Engineering Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Reliability Assessment Model Of Network Operating System Based On Convolution Neural Network, Jamal N. Hasoon, Sarah S. Qasim, Mohammed A. Alshomali, Jane J. Stephan

Al-Esraa University College Journal for Engineering Sciences

The paper's subject is one of the points of fundamental significance in improving the development of complex computer systems is the effect of errors since their probability of occurrence in a widely distributed system is exceptionally high. Thus, the computer system must be dependable and provide comprehensive support for fault tolerance, fault detection, signal recovery mechanisms, failure prediction, etc. The goal is to develop a way to evaluate the reliability of the Red Hat Linux operating system utilizing data sets of system failures obtained from system injection with error reports using the Fault Injection Benchmarking and Reliability) FIBR( (for a …

Investing Traditional Architecture That Fulfills The Supreme Human Needs With Its Spiritual Dimension In Reconstruction / The Architecture Of Old Mosul City, A Case Study, Sinan Mohammad Talee Al-Saffar, Anwar Subhi Ramdan Al - Qaraghuli

Al-Esraa University College Journal for Engineering Sciences

Architecture has sought since time immemorial to meet multiple human needs, starting from the basic physiological needs for human survival, psychological needs (social and individual) to needs related to human progress, such as taking into account the aesthetic and spiritual aspects, which represent the highest levels of those needs, through a set of design aspects and characteristics. This research is based on the study of the spiritual dimension of higher human needs in general that architecture seeks to meet, by studying that in the architecture of traditional cities, in particular, to enhance architectural knowledge with regard to the importance of …

The Role Of Algorithms In Formulating The Architectural Formation, Ghada Ghalib Abdul Wahab, Younis Mahmood M. Salem

Al-Esraa University College Journal for Engineering Sciences

Algorithms are mathematical processes that provide step-by-step instructions for solving a specific problem. They are commonly used in computer science and other technical fields to automate processes and solve complex problems. One great application of algorithms is the generation of shapes. Algorithms can be used to create complex shapes and patterns that are difficult or impossible to create manually. We will explore how algorithms can be used as a mechanism to generate shapes by adopting the Voronoi algorithm because it provides a wide environment for creativity through new intellectual processes that may not occur at all in the human mind …

The Detection Of Android Malwares Using The Features Selection Technique, Farah Rafid Salman, Amer Abdulmajeed Abdulrahman

Al-Esraa University College Journal for Engineering Sciences

The use of Android smartphones has been rising quickly as Internet-based services gain more popularity and develop. The Android operating system's enormous popularity has drawn malware attacks on these devices. It is difficult and ineffective to detect malware versions with features that modify their behavior in order to avoid detection by machine learning (ML) techniques. Effective feature selection plays a crucial role in detecting malware characteristics and reduces the dimensionality of a large dataset by removing unnecessary features that are not useful and keeping those relevant features that increase classification accuracy and detection rate. This helps to solve the problems …

A Review Of Polymer – Particles Composite Materials, Ismail Ibrahim Marhoon, Ayad Abbood Abdul Al-Hassan, Mohammed Ali Abdulrehman

Al-Esraa University College Journal for Engineering Sciences

In several engineering applications traditional materials are replacedby composite materials. Filled composite materials consist of the continuousmatrix and the filling particles. The primary purpose of introducing inorganicsolid particles into polymers is to essentially increase mechanical and physicalproperties. The wear properties of polymer composite can be changed to agreater degree by modifying the process of preparing the filled compositematerials. In the present review, a large-scale research has been conductedon the effect of wear on the composites of polymers. The effect of filler onthe polymer composites wear behavior has been thoroughly explained

Ability Of Replacing The Steel Strands By Cfrp In Pre-Stressed Concrete Girders: Art Review, Ahmed Salim Edan, Wael Shawky Abdulsahib

Al-Esraa University College Journal for Engineering Sciences

Fiber-reinforced polymer (FRP) composites are the modern,trustworthy alternatives to steel tendons and rebars. The bulk of currentresearch is devoted to establishing the feasibility of incorporating carbonfibre-reinforced polymer (CFRP) into reinforced concrete girders byevaluating the strength and reliability of CFRP and concrete components.In order to improve fatigue and corrosion resistance, CFRPs are crucial.Comparing reinforced prestressed concrete bridge girders strengthenedwith conventional steel reinforcement to those reinforced with CFRPs offersthe possibility of greatly increasing service life. Also widely researchedand used in bridge engineering as a corrosion-resistant substitute for steelreinforcement is CFRP composite material. The use of carbon fiber-reinforcedplastic (CFRP) reinforcement for prestressing concrete …

