Engineering Commons^™

Expedited Pcr With Stirring, Hendrik Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Disclosed are an apparatus and methods for rapid amplification of nucleic acids. More particularly, the present dis closure relates to an apparatus for mixing a reaction solution during amplification of nucleic acids and to methods for amplifying nucleic acids. Also disclosed are methods for lysing cells in a sample and amplifying nucleic acids.

Computer Simulation For Continuous Centrifugation Of High-Density Cell Cultures, Hironori Tomizawa

USF Tampa Graduate Theses and Dissertations

Perfusion bioreactors are used for cell production for cell therapies. The system uses cell separation devices such as centrifuge to facilitate cell growth by separating cells and spent media and allows constant media replacement. However, current cell separation technologies can increase shear stress, are generally not continuous processes, and are not as efficient as desired. These limit the amount of media replaced per unit time. Therefore, there is a need for a new system or a method that operates continuously to minimize cell damage, yield high cell concentration, and exchange media effectively. A set of research questions was formulated: (1) …

Creating Reel Designs: Reflecting On Arthrogryposis Multiplex Congenita In The Community, Iris Layadi

Purdue Journal of Service-Learning and International Engagement

Because of its extreme rarity, the genetic disease arthrogryposis multiplex congenita (AMC) and the needs of individuals with the diagnosis are often overlooked. AMC refers to the development of nonprogressive contractures in disparate areas of the body and is characterized by decreased flexibility in joints, muscle atrophy, and developmental delays. Colton Darst, a seven-year-old boy from Indianapolis, Indiana, was born with the disorder, and since then, he has undergone numerous surgical interventions and continues to receive orthopedic therapy to reduce his physical limitations. His parents, Michael and Amber Darst, have hopes for him to regain his limbic motion and are …

Pairwise Correlation Analysis Of The Alzheimer’S Disease Neuroimaging Initiative (Adni) Dataset Reveals Significant Feature Correlation, Erik D. Huckvale, Matthew W. Hodgman, Brianna B. Greenwood, Devorah O. Stucki, Katrisa M. Ward, Mark T. W. Ebbert, John S. K. Kauwe, The Alzheimer’S Disease Neuroimaging Initiative, The Alzheimer’S Disease Metabolomics Consortium, Justin B. Miller

Sanders-Brown Center on Aging Faculty Publications

The Alzheimer’s Disease Neuroimaging Initiative (ADNI) contains extensive patient measurements (e.g., magnetic resonance imaging [MRI], biometrics, RNA expression, etc.) from Alzheimer’s disease (AD) cases and controls that have recently been used by machine learning algorithms to evaluate AD onset and progression. While using a variety of biomarkers is essential to AD research, highly correlated input features can significantly decrease machine learning model generalizability and performance. Additionally, redundant features unnecessarily increase computational time and resources necessary to train predictive models. Therefore, we used 49,288 biomarkers and 793,600 extracted MRI features to assess feature correlation within the ADNI dataset to determine the …

Posterior Segment Ophthalmic Drug Delivery: Role Of Muco-Adhesion With A Special Focus On Chitosan., Ayah Mohammad Burhan, Butsabarat Klahan, Wayne Cummins, Vanessa Andrés-Guerrero, Mark Byrne, Niall J O'Reilly, Anuj Chauhan, Laurence Fitzhenry, Helen Hughes

Henry M. Rowan College of Engineering Departmental Research

Posterior segment eye diseases (PSEDs) including age macular degeneration (AMD) and diabetic retinopathy (DR) are amongst the major causes of irreversible blindness worldwide. Due to the numerous barriers encountered, highly invasive intravitreal (IVT) injections represent the primary route to deliver drugs to the posterior eye tissues. Thus, the potential of a more patient friendly topical route has been widely investigated. Mucoadhesive formulations can decrease precorneal clearance while prolonging precorneal residence. Thus, they are expected to enhance the chances of adherence to corneal and conjunctival surfaces and as such, enable increased delivery to the posterior eye segment. Among the mucoadhesive polymers …

