Biomedical Engineering and Bioengineering Commons^™

Effects Of Indole Derivative Idc16 On Cell Proliferation, Transfection, And Alternative Splicing In Production Of Lentiviral Vectors By Transient Co-Transfection, Nataly Mier

All Graduate Theses and Dissertations, Fall 2023 to Present

Viruses can efficiently introduce genetic material into a variety of cells through cell infection. Therefore, viral vectors, defined as virus-based gene delivery systems, effectively transfer functional gene constructs to target cells. Among different viral vectors, lentiviral vectors are of interest due to the advantages offered to research and therapeutic applications. Low productivity of lentiviral vectors in mammalian producer cells and high production cost, however, remain barriers to the vectors’ routinary use, particularly in clinical settings.

Since most lentiviral vectors are derived from human immunodeficiency virus type I, their genome has been engineered to increase safety. Nevertheless, modifications of the lentiviral …

Evaluating Differences In Optical Properties Of Indolent And Aggressive Murine Breast Tumors Using Quantitative Diffuse Reflectance Spectroscopy, Joel Rodriguez Troncoso, Umme Marium Mim, Jesse D. Ivers, Santosh K. Paidi, Mason G. Harper, Khue G. Nguyen, Sruthi Ravindranathan, Lisa Rebello, David E. Lee, David A. Zaharoff, Ishan Barman, Narasimhan Rajaram

Biomedical Engineering Faculty Publications and Presentations

We used diffuse reflectance spectroscopy to quantify tissue absorption and scattering-based parameters in similarly sized tumors derived from a panel of four isogenic murine breast cancer cell lines (4T1, 4T07, 168FARN, 67NR) that are each capable of accomplishing different steps of the invasion-metastasis cascade. We found lower tissue scattering, increased hemoglobin concentration, and lower vascular oxygenation in indolent 67NR tumors incapable of metastasis compared with aggressive 4T1 tumors capable of metastasis. Supervised learning statistical approaches were able to accurately differentiate between tumor groups and classify tumors according to their ability to accomplish each step of the invasion-metastasis cascade. We investigated …

Representativeness Evaluation Of Delta-Flux Eddy Covariance Towers For Assessing Greenhouse Gas Emissions From Rice Fields In The Mid-South Region, Katherine Skiles

Biological and Agricultural Engineering Undergraduate Honors Theses

Rice grown in 5 states across the Mid-South (AR, LA, MS, TX, and MO) account for nearly 80% of all domestic U.S. rice production. Methane emissions produced during rice farming and the large seasonal water demand to maintain flooded fields have created a need for alternative irrigation research that can reduce methane emissions and conserve water. Structures called eddy covariance towers (ECTs) can observe methane and other flux responses to changing irrigation styles, and their data is shared across flux tower networks such as Delta-Flux in the Mid-South. The Delta-Flux network is relatively new, and its data-sharing capacity is not …

Characterizing Intervertebral Disc Strain Under Dynamic Loading Conditions Using Ultrasound Texture Analysis, Radhika Kulkarni

Discovery Undergraduate Interdisciplinary Research Internship

Herniated discs in the spine are a significant patient burden, with potential links to lower back and leg discomfort and a considerable impact on daily life. These discs, located between spinal vertebrae, are comprised of the annulus fibrosus (AF) and the nucleus pulposus (NP). Herniations happen when the NP protrudes through a full-thickness annular tear, possibly compressing spinal nerves. The mechanical factors underlying herniated discs are poorly understood, necessitating research into these mechanisms and accessible diagnostic techniques. Our study employs high-resolution ultrasound and texture correlation to quantify strain patterns in intervertebral discs during dynamic loading.