A Review Article On The Performance Based Seismic Design Of Structures, Reem Hatem Ahmed, Sahar Elaiwi, Shelan Hameed Ameen

Al-Esraa University College Journal for Engineering Sciences

For the most part, seismic design builds complex structural systems using the same small number of essential structural components as non-seismic design projects. Based on the building regulations, structures are frequently designed to "withstand" the largest earthquake with a given likelihood that is projected to happen at their location. This means that by avoiding structures from collapsing, the number of fatalities must be maintained to a minimal. Seismic design involves knowing the many failure modes regarding a structure and giving it the right stiffness, strength, ductility, and layout for ensuring that these modes do not take place. In this essay, …

In Silico Prediction Of Sodium-Glucose Co-Transporter-2 (Sglt2) Inhibition Activity By Allium Fistulosum Compound Based On Skelspheres Molecular Descriptor, Rudy Heryanto, Aryo Tedjo, Dimas Noor

Indonesian Journal of Medical Chemistry and Bioinformatics

The Sodium-Glucose co-transporter-2 (SGLT2) inhibitor represents a novel agent for the treatment of type 2 diabetes. Drugs of this class function by inhibiting glucose reabsorption in the kidneys, thereby controlling blood glucose levels. It is known that SGLT2 inhibitors activate the AMPK signaling pathway by increasing the expression and activity of AMP-activated protein kinase (AMPK). In vivo tests have demonstrated that ethanolic and aqueous extracts of Welsh onion leaves (Allium fistulosum L) can reduce body weight, liver weight, adipocyte size, and enhance AMP-activated protein kinase (AMPK) expression. In this study, the inhibitory activity (IC50) of compounds within Allium fistulosum against …

Bioinspired Materials For Underwater Adhesion With Pathways To Switchability, Chanhong Lee, Huiqi Shi, Jiyoung Jung, Bowen Zheng, Kan Wang, Ravi Tutika, Rong Long, Bruce Lee, Grace X. Gu, Michael D. Bartlett

Michigan Tech Publications

Strong adherence to underwater or wet surfaces for applications like tissue adhesion and underwater robotics is a significant challenge. This is especially apparent when switchable adhesion is required that demands rapid attachment, high adhesive capacity, and easy release. Nature displays a spectrum of permanent to reversible attachment from organisms ranging from the mussel to the octopus, providing inspiration for underwater adhesion design that has yet to be fully leveraged in synthetic systems. Here, we review the challenges and opportunities for creating underwater adhesives with a pathway to switchability. We discuss key material, geometric, modeling, and design tools necessary to achieve …

A Portable And Reliable Tool For On-Site Physical Reaction Time (Rt) Measurement, Brent Harper, Michael Shiraishi, Rahul Soangra

Physical Therapy Faculty Articles and Research

The drop-stick test system (DTS) invention has the capability to measure reaction accurately for sideline mild traumatic brain injury (mTBI) assessment. The reaction time (RT) measurements showed moderate to good inter-instrument reliability with an overall ICC of 0.82 (95 % CI 0.78–0.85). RT is a useful biomarker of mTBI or concussion, but existing technologies in controlled laboratory environments are not feasible for assessments in the field. With wearable technologies and wireless connection with smartphones, it is now easier to conduct RT assessments on the field. The purpose was to develop a portable DTS involving wearable inertial sensors translatable from the …

Exploration Of Corona Charge As A Novel In Vitro Human T Cell Dna Transfection Method, Molly A. Skinner

USF Tampa Graduate Theses and Dissertations

With gene-based immunotherapies on the rise to treat a multitude of diseases, the ability to genetically modify cells in a rapid and efficient fashion is necessary to keep up with demand. Gene electrotransfer (gene transfer by electroporation) is an appealing transfection method due to its low cost, high efficiency compared to other physical forms of gene delivery, and low toxicity compared to liposomal or viral vectors.

Traditional gene delivery via electroporation is done within a cuvette where the cell suspension is placed between two plate electrodes. This method requires cells to be moved from the treatment cuvette to a growth …