Multi-Organs-On-Chips For Testing Small-Molecule Drugs: Challenges And Perspectives., Berivan Cecen, Christina Karavasili, Mubashir Nazir, Anant Bhusal, Elvan Dogan, Fatemeh Shahriyari, Sedef Tamburaci, Melda Buyukoz, Leyla Didem Kozaci, Amir K Miri

Henry M. Rowan College of Engineering Departmental Research

Organ-on-a-chip technology has been used in testing small-molecule drugs for screening potential therapeutics and regulatory protocols. The technology is expected to boost the development of novel therapies and accelerate the discovery of drug combinations in the coming years. This has led to the development of multi-organ-on-a-chip (MOC) for recapitulating various organs involved in the drug-body interactions. In this review, we discuss the current MOCs used in screening small-molecule drugs and then focus on the dynamic process of drug absorption, distribution, metabolism, and excretion. We also address appropriate materials used for MOCs at low cost and scale-up capacity suitable for high-performance …

Artificial Image Objects For Classification Of Breast Cancer Biomarkers With Transcriptome Sequencing Data And Convolutional Neural Network Algorithms, Xiangning Chen, Daniel G. Chen, Zhongming Zhao, Justin M. Balko, Jingchun Chen

School of Medicine Faculty Research

Background: Transcriptome sequencing has been broadly available in clinical studies. However, it remains a challenge to utilize these data effectively for clinical applications due to the high dimension of the data and the highly correlated expression between individual genes. Methods: We proposed a method to transform RNA sequencing data into artificial image objects (AIOs) and applied convolutional neural network (CNN) algorithms to classify these AIOs. With the AIO technique, we considered each gene as a pixel in an image and its expression level as pixel intensity. Using the GSE96058 (n = 2976), GSE81538 (n = 405), and GSE163882 (n = …

Novel Insights Into Negative Pressure Wound Healing From An In Situ Porcine Perspective, Jacob G. Hodge, Ashley L. Pistorio, Christopher A. Neal, Hongyan Dai, Jennifer G. Nelson-Brantley, Molly E. Steed, Richard A. Korentager, David S. Zamierowski, Adam J. Mellott

School of Medicine Faculty Research

Negative pressure wound therapy (NPWT) is used clinically to promote tissue formation and wound closure. In this study, a porcine wound model was used to further investigate the mechanisms as to how NPWT modulates wound healing via utilization of a form of NPWT called the vacuum-assisted closure. To observe the effect of NPWT more accurately, non-NPWT control wounds containing GranuFoam™ dressings, without vacuum exposure, were utilized. In situ histological analysis revealed that NPWT enhanced plasma protein adsorption throughout the GranuFoam™, resulting in increased cellular colonization and tissue ingrowth. Gram staining revealed that NPWT decreased bacterial dissemination to adjacent tissue with …

Defining The Innate Immune Responses For Sars-Cov-2-Human Macrophage Interactions, Mai M. Abdelmoaty, Pravin Yeapuri, Jatin Machhi, Katherine E. Olson, Farah Shahjin, Vikas Kumar, You Zhou, Jingjing Liang, Kabita Pandey, Arpan Acharya, Siddappa N. Byrareddy, R. Lee Mosley, Howard E. Gendelman

Nebraska Center for Biotechnology: Faculty and Staff Publications

Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end-organ malfunctions. All follow the presence of persistent viral components and virions without evidence of viral replication. To elucidate SARS-CoV- 2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the …

Systematic Review And Regression Modeling Of The Effects Of Age, Body Size, And Exercise On Cardiovascular Parameters In Healthy Adults, Aseem Pradhan, John Scaringi, Patrick Gerard, Ross Arena, Jonathan Myers, Leonard A. Kaminsky, Ethan Kung

Publications

Purpose

Blood pressure, cardiac output, and ventricular volumes correlate to various subject features such as age, body size, and exercise intensity. The purpose of this study is to quantify this correlation through regression modeling.

