Biomedical Engineering and Bioengineering Commons^™

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 …

Microbial Glycosylation Of Antitubercular Agent Chlorflavonin, Jie Ren, Jixun Zhan

Biological Engineering Faculty Publications

Flavonoids have shown health-benefiting properties, such as antioxidative and anti-inflammatory activities, and are commonly used as nutraceuticals and pharmaceuticals. Although flavonoids are predominantly identified from plants, several filamentous fungal species have also been reported to produce bioactive flavonoids, including chlorflavonin from Aspergillus candidus, a novel halogenated flavonoid with potent antifungal and antitubercular (anti-TB) activities. Unfortunately, the low water-solubility of this molecule may hinder its bioavailability. Glycosylation is an effective method to enhance the polarity of natural products and alter their physicochemical properties. This work focuses on the development of novel water-soluble chlorflavonin derivatives to combat the threat of drug-resistant …

Autofluorescence Imaging Of Endogenous Metabolic Cofactors In Response To Cytokine Stimulation Of Classically Activated Macrophages, Shelby N. Bess, Matthew J. Igoe, Abby C. Denison, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Background

Macrophages are one of the most prevalent subsets of immune cells within the tumor microenvironment and perform a range of functions depending on the cytokines and chemokines released by surrounding cells and tissues. Recent research has revealed that macrophages can exhibit a spectrum of phenotypes, making them highly plastic due to their ability to alter their physiology in response to environmental cues. Recent advances in examining heterogeneous macrophage populations include optical metabolic imaging, such as fluorescence lifetime imaging (FLIM), and multiphoton microscopy. However, the method of detection for these systems is reliant upon the coenzymes NAD(P)H and FAD, which …

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 …

Sarcopenia Is Associated With Osteopenia And Impaired Quality Of Life In Children With Genetic Intrahepatic Cholestatic Liver Disease, Julia Boster, Nathan P. Goodrich, Cathie Spino, Kathleen M. Loomes, Estella M. Alonso, Binita M. Kamath, Ronald J. Sokol, Saul J. Karpen, Alexander Miethke, Benjamin L. Shneider, Jean P. Molleston, Rohit Kohli, Simon P. Horslen, Philip Rosenthal, Pamela L. Valentino, Jeffrey Teckman, Thomas N. Hangartner, Sundaram Shikha

Biomedical, Industrial & Human Factors Engineering Faculty Publications

Background:
Sarcopenia occurs in pediatric chronic liver disease, although the prevalence and contributing factors in genetic intrahepatic cholestasis are not well-described. The objective of this study was to measure muscle mass in school-aged children with genetic intrahepatic cholestasis and assess relationships between sarcopenia, clinical variables, and outcomes.

Methods:
Estimated skeletal muscle mass (eSMM) was calculated on dual-energy x-ray absorptiometry obtained in a Childhood Liver Disease Research Network study of children with bile acid synthesis disorders(BASD) alpha-1 antitrypsin deficiency (a1ATd), chronic intrahepatic cholestasis (CIC), and Alagille syndrome (ALGS). Relationships between eSMM, liver disease, and transplant-free survival were assessed.

Results:
eSMM was …

Computational Methodology For Generating Patient-Specific Soft Tissue Representations, Ahilan Anantha Krishnan

Electronic Theses and Dissertations

This dissertation focused on modeling specimen-specific soft tissue structures in the context of joint replacement surgery. The research addressed four key aspects. The first study involved developing a workflow for creating finite element models of the hip capsule to replicate its torque-rotational response. Experimental data from ten cadaveric hips were used to calibrate the models, resulting in improved accuracy and relevance for surgical planning and implant design. The second study tackled the challenge of expediting the calibration of mechanical properties of the hip capsule to match patient-specific laxities. A statistical shape function model was proposed to generate patient-specific finite element …

Exploration Of Motion Capture System To Investigate Human Shoulder Kinematics, Ola Alsaadi

Electronic Theses and Dissertations

The glenohumeral joint (GH) is commonly conceptualized as a ball-and-socket joint [1], and its center of rotation (COR) is presumed to coincide with the geometric center of the medial-superior region of the humeral head [2]. Recent research has endorsed improvements in COR estimation through invasive and noninvasive techniques, including cadaver studies, stereophotogrammetry, and motion capture (MOCAP) systems. Despite increased interest in wearable technology within human movement analysis, the problem of COR estimation employing MOCAP systems and its validation against bi-planar fluoroscopy remains relatively unexplored.

This study employed a marker-based MOCAP system to compare the accuracy, error, and precision of three …

Kinematic Analysis Of Gait And Deep Knee Flexion For Pre- And Post-Operative Total Knee Arthroplasty, Samantha Collins

Electronic Theses and Dissertations

Osteoarthritis (OA) is a form of arthritis that develops in the joint due to overuse and aging causing pain, discomfort, and disability. Total Knee Arthroplasty (TKA) is a surgical procedure performed when OA symptoms are severe with an estimated 600,000 patients in the United States currently receiving TKA. Studies have reported dissatisfaction of the knee for 14-39% of patients. This study collected knee kinematics before and after surgery using stereo radiography for precise measurement of gait and deep knee flexion activities. Results showed healthy knee kinematics were not restored and no significant changes could be seen from OA kinematics in …

Digital Twins Of The Living Knee: From Measurements To Model, Thor Erik Andreassen

