Biomedical Engineering and Bioengineering Commons^™

A Method For Ultrasound Servo Tracking For Puncture Needle, Shitong Ye, Bo Yang, Hao Quan, Shan Liu, Minyu Tang, Jiawei Tian

Electrical & Computer Engineering Faculty Publications

Computer-aided surgical navigation technology helps and guides doctors to complete the operation smoothly, which simulates the whole surgical environment with computer technology, and then visualizes the whole operation link in three dimensions. At present, common image-guided surgical techniques such as computed tomography (CT) and X-ray imaging (X-ray) will cause radiation damage to the human body during the imaging process. To address this, we propose a novel Extended Kalman filter-based model that tracks the puncture needle-point using an ultrasound probe. To address the limitations of Kalman filtering methods based on position and velocity, our method of Kalman filtering uses the position …

A Customized Large Single-Piece Bifrontal Implant For Post-Craniectomy Defect Reconstruction: A Case Study, Omid Ghaderzadeh, Ehsan Amirbeyk, Seyed Roholah Ghodsi, Zahra Namazi, Lobat Tayebi

Electrical & Computer Engineering Faculty Publications

Background: Large bifrontal defects pose unique reconstruction challenges due to their complex curvature and mechanical requirements. This case demonstrated how computer-aided design/manufacturing (CAD/CAM) enabled precise single-piece polymethyl methacrylate (PMMA) implant fabrication, thereby overcoming traditional limitations. Case presentation: A 25-year-old male who had undergone bifrontal decompressive craniectomy suffered a severe traumatic brain injury. The autologous bone flap had been temporarily stored in a subcutaneous fat area of the abdomen for 3 months to preserve its viability. A secondary cranioplasty was then performed using titanium miniplates and self-tapping screws for final fixation. After 2 years, the patient developed empyema and a brain …

Development Of 2d Microfluidics Surface With Low-Frequency Electric Fields For Cell Separation Applications, Madushan Wickramasinghe, Dharmakeerthi Nawarathna

Electrical & Computer Engineering Faculty Publications

Cell separation techniques are widely used in many biomedical and clinical applications for the development of screening, diagnosis and therapeutic tests. Current 3D microfluidics-based cell separation methods have limited applications in part due to low throughput and technical complexity. To address these critical needs, we have developed a 2D microfluidics surface which is the miniaturized version of a 3D microfluids cell separation device. Using low-frequency electric fields (1–10 Vpp and 1 kHz–20 MHz), we have first studied dielectrophoresis, AC electro-osmosis and capillary flow within a sessile drop, and finally utilized the results to develop the 2D cell separation surface. Our …

Benchmarking Batch-Effect Correction Methods Towards The Construction Of A Triple-Negative Breast Cancer Cell Atlas, Peter Scheible, Amy H. Tang, Jing He, Jiangwen Sun

Computer Science Faculty Publications

Triple-negative breast cancer (TNBC) requires detailed cellular mapping given its aggressive nature, immense tumor heterogeneity and genetic diversity. We integrated 156,794 cells from six scRNA-seq datasets—including tumors, metastases, and cell lines—to build a TNBC scRNA cell atlas, focusing on batch effect mitigation while maintaining biological and molecular details. Preprocessing f ilters noise, normalizes data, and leverages PCA for integration readiness. We utilized scANVI, a semi-supervised tool, to align datasets, preserving TNBC’s complex tumor heterogeneity via marker annotations [1]. UMAPs demonstrate biological clustering in integrated data, contrasted with datasetdriven unintegrated patterns. Assessments verifying effective batch correction. This method aligns with NASA’s …

Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for molecular flexibility and the high sparsity of CPI data. Here, we introduce ColdstartCPI, a framework inspired by induced-fit theory, which leverages unsupervised pre-training features and a Transformer module to learn both compound and protein characteristics. ColdstartCPI treats proteins and compounds as flexible molecules during inference, aligning with biological insights. It outperforms state-of-the-art sequence-based models, particularly for unseen compounds and proteins, and shows strong generalization capability …

Insights In Adaptation: Examining Self-Reflection Strategies Of Job Seekers With Visual Impairments In India, Akshay Kolgar Nayak, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok

Computer Science Faculty Publications

Significant changes in the digital employment landscape, driven by rapid technological advancements and the COVID-19 pandemic, have introduced new opportunities for blind and visually impaired (BVI) individuals in developing countries like India. However, a significant portion of the BVI population in India remains unemployed despite extensive accessibility advancements and job search interventions. Therefore, we conducted semi-structured interviews with 20 BVI persons who were either pursuing or recently sought employment in the digital industry. Our findings reveal that despite gaining digital literacy and extensive training, BVI individuals struggle to meet industry requirements for fulfilling job openings. While they engage in self-reflection …

In Vitro Comparative Study Of Composite Coatings For Magnesium-Based Bone Implants, Abdelrahman Amin, Bryce Williams, Thomas Mcgehee, Alyssandra Navarro, Vipul Patil, Mostafa Elsaadany, Hanna Ibrahim

Biomedical Engineering Faculty Publications and Presentations

This study provides a comparative assessment of the corrosion, morphology, and biological properties of four of the most promising coating methods for magnesium in biomedical applications, namely micro-arc oxidation (MAO), graphene oxide (GO)-containing MAO coating, MAO/sol-gel composite coating, and MAO/polycaprolactone (PCL) polymer dip coating approaches. Despite the abundance of research focused on these promising coating approaches, there is a notable lack of comparative studies evaluating their properties. To this end, the investigated composite coatings are ZK60+MAO, ZK60+MAO/GO, ZK60+MAO/Sol-gel, and ZK60+MAO/PCL composite coating. Several tests were used to assess various properties of the prepared groups such as in vitro corrosion characteristics, …

Finite Element Simulation Of Interstitial–Lymphatic Fluid Flow And Nanodrug Transport In A Solid Tumor: An Intratumoral Injection Approach, Gobinda Debnath, Buddakkagari Vasu, Rama Subba Reddy Gorla

Faculty Publications

Objective: This study presents a mathematical model and finite element simulations to investigate interstitial fluid flow and nanodrug transport in a solid tumor, incorporating transvascular exchange, convection–diffusion–reaction dynamics, and intratumoral injection mechanisms. Impact Statement: Optimizing nanodrug distribution remains a critical challenge in cancer therapy. The proposed model advances nanomedicine by enhancing the mechanistic understanding of nanodrug transport in a solid tumor. Introduction: Cancer, a global threat, often manifests as solid tumors driven by uncontrolled cell growth. The heterogeneous microenvironment, lymphatic drainage, nano-bio interactions, and elevated interstitial fluid pressure (IFP) hinder effective nanodrug delivery. Nanoparticle (NP)-based drug delivery systems offer a …

Evaluation Of The Dnazyme Gr5 For The Determination Of Lead Speciation In Natural Waters, Gaganprit Gill

Theses and Dissertations (Comprehensive)

This thesis explores the development and application of a DNAzyme-based biosensor designed to detect labile metal species in environmental samples. Real time and on-site monitoring of labile metal fractions would make a valuable contribution to environmental management, as these fractions are the most bioavailable and pose significant toxicity risks to aquatic organisms. Conventional methods for detecting labile metals, while effective, are often burdened by high costs, complexity, and lengthy processing times, making them less ideal for rapid and widespread environmental assessments.

The first manuscript of this thesis (chapter 2) establishes the fundamental capabilities of the Pb²⁺-specific DNAzyme GR5 …

Optical Methods For Time-Resolved Dosimetry And Oximetry Of Ultra-High Dose Rate Radiation Therapy, Megan A. Clark

Dartmouth College Ph.D Dissertations

Radiotherapy (RT) is a cornerstone method used to treat over 50% of the 2 million new cancer diagnoses each year in the United States. The success of RT directly relies on an optimal balance between maximizing the dose to the tumor while minimizing dose to surrounding normal tissues. Achieving this balance is often challenging due to underlying radiation transport and the presence of anatomical constraints that limit the beam delivery geometry. In turn, minimizing healthy tissue toxicity prevents use of a more aggressive tumor killing approach, and even in curative cases may decrease the patient’s quality of life due to …