Methods

We conducted a systematic review to compile reference data of healthy subjects for several cardiovascular parameters and subject features. Regression algorithms used these aggregate data to formulate predictive models for the outputs—systolic and diastolic blood pressure, ventricular volumes, cardiac output, and heart rate—against the features—age, height, weight, and exercise intensity. A simulation-based procedure generated data of virtual subjects to test whether these regression models built …

Plaque Contact Surface Area And Flow Lumen Volume Predict Stroke Risk In Extracranial Carotid Artery Stenosis, Ryan Gendey, Ethan Kung, Veena Mehta, Adam Brown, Matthew Bridges, Ravi Veeraswamy

Publications

The standard indication for intervention in asymptomatic disease is currently percent stenosis in the internal carotid artery as measured by the NASCET method, which remains limited in discriminating power. CT angiography (CTA) is widely used to calculate NASCET stenosis but also offers the opportunity to analyze carotid artery plaques from a morphological perspective that has not been widely utilized. We aim to improve stroke risk stratification of patients with carotid artery stenosis using plaque 3D modeling and image analysis. Patients with CTAs appropriate for 3D reconstruction were identified from an NIH designated stroke center database, and carotid arteries were segmented …

Investigation Of Combinations Of Rationally Selected Bioengineered Nisin Derivatives For Their Ability To Inhibit Listeria In Broth And Model Food Systems, Laura Nyhan, Des Field, Colin Hill, Michael J. Callanan, Máire Begley

Department of Biological Sciences Publications

In this study, we examined the ability of nisin A and a rationally assembled bank of 36 nisin derivative producing Lactococcus lactis strains to inhibit Listeria. A broth-based bioluminescence assay for screening single and combinations of bioengineered nisin derivatives using cell-free supernatants (CFS) from nisin derivative producing strains was developed. In this way, we screened 630 combinations of nisin derivative producing strains, identifying two (CFS from M17Q + N20P and M17Q + S29E) which exhibited enhanced anti-listerial activity when used together compared to when used alone, or to the nisin A producing strain. Minimal inhibitory concentration assays performed with purified …

Physiological Processes, Chirag B. Raval

Open Educational Resources

Physiological Processes is designed to introduce fundamental concepts of physiology to biomedical engineering learners. Areas covered include: neural, muscular, cardiovascular, respiratory and renal system function; bioelectrical signals, capillary-level transport, organ-level exchange. Whenever possible, analysis will be quantitative in order to fulfill the course goals and to build the foundation for the subsequent biomedical engineering curriculum. This course is for Biomedical Engineering majors only.

Fibrin Gel Enhances The Antitumor Effects Of Chimeric Antigen Receptor T Cells In Glioblastoma, Edikan A. Ogunnaike, Alain Valdivia, Mostafa Yazdimamaghani, Ernesto Leon, Seema Nandi, Hannah Hudson, Hongwei Du, Simon Khagi, Zhen Gu, Barbara Savoldo, Frances S. Ligler, Shawn Hingtgen, Gianpietro Dotti

Chemical and Biochemical Engineering Faculty Research & Creative Works

Regional delivery of chimeric antigen receptor (CAR) T cells in glioblastoma represents a rational therapeutic approach as an alternative to intravenous administration to avoid the blood-brain barrier impediment. Here, we developed a fibrin gel that accommodates CAR-T cell loading and promotes their gradual release. Using a model of subtotal glioblastoma resection, we demonstrated that the fibrin-based gel delivery of CAR-T cells within the surgical cavity enables superior antitumor activity compared to CAR-T cells directly inoculated into the tumor resection cavity.