Electronic Theses and Dissertations

Modern medicine has dramatically improved the lives of many. In orthopaedics, robotic surgery has given clinicians superior accuracy when performing interventions over conventional methods. Nevertheless, while these and many other methods are available to ensure treatments are performed successfully, far fewer methods exist to predict the proper treatment option for a given person. Clinicians are forced to categorize individuals, choosing the best treatment on “average.” However, many individuals differ significantly from the “average” person, for which many of these treatments are designed. Going forward, a method of testing, evaluating, and predicting different treatment options' short- and long-term effects on an …

Knowledge Integration In Domain-Informed Machine Learning And Multi-Scale Modeling Of Nonlinear Dynamics In Complex Systems, Phat K. Huynh

USF Tampa Graduate Theses and Dissertations

Nonlinear dynamical systems have been extensively used to model various phenomena in the changing world around us, especially in science and engineering fields. Thanks to breakthrough advancements in sensing technologies, an increasingly high volume of multi-modal sensor data has been collected, which enables us gain better insights into complex systems dynamics and build sophisticated data-driven machine-learning-based dynamic models without having the access to the underlying governing equations. However, integrating domain-specific knowledge in machine learning algorithms remains pivotal for various reasons: it promises enhanced predictive accuracy, better model interpretability, and increased generalizability. This dissertation delves into three core research questions, each …

Effect Of Fire Flame On Some Mechanical Properties Of Self-Compacting Concrete, Haider Sadiq M. Ali, Nabeel A-M. Albayati, Basman R. Mohammed, Adil M. Jabbar

Al-Esraa University College Journal for Engineering Sciences

This paper presents an experimental investigation of the effect of fire flame on self-compacting concrete. The experimental program included casting cylinder and prism concrete specimens for compressive strength, modulus of elasticity, modulus of rupture, and concrete density tests. The specimens are exposed to fire flame at 800 ºC approximately for 2 hours or 6 hours. Then the specimens were cooled either in a fast or slow manner. Test results show that the compressive strength was reduced by about (54 - 61)% for fire exposure of 6 hours and by (27 - 37)% for 2 hours of exposure and cooled slowly …

Manual Preparation Of Eyeglasses Based On Corneal Topographical Images For Keratoconus Patients, Bassma Sabah Majeed, Faiz F. Mustafa, Nebras H. Ghaeb

Al-Esraa University College Journal for Engineering Sciences

keratoconus (KCN) is a non-inflammatory, progressive thinning process of the cornea. It is considered one of the advanced biomechanical changes on the corneal surface, and methods of treatment in late cases are special designed contact lenses or surgical intervention. The objective of this paper is to customize the standard eyeglass lens in a way so that it fits with the abnormal shape and changes of the surface of the cornea of a patient suffering from KCN disease.The proposed method here, based on manual scratching of the external surface of the standard eyeglass lens under supervising of an expert optometrist, where …

Age-Friendly Educational Buildings Primary Schools In Kerbala - A Case Study, Anwar Fadhil Hussein, Ibrahim Jawad Kadhim

Al-Esraa University College Journal for Engineering Sciences

The concept of age-friendly societies has gained international attention among researchers, policy makers, and community organizations since the World Health Organization launched the Friendly Communities Project in 2006, to address challenges in some countries, as these challenges affect all aspects of society, and the educational environment represents an important joint of those joints, being the environment that is the most effective and influential in shaping human behavior. The age stage that is most affected and capable of learning and shaping behavior is of importance, which is the childhood stage. Therefore, the research focused on school buildings, as they represent an …

The Role Of Enhancing Interaction With The Natural Environment In Achieving Social Interaction For Children In Orphanage Institutions, Shamael M. W. Al Dabbagh, Zainab Khalid Rashad Al Khafaji

Al-Esraa University College Journal for Engineering Sciences

The child deprived of family care is considered the child most in need of attention and care. When the orphan child enters a new environment for him, it is obvious that he feels alienated, isolated, and loses the sense of interaction and communication with society. The research sees the possibility of mitigating this feeling by enhancing interaction with the natural environment within the internal spaces of the orphanage building and at the neighborhood level. In order to solve the research problem, the research adopted a hypothesis stating that "interaction with the natural environment enhances the achievement of social interaction for …

The Role Of Academic Competitions In Promoting Architectural Education: Tamayouze Excellence Award In Iraqi Architectural Education - Case Study, Nairy Mugardich Krikor, Anwar Subhi Ramadan

Al-Esraa University College Journal for Engineering Sciences

The importance of architectural competitions has emerged in finding the best designs, upgrading and architectural advancement in both practice and thinking. Architectural competitions have become intellectual meetings that contribute to stimulating self-learning and encouraging creativity. They act as an educational tool that leads to competition, giving motivation to the development of skills and learning, in a way that enhances the integration between architectural theory and practical practice for both engineers and architecture students. The research was concerned with studying the effective role of academic competitions in architectural education as one of the ways to improve teaching and learning, and to …

Analysis And Mitigation Of Cyber-Attacks Targeting Infrastructures Operated By Iot Systems, Raja Salih Mohammed Hasan, Nadia Mahmood Ali, Ihsan Jabbar Hasan

Al-Esraa University College Journal for Engineering Sciences

Numerous countries have a high impact on providing the planet with critical infrastructures offering very important services employed in different fields such as water resources management, public services, power grids, telecoms, commercials, and transportation. The increasing solutions in IoT systems made it possible to exploit internet connection services for supporting the critical infrastructures. The latest are being targeted by various types of cyber-attacks due to the advancement in internet services. Therefore, improving the security systems and the ways to detect the threats is highly required. Meanwhile, protecting the critical infrastructures from hostile cyber-attacks is of high significance. This article examines …