Increased Visual Response Delay Impact On Sensorimotor Control In Persons With Multiple Sclerosis, Julie C. Wagner, Frankie M. Ingram, Vincenzo Daniele Boccia, Matilde Inglese, Maura Casadio, Camilla Pierella, Andrea Canessa, Robert A. Scheidt, Scott A. Beardsley

Biomedical Engineering Faculty Research and Publications

Multiple Sclerosis negatively affects hand function in 60% of cases. Upper extremity dysfunction in persons with Multiple Sclerosis (PwMS) has previously been linked to slower, more variable movement, increased visual response delays (T_v), and neuroimaging evidence of altered brain activity; yet no one knows how these aspects relate to each other. This work combines clinical, kinematic, sensorimotor control, and neural imaging techniques to gain a more complete understanding of how upper extremity dysfunction arises in PwMS. Twenty PwMS and 20 Controls completed a reach and hold task with simultaneous electroencephalography recorded to determine if increased T_v in …

Lung Uptake Of Two Spect Markers Identifies Sensitivity To Hyperoxia-Induced Acute Respiratory Distress Syndrome In Rats, Anne V. Clough, Taheri Pardis, Guru P. Sharma, Ming Zhao, Elizabeth R. Jacobs, Said H. Audi

Biomedical Engineering Faculty Research and Publications

Introduction: Exposure of adult rats to hyperoxia is a well-established model of human Acute Respiratory Distress Syndrome (ARDS). Although rats exposed to 100% O₂ display clinical evidence of lung injury after ∼40 h and death by 72 h, rats exposed to 60% O₂ for up to 7 days show little sign of injury. However, when subsequently exposed to hyperoxia, these pre-exposed rats become more susceptible to ARDS. The objective of this study is to evaluate the ability of imaging biomarkers to track this hyperoxia susceptibility and to elucidate underlying mechanisms.

Methods: Sprague-Dawley rats were exposed to either room …

Scoping Review Of Machine Learning Techniques In Marker-Based Clinical Gait Analysis, Kevin N. Dibbern, Maddalena G. Krzak, Alejandro Olivas, Mark V. Albert, Joseph J. Krzak, Karen M. Kruger

Biomedical Engineering Faculty Research and Publications

The recent proliferation of novel machine learning techniques in quantitative marker-based 3D gait analysis (3DGA) has shown promise for improving interpretations of clinical gait analysis. The objective of this study was to characterize the state of the literature on using machine learning in the analysis of marker-based 3D gait analysis to provide clinical insights that may be used to improve clinical analysis and care. Methods: A scoping review of the literature was conducted using the PubMed and Web of Science databases. Search terms from eight relevant articles were identified by the authors and added to by experts in clinical gait …

Determination Of Electrochemical Parameters For Predicting Reaction Mechanism And Algorithmic Approaches To Pain Assessment, Huize Xue

Dissertations

This dissertation introduces novel advancements in electrochemical kinetics and pain assessment, structured into two main parts. The first part focuses on the comprehensive analysis of the kinetic and mechanistic aspects of electrochemical reactions, utilizing a combination of experimental techniques and simulation methods. A new software tool, Envismetrics, was developed using Python to facilitate the analysis of complex electrochemical data, including cyclic voltammetry (CV), chronoamperometry (CA), and hydrodynamic voltammetry (HDV). The software was rigorously tested and validated with well-characterized redox systems such as the ferricyanide/ferrocyanide couple, dimethylamine borane (DMAB), and Per- and Polyfluoroalkyl Substances (PFAS). It was successfully used to determine …

Automated Segmentation Of The Ulnar Nerve In Mri Using Deep Learning Techniques, Akhil Nagulapalli

Theses

Cubital Tunnel Syndrome (CuTS), a condition caused by compression of the ulnar nerve, results in numbness, tingling, pain, and even muscle atrophy, affecting fine motor skills and diminishing patient quality of life. Accurate diagnosis of CuTS is challenging, as current diagnostic methods—including clinical exams, nerve conduction studies, and unaided MRI—often lack the precision to reliably identify the nerve and detect compression in its early stages. Deep learning-based segmentation offers a promising solution, enabling precise and automated identification of nerve structures in MRI images, which could significantly improve diagnostic accuracy and support timely intervention.