A motion segment from the …

Controlled Radiation Capsule For Precision And Rapid Cancer Treatment, Hoseon Lee, Zsolt Kollar, Bailey R. White, Junia Nguyen, David Roque, Sowjanya Palagani

Symposium of Student Scholars

This research aims to transform cancer treatment through the optimization of brachytherapy, with a focus on reducing treatment duration, setup complexities, and financial burdens, all while emphasizing patient safety. Patients living at a distance from radiation clinics, particularly those undergoing extended Low Dose Radiation brachytherapy, often struggle with the formidable financial challenges associated with securing nearby accommodations. In response to these issues, the research introduces a radiation capsule designed to condense the conventional six-month treatment period to approximately just one week, thereby significantly reducing the duration of required accommodations. This capsule is especially relevant considering the construction cost of $40 …

Deep Multi-Stage System For Liver And Lesions Segmentation Using Ct Images, Nermeen Elmenabawy, Mervat El-Seddek, Hossam El-Din Moustafa, Ahmed Elnakib

Mansoura Engineering Journal

Accurate tumor segmentation plays a pivotal role in cancer diagnosis and treatment planning. This study introduces an automated system for segmenting liver and tumors in CT images through a multi-stage process. Initial preprocessing improves image quality, followed by feature extraction using pretrained VGG16-Segnet and FCNAlexnet models. Outputs from both models are combined using a parallel fusion operation. Finally, pixel-wise classification designates pixels as liver, tumor, or background. Evaluation on the MICCAI'2017 LiTS database yielded a Dice coefficient of 95.3% for liver and 78.1% for tumors using 5-fold cross-validation. Comparative studies highlight the superior accuracy of our approach in liver and …

Occlusive Membranes For Guided Regeneration Of Inflamed Tissue Defects., Woojin Choi, Utkarsh Mangal, Jin-Young Park, Ji-Yeong Kim, Taesuk Jun, Ju Won Jung, Moonhyun Choi, Sungwon Jung, Milae Lee, Ji-Yeong Na, Du Yeol Ryu, Jin Man Kim, Jae-Sung Kwon, Won-Gun Koh, Sangmin Lee, Patrick T J Hwang, Kee-Joon Lee, Ui-Won Jung, Jae-Kook Cha, Sung-Hwan Choi, Jinkee Hong

Henry M. Rowan College of Engineering Departmental Research

Guided bone regeneration aided by the application of occlusive membranes is a promising therapy for diverse inflammatory periodontal diseases. Symbiosis, homeostasis between the host microbiome and cells, occurs in the oral environment under normal, but not pathologic, conditions. Here, we develop a symbiotically integrating occlusive membrane by mimicking the tooth enamel growth or multiple nucleation biomineralization processes. We perform human saliva and in vivo canine experiments to confirm that the symbiotically integrating occlusive membrane induces a symbiotic healing environment. Moreover, we show that the membrane exhibits tractability and enzymatic stability, maintaining the healing space during the entire guided bone regeneration …

The Effects Of Engineering Summer Camps On Middle And High School Students’ Engineering Interest And Identity Formation: A Multi-Methods Study, Timothy Robinson, Adam Kirn, Jenny Amos, Indira Chatterjee

Journal of Pre-College Engineering Education Research (J-PEER)

This multi-methods study explores changes in engineering interest and identity of middle and high school students (n = 79) attending introductory-level engineering summer camps at a large western land grant university. Middle school is a critical time when student interest, identity, and subsequently career choice begin to emerge and hence it is important that at this age students are given accurate information about engineering majors in college and future career opportunities in engineering. Data were collected over a period of two years in six summer camps. Three separate populations of middle and high school students participated in the summer …

Real-Time Arrhythmia Detection Using Convolutional Neural Networks, Thong Vu, Tyler Petty, Kemal Yakut, Muhammad Usman, Wei Xue, Francis M. Haas, Robert A. Hirsh, Xinghui Zhao

Henry M. Rowan College of Engineering Departmental Research

Cardiovascular diseases, such as heart attack and congestive heart failure, are the leading cause of death both in the United States and worldwide. The current medical practice for diagnosing cardiovascular diseases is not suitable for long-term, out-of-hospital use. A key to long-term monitoring is the ability to detect abnormal cardiac rhythms, i.e., arrhythmia, in real-time. Most existing studies only focus on the accuracy of arrhythmia classification, instead of runtime performance of the workflow. In this paper, we present our work on supporting real-time arrhythmic detection using convolutional neural networks, which take images of electrocardiogram (ECG) segments as input, and classify …