The Immune Modulatory Role Of Endocannabinoid Anandamide To Suppress Inflammation Through Regulation Of Microrna And Microbiome, Muthanna Ali Sultan

Theses and Dissertations

Cannabinoids are group of compounds that exerts their anti-inflammatory action through activation of CB1 and CB2 receptors and other minor receptors. In the current study, we investigated the effect of Anandamide (AEA) on Acute Respiratory Distress Syndrome (ARDS) induced by exposure to Staphylococcus Enterotoxin B (SEB) intranasally. We found that C57BL/6 mice treated with AEA showed improvement in the clinical functions of the lungs, accompanied by a decrease in the infiltration of inflammatory cells in the lung tissue, and a decrease in the secretion of pro-inflammatory cytokines. Furthermore, AEA regulated the miRNA profile of the mononuclear cells in the lungs …

The Effect Of Visual Field Manipulations On Standing Balance Control In People With Multiple Sclerosis, Lara I. Riem, Scott A. Beardsley, Brian D. Schmit

Biomedical Engineering Faculty Research and Publications

Background

Multiple sclerosis (MS) is associated with an increased risk of falls, degeneration of sensory organization, and possible increased reliance on vision for balance control.

Research question

The aim of this study was to assess differences in standing postural control between people with MS and age and sex matched controls during medial-lateral (ML) oscillations of the visual field, with and without blinders to the lower periphery.

Methods

Ten persons with MS (mean age 54.0 ± 5.3 years) and ten age and sex matched controls (mean age: 56.3 ± 6.0 years) participated in this study. Balance control was assessed while participants …

Settingsorder Article Reprints Open Accessarticle Generation And Characterization Of Human Mesenchymal Stem Cell-Derived Smooth Muscle Cells, Srikanth Sivaraman, Jackson Hedrick, Samia Ismail, Chris Slavin, Raj R. Rao

Biomedical Engineering Faculty Publications and Presentations

Cardiovascular diseases are the leading cause of death worldwide. A completely autologous treatment can be achieved by using elastogenic mesenchymal stem cell (MSC)-derived smooth muscle cells (SMC) at the affected tissue site of vascular diseases such as abdominal aortic aneurysms (AAA). Thus, our work focused on evaluating the efficacy of (a) the combination of various growth factors, (b) different time periods and (c) different MSC lines to determine the treatment combination that generated SMCs that exhibited the greatest elastogenicity among the tested groups using Western blotting and flow cytometry. Additionally, total RNA sequencing was used to confirm that post-differentiation cells …

Generation And Characterization Of Human Mesenchymal Stem Cell-Derived Smooth Muscle Cells, Srikanth Sivaraman, Jackson Hedrick, Samia Ismail, Chris Slavin, Raj R. Rao

Biomedical Engineering Faculty Publications and Presentations

Cardiovascular diseases are the leading cause of death worldwide. A completely autologous treatment can be achieved by using elastogenic mesenchymal stem cell (MSC)-derived smooth muscle cells (SMC) at the affected tissue site of vascular diseases such as abdominal aortic aneurysms (AAA). Thus, our work focused on evaluating the efficacy of (a) the combination of various growth factors, (b) different time periods and (c) different MSC lines to determine the treatment combination that generated SMCs that exhibited the greatest elastogenicity among the tested groups using Western blotting and flow cytometry. Additionally, total RNA sequencing was used to confirm that post-differentiation cells …

Poly(2-Hydroxyethyl Methacrylate) Hydrogels For Contact Lens Applications–A Review, Kushendarsyah Saptaji, Nurlaely Rohmatul Iza, Sinta Widianingrum, Vania Katherine Mulia, Iwan Setiawan

Makara Journal of Science

The emerging technology in biomedical engineering requires biocompatible materials, which are also referred to as biomaterials. For a material to be considered biocompatible, it should not interact with human tissues in a harmful way, and vice versa. Various properties of biocompatible materials, such as mechanical and optical properties, have to be considered for different biomedical applications. One of the most popular applications of biomaterials is for contact lenses. Hydrogels, specifically poly(2-hydroxyethyl methacrylate) (PHEMA) hydrogels, are among the most popular ones in ophthalmologic applications, especially in soft contact lenses. This paper reviews the use of PHEMA hydrogels as one of the …

Delivery Optimization And Evaluation Of Biomechanics Of An Injectable Nucleus Pulposus Replacement Device, Zachary Rustin Brown