A novel deep learning model for segmenting …

Energy-Efficient Technologies For Drying Mulberry Silkworm Cocoons Using Infrared Radiation, Doston Ishmukhammat Ugli Samandarov

Technical science and innovation

The article presents the results of theoretical and experimental studies on drying of mulberry silkworm cocoons. Based on the analysis of drying efficiency and silk quality, the use of infrared radiation (IR) at a temperature of 70 °C was found to be optimal. The experimental data were tested on six mathematical models, among which the Midilli model most accurately described the drying process. The effective moisture diffusion coefficient was found to vary in the range of 1.847×10^-⁹-4.339×10^-⁹ m²/s, and the drying rate was found to be 0.32-0.79 kg of water/hour. IR radiation promotes accelerated evaporation of …

Energy Saving Technology For Drying Garlic (Allium Sativum), Jasur Esirgapovich Safarov, Shakhnoza Abduvaxitovna Sultanova, А M. Mirkomilov

Technical science and innovation

Food drying is a widely used preservation method aimed at reducing water content to extend shelf life, decrease weight, and enhance storage efficiency. This process, particularly in garlic, involves rapid initial moisture loss followed by a slower phase due to the increasing difficulty of extracting residual water. Drying methods include natural solar drying and advanced mechanical techniques such as hot air and vacuum drying, each influencing product quality, drying efficiency, and economic feasibility. Dehydrated garlic exhibits specific sensory, physico-chemical, and microbiological characteristics, making it suitable for various applications, including powder production. Advanced drying equipment optimizes air volume, temperature, and material …

Influence Of Fused Deposition Modeling Process Parameters On The Constitutive Model Of Hyperelastic Thermoplastic Polyurethane, Lucas Gallup, Mohamed Trabia, Brendan O'Toole, Youssef Fahmy

Mechanical Engineering Faculty Research

Thermoplastic polyurethanes (TPUs) are suited for fused deposition modeling (FDM) of parts that require high levels of flexibility and strength. Predicting the deformation of TPU parts produced using FDM may be difficult, especially under large deformations, as their constitutive models depend on the printing process parameters. The lack of understanding led to the absence of constitutive models for TPU parts produced using FDM. This work aims to identify accurate hyperelastic constitutive models. Six groups of uniaxial tensile specimens were produced using FDM. These groups were made with variations in two process parameters, which were infill geometry and extrusion nozzle temperature. …

Movian: Advancing Human Motion Analysis With 3d Visualization And Annotation, Trudi Di Qi, Isaac Browen, David Zhang, Hector M. Camarillo-Abad, Franceli L. Cibrian

Engineering Faculty Articles and Research

Human motion analysis, including data visualization and annotation, is crucial for understanding human behavior and intentions during various activities, aiding in the development of innovative tools that support independent living. Current wearable sensing technology provides rich 3D spatial movement data but generates multimodal complex datasets that require specialized skills for effective analysis. Despite the need, limited research exists on tools for effective visualization and easy annotation of such complex motion data. MoViAn (Motion Data Visualization and Annotation) is an innovative 3D data analysis system offering enriched visual representations of 3D human motion data (e.g., gaze, hand movements), along with an …

Microwell Fabrication For Impedance And Ac Measurements Of Isolated Ventricular Cardiomyocytes, Fallon Wenck

Multidisciplinary Studies Theses and Dissertations

Electrophysiological behavior of human hearts have been extensively studied for hundreds of years. Even with elucidation of not just biological function, but also time and frequency-dependent current flow, the sheer intricacy of in vivo cardiac tissue function remains somewhat enigmatic. All while heart disease has been the leading cause of death in the United States for over a century, with its rates of occurrence still increasing annually [1]. Thus, new research techniques and tools to quantify cardiac function are still being pursued at smaller and smaller scales to decrease research/innovation time, cost, and diagnostic ambiguity. In fact, it remains incredibly …