Evolutionary Conservation And Times Of Action Of Heterochronic Genes, Maria Ivanova

Theses and Dissertations

The heterochronic pathway of C. elegans is the most well-characterized system to date for controlling the sequence and timing of developmental events. However, we still have critical unanswered questions to address. First, little is known about the evolution of the heterochronic pathway, and of developmental timing in general. To determine if the roles of major heterochronic genes are conserved, I made mutants in orthologs of these genes in C. briggsae, using CRISPR/Cas9. My studies revealed a significant drift in the roles of some of the genes, although all of them are still involved in the developmental timing regulation, and several …

Differential Impact Of Blood Pressure Control Targets On Epicardial Coronary Flow After Transcatheter Aortic Valve Replacement, Brennan Vogl, Alejandra Chavez-Ponce, Adam Wentworth, Eric Erie, Pradeep Yadav, Vinod H. Thourani, Lakshmi Prasad Dasi, Brian Lindman, Mohamad Alkhouli, Hoda Hatoum

Michigan Tech Publications

Background: The cause for the association between increased cardiovascular mortality rates and lower blood pressure (BP) after aortic valve replacement (AVR) is unclear. This study aims to assess how the epicardial coronary flow (ECF) after AVR varies as BP levels are changed in the presence of a right coronary lesion. Methods: The hemodynamics of a 3D printed aortic root model with a SAPIEN 3 26 deployed were evaluated in an in vitro left heart simulator under a range of varying systolic blood pressure (SBP) and diastolic blood pressure (DBP). ECF and the flow ratio index were calculated. Flow index value …

Transport Barriers Influence The Activation Of Anti-Tumor Immunity: A Systems Biology Analysis, Mohammad R. Nikmaneshi, James W. Baish, Hengbo Zhou, Lance L. Munn

Faculty Journal Articles

Effective anti-cancer immune responses require activation of one or more naïve T cells. If the correct naïve T cell encounters its cognate antigen presented by an antigen presenting cell, then the T cell can activate and proliferate. Here, mathematical modeling is used to explore the possibility that immune activation in lymph nodes is a rate-limiting step in anti-cancer immunity and can affect response rates to immune checkpoint therapy. The model provides a mechanistic framework for optimizing cancer immunotherapy and developing testable solutions to unleash anti-tumor immune responses for more patients with cancer. The results show that antigen production rate and …

Integrative Transcriptomics And Proteomics Profiling Of Arabidopsis Thaliana Elucidates Novel Mechanisms Underlying Spaceflight Adaptation, Gbolaga O. Olanrewaju, Natasha J. Haveman, Michael J. Naldrett, Anna-Lisa Paul, Robert J. Ferl, Sarah E. Wyatt

Nebraska Center for Biotechnology: Faculty and Staff Publications

Spaceflight presents a unique environment with complex stressors, including microgravity and radiation, that can influence plant physiology at molecular levels. Combining transcriptomics and proteomics approaches, this research gives insights into the coordination of transcriptome and proteome in Arabidopsis’ molecular and physiological responses to Spaceflight environmental stress. Arabidopsis seedlings were germinated and grown in microgravity (μg) aboard the International Space Station (ISS) in NASA Biological Research in Canisters – Light Emitting Diode (BRIC LED) hardware, with the ground control established on Earth. At 10 days old, seedlings were frozen in RNA-later and returned to Earth. RNA-seq transcriptomics and TMTlabeled LC-MS/MS proteomic …

Computational Modeling Using A Novel Continuum Approach Coupled With Pathway-Informed Neural Networks To Optimize Dynein-Mediated Centrosome Positioning In Polarized Cells, Arkaprovo Ghosal, Padmanabhan Seshaiyar Dr., Adriana Dawes Dr., General Genomics Inc.

