, as seen in the technological augmentation of plants and living entities. This investigation delves into how this intersection, alongside empathy towards these creations, contributes to fears of uncontrollability and the risks of addiction and excessive dependence on technology.

Bioengineering and genetic modification have cultivated unprecedented developments, allowing humans to manipulate the fundamental building blocks of life. My research speculates on this technology further, modifying the genetic code of organisms and creating bioengineered wearable entities with enhanced traits or entirely new functionalities. The primary objective …

Smart Cushion Device For Elderly Aging In Place, Anna Dion, Nate Colley, Leonardo Bravo

Biomedical Engineering

Our task at hand is to develop a consumer-focused solution for improving elder care to provide additional peace of mind for seniors and caregivers using technology to extend independent living. We intend to create a device that will improve the quality of life of elderly individuals living alone by encouraging periodical movement throughout the day, along with monitoring pressure distribution and alerting when pressure concentration is potentially harmful. It will also alert users to the presence of moisture which can arise from spills or incontinence. The key stakeholders of this project include elderly adults over the age of 65 who …