Theses and Dissertations

Lower back pain effects up to 80% of people at some point in their life, a majority of cases being the result of degenerative disc disease. Treatment options for degenerative disc disease are limited, jumping from physical therapy to major spinal fusion and total disc replacement surgery with little to no approaches in between. Furthermore, surgical treatments have not shown to be more effective than conservative treatments and reducing pain and disability over the long term. Hydrogels have shown promise as a potential nucleus pulposus replacement device. Their properties are controllable and can be implanted into the body through minimally …

Combined Devices Of Facts Technology, Bahrom Ravshanovich Normuratov Associate Lecturer, Misrikhan Misrikhanov, Shukhrat Khamidov

Technical science and innovation

FACTS - Flexible Alternative Current Transmission System technology is a family of devices, each of which can be used individually and in concert with other devices to control the interrelated parameters of the electrical power system. The mission of FACTS technology is to improve the control of power flows in both steady-state and transient modes of EPS. Flexibility of Electric Power Transmission, applied as "The ability to adapt to changes in transmission system or operating conditions while maintaining sufficient operating limits in steady-state and transient modes". Controlled Flexible AC Transmission Lines - Flexibility from Electric Power Transmission means "AC Power …

Synthesis And Polymerization Processes Of 1-Chlorine-3- Piperidine -2-Propylmethacrylate Monomer, N U. Pulatova, O S. Maksumova, Izabela Barszczewska Rybarek

Technical science and innovation

An amino alcohol was synthesized on the basis of piperidine and epichlorohydrin. The esterification reaction of methacrylic acids with the obtained amino alcohol was studied. In order to identify optimal synthesis conditions, the influence of temperature, reaction duration and ratio of reactive reagents was investigated. The processes of obtaining unsaturated esters by esterification reactions with 1-chlorine-3-piperidine-2-propanol and acrylic-, methacrylic acids have been studied. The effect of monomer concentration on the rate of polymerization reaction and the yield of polymer formation was studied . The radical polymerization of a new monomer with a piperidine cycle in the presence of a nitrogen-containing …

Covid-19 Et Gestion Des Troubles Gastro-Intestinaux : Expérience D’Un Centre Hospitalier Marocaincovid-19, Gastrointestinal Disorders, Pandemic., Hanane Delsa, Mohamed Cherkaoui Jaouad Reda, Amine Benfaida, Anass Nadi, Fedoua Rouibaa

Health Sciences

Pandemic Covid-19 is a real challenge for the medical profession. SARS-CoV-2 virus attacks several human organs, including the digestive tract. Digestive disorders have been described as revealing symptoms or accompanying signs of infection. The treatment of these symptoms must be early and codified. At Cheikh Khalifa International University Hospital in Casablanca, a codified treatment protocol has been proposed to facilitate the management of these disorders.

Mechanical And Material Characterization Of Advanced Materials For Tissue Regeneration, Bailey Kylara Ricketts Jackson

Theses and Dissertations

In natural disasters and military deployment operations, injury to long bone can cause extensive damage and be difficult to treat and heal quickly. Explosive devices and trauma often produce long-bone (>2-cm length) wounds that are more complicated than common fractures. Due to the size and complexity of these injuries, they can be difficult to treat in a battlefield environment and take a long time to heal completely and properly. Even after the long healing period, these injuries often require rehabilitation to strengthen the muscles that have weakened in the wounded limb. For military applications especially, these effects can put …

Build Your Own Body Mod: Empowerment Through Prototyping And Design, Anaiss Arreola, Katherine R. Ganim

Journal of Science Education for Students with Disabilities

When you don’t have a hand, what could you have instead? This article introduces the impact of inviting youth with disabilities to learn tools and technology to design their own solutions and advocate for their own future. This approach to programming is rooted in a mindset of designing WITH, not FOR. Not only are design outcomes improved when users are incorporated into the process, but this approach has been shown to improve confidence in creating one’s own solutions. These programs include hands-on “design-your-own-body-mod” workshops, as well as a budding inclusive design consultancy led by youth with disabilities. Through this programming, …