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Multicellular And Multiscale Models Of Microbes And Host Systems, Elebeoba May

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Multi-Organ Maize Metabolic Model Connects Temperature Stress With Energy Production And Reducing Power Generation, Niaz Bahar Chowdhury, Margaret Simons- Senftle, Berengere Decouard, Isabelle Quillere, Martine Rigault, Karuna Anna Sajeevan, Bibek Acharya, Ratul Chowdhury, Bertrand Hirel, Alia Dellagi, Costas Maranas, Rajib Saha

Department of Chemical and Biomolecular Engineering: Faculty Publications

Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolicmodel, iZMA6517, and contextualized itwith heat and cold stress transcriptomics data using expression distributed reaction flux measurement (EXTREAM) algorithm. Furthermore, implementing metabolic bottleneck analysis on contextualized models revealed differences between these stresses. While both stresses had reducing power bottlenecks, heat stress had additional energy generation bottlenecks.We also performed thermodynamic driving force analysis, revealing thermodynamics-reducing power-energy generation axis dictating the nature of temperature stress responses. Thus, a temperaturetolerant maize ideotype can …

S-Net: A Multiple Cross Aggregation Convolutional Architecture For Automatic Segmentation Of Small/Thin Structures For Cardiovascular Applications, Nan Mu, Zonghan Lyu, Mostafa Rezaeitaleshmahalleh, Cassie Bonifas, Jordan Gosnell, Marcus Haw, Joseph Vettukattil, Jingfeng Jiang

Michigan Tech Publications

With the success of U-Net or its variants in automatic medical image segmentation, building a fully convolutional network (FCN) based on an encoder-decoder structure has become an effective end-to-end learning approach. However, the intrinsic property of FCNs is that as the encoder deepens, higher-level features are learned, and the receptive field size of the network increases, which results in unsatisfactory performance for detecting low-level small/thin structures such as atrial walls and small arteries. To address this issue, we propose to keep the different encoding layer features at their original sizes to constrain the receptive field from increasing as the network …

Novel Method Of The Quantification Of Turbulent Fluid Flow In Silicone Artery Phantoms Using Acoustic Analysis, Julia Wong

Master's Theses

Cardiovascular disease is the leading cause of death globally and is responsible for taking 17.9 million lives per year. Despite the use of clinical treatments and detection methods, there remains a large population of individuals that suffer from CVD whose symptoms are left undetected and untreated prior to a life-threatening cardiac event. This highlights a need for an early detection method that can prevent the manifestation and worsening of the disease as well as address limitations of current early detection methods. An area of interest for early detection of CVD is subclinical atherosclerosis, which is the long, early, asymptomatic stage …

Development Of An Angiogenic Tissue-On-A-Chip Microenvironment, Eric Stuehr

Master's Theses

Preclinical testing is necessary to investigate the safety and efficacy of novel therapeutics before moving to clinical trials, yet approximately 90% of these therapies fail once tested in humans. This has led to increased interest in developing robust preclinical models that accurately mimic the complex human in vivo physiology. Microfluidic devices that can introduce dynamic conditions to 3D cell/organoid cultures, also known as tissue-on-a-chip, have emerged as physiologically relevant in vitro preclinical models that can achieve high throughput screening of therapeutics. The research presented here aimed to develop an angiogenic environment within a novel microfluidic device to stimulate formation of …

Pedicle Screw Placement Accuracy In Robot-Assisted Spinal Fusion In A Multicenter Study, Victoria L. Volk, Keegan A. Steele, Mia Cinello‑Smith, Richard V. Chua, John Pollina, Gregory Poulter, Eiman Shafa, Peter Busselberg, Clare K. Fitzpatrick

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Pedicle screw fixation is a spinal fusion technique that involves the implantation of screws into vertebral pedicles to restrict movement between those vertebrae. The objective of this research is to measure pedicle screw placement accuracy using a novel automated measurement system that directly compares the implanted screw location to the planned target in all three anatomical views. Preoperative CT scans were used to plan the screw trajectories in 122 patients across four surgical centers. Postoperative scans were fused to the preoperative plan to quantify placement accuracy using an automated measurement algorithm. The mean medial–lateral and superior–inferior deviations in the pedicle …