Metasurface Cloaks To Decouple Closely Spaced Printed Dipole Antenna Arrays Fed By A Microstrip-To-Balanced Transmission-Line Transition, Doojin Lee, Alexander B. Yakovlev

Faculty and Student Publications

In this work, we present a numerical study of 1D and 2D closely spaced antenna arrays of microstrip dipole antennas covered by a metasurface in order to properly cloak and decouple the antenna arrays operating at neighboring frequencies. We show that the two strongly coupled arrays fed by a microstrip-to-balanced transmission-line transition are effectively decoupled in 1D and 2D array scenarios by covering the dipole antenna elements with an elliptically shaped metasurface. The metasurface comprises sub-wavelength periodic metallic strips printed on an elliptically shaped dielectric cover around the dipole antennas and integrated with the substrate. We present a practical design …

Layered Double Hydroxide-Based Nanocomposite Scaffolds In Tissue Engineering Applications, Burcin Izbudak, Berivan Cecen, Ingrid Anaya, Amir K. Miri, Ayca Bal-Ozturk, Erdal Karaoz

Henry M. Rowan College of Engineering Departmental Research

Layered double hydroxides (LDHs), when incorporated into biomaterials, provide a tunable composition, controllable particle size, anion exchange capacity, pH-sensitive solubility, high-drug loading efficiency, efficient gene and drug delivery, controlled release and effective intracellular uptake, natural biodegradability in an acidic medium, and negligible toxicity. In this review, we study potential applications of LDH-based nanocomposite scaffolds for tissue engineering. We address how LDHs provide new solutions for nanostructure stability and enhance in vivo studies' success.

During Natural Viewing, Neural Processing Of Visual Targets Continues Throughout Saccades, Atanas D. Stankov, Jonathan Touryan, Stephen Gordon, Anthony J. Ries, Jason Ki, Lucas C. Parra

Publications and Research

Relatively little is known about visual processing during free-viewing visual search in realistic dynamic environments. Free-viewing is characterized by frequent saccades. During saccades, visual processing is thought to be suppressed, yet we know that the presaccadic visual content can modulate postsaccadic processing. To better understand these processes in a realistic setting, we study here saccades and neural responses elicited by the appearance of visual targets in a realistic virtual environment. While subjects were being driven through a 3D virtual town, they were asked to discriminate between targets that appear on the road. Using a system identification approach, we separated overlapping …

Bone Quality And Fractures In Women With Osteoporosis Treated With Bisphosphonates For 1 To 14 Years, Hartmut H. Malluche, Jin Chen, Florence Lima, Lucas J. Liu, Marie-Claude Monier-Faugere, David A. Pienkowski

Internal Medicine Faculty Publications

Oral bisphosphonates are the primary medication for osteoporosis, but concerns exist regarding potential bone-quality changes or low-energy fractures. This cross-sectional study used artificial intelligence methods to analyze relationships among bisphosphonate treatment duration, a wide variety of bone-quality parameters, and low-energy fractures. Fourier transform infrared spectroscopy and histomorphometry quantified bone-quality parameters in 67 osteoporotic women treated with oral bisphosphonates for 1 to 14 years. Artificial intelligence methods established two models relating bisphosphonate treatment duration to bone-quality changes and to low-energy clinical fractures. The model relating bisphosphonate treatment duration to bone quality demonstrated optimal performance when treatment durations of 1 to 8 …

Engineering A High-Throughput Screening Platform For Assessing Developmental Neurotoxicity Throughout Head- Regeneration In Schmidtea Mediterranea, Johnathan James Morris

Theses and Dissertations

The increase in commercially used chemicals that are inadequately evaluated for safety and risk to development has created a reticent threat to human health. Addressing these deficiencies is compounded by limited methodologies to determine the etiology of exposure-related developmental neurotoxicity (DNT). Current means of assessing DNT are largely retrospective and limited by the expensive, time-consuming, and labor-intensive use of laboratory animal models, thereby motivating a global research effort to produce alternative chemical screening assays. In this work, we have developed a novel high- throughput platform that serves as a new tool to evaluate the effects of exogenous chemical exposure on …