Engineering Commons^™

Receptor-Targeted Next-Generation Probiotics Ameliorate Mammalian Colitis, Nicholas L. F. Gallina, Vignesh Nathan, Akshay Krishnakumar, Dongqi Liu, Rishi Drolia, Nicole Irrizary Tardi, Yang Fu, Manalee Samadar, Shivendra Tenguria, Alvin Cai, Ruth Eunice Centeno-Martinez, Timothy A. Johnson, Abigail Cox, Lavanya Reddivari, Bruce Applegate, Xingjian Bai, Luping Xu, Deepti Tanjore, Ramesh Vemulapalli, Rahim Rahimi, Arun K. Bhunia

Biological Sciences Faculty Publications

Introduction: a loss of intestinal barrier function, inflammation, and an elevated expression of epithelial heat shock protein 60 (Hsp60) are features of an inflamed bowel. Probiotics have been used to alleviate colitis-induced pathologies, but offer poor adhesion and adaptation to the diseased gut. We hypothesize that enhancing probiotic adhesion in the inflamed bowel may ameliorate such pathologies. Listeria adhesion protein (LAP; 94-kDa acetaldehyde alcohol dehydrogenase) aids Listeria attachment to the epithelial cells by interacting with the mammalian receptor Hsp60. Bioengineered Lactobacillus casei probiotics (BLPs) expressing LAP showed strong interaction with epithelial Hsp60, a high immunomodulatory response, and sustained epithelial barrier …

Measurement Of The Local Static Mechanical Pressure Of Earplugs, Luiz G.C. Melo, Ahmed S. Dalaq, Franck Sgard, Olivier Doutres, Laurianne Legroux, Eric Wagnac

Études primaires

Earplugs are used in various critical industrial sectors, such as construction, aviation, military and defense, transportation, and healthcare. However, they present inherent drawbacks, notably discomfort that can lead to inconsistent and incorrect use, thereby leaving a significant proportion of workers vulnerable to irreversible hearing damage, ranging from tinnitus to deafness. This discomfort is closely linked to a physical parameter known as static mechanical pressure (SMP), representing the pressure exerted by earplugs on the earcanal walls. Determining the SMP is crucial for developing earplugs that prioritize comfort. However, experimental studies in this area are scarce and there is no experimental set-up …

Ai And Ml-Based Risk Assessment Of Chemicals: Predicting Carcinogenic Risk From Chemical-Induced Genomic Instability, Ajay Vikram Singh, Preeti Bhardwaj, Peter Laux, Prachi Pradeep, Madleen Busse, Andreas Luch, Akihiko Hirose, Christopher J. Osgood, Michael W. Stacey

Biological Sciences Faculty Publications

Chemical risk assessment plays a pivotal role in safeguarding public health and environmental safety by evaluating the potential hazards and risks associated with chemical exposures. In recent years, the convergence of artificial intelligence (AI), machine learning (ML), and omics technologies has revolutionized the field of chemical risk assessment, offering new insights into toxicity mechanisms, predictive modeling, and risk management strategies. This perspective review explores the synergistic potential of AI/ML and omics in deciphering clastogen-induced genomic instability for carcinogenic risk prediction. We provide an overview of key findings, challenges, and opportunities in integrating AI/ML and omics technologies for chemical risk assessment, …

Enhanced Skin Cancer Diagnosis Through Grid Search Algorithm-Optimized Deep Learning Models For Skin Lesion Analysis, Rudresh Pillai, Neha Sharma, Sheifali Gupta, Deepali Gupta, Sapna Juneja, Saurav Malik, Hong Qin, Mohammed S. Alqahtani, Amel Ksibi

Computer Science Faculty Publications

Skin cancer is a widespread and perilous disease that necessitates prompt and precise detection for successful treatment. This research introduces a thorough method for identifying skin lesions by utilizing sophisticated deep learning (DL) techniques. The study utilizes three convolutional neural networks (CNNs)-CNN1, CNN2, and CNN3-each assigned to a distinct categorization job. Task 1 involves binary classification to determine whether skin lesions are present or absent. Task 2 involves distinguishing between benign and malignant lesions. Task 3 involves multiclass classification of skin lesion images to identify the precise type of skin lesion from a set of seven categories. The most optimal …

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

In Vivo Measurement Of Nadh Fluorescence Lifetime In Skeletal Muscle Via Fiber-Coupled Time-Correlated Single Photon Counting, Kathryn M. Priest, Jacob V. Schluns, Nathania Nischal, Colton L. Gattis, Jeffery C. Wolchok, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Nicotinamide adenine dinucleotide (NADH) is a cofactor that serves to shuttle electrons during metabolic processes such as glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation (OXPHOS). NADH is autofluorescent, and its fluorescence lifetime can be used to infer metabolic dynamics in living cells. Fiber-coupled time-correlated single photon counting (TCSPC) equipped with an implantable needle probe can be used to measure NADH lifetime in vivo, enabling investigation of changing metabolic demand during muscle contraction or tissue regeneration. This study illustrates a proof of concept for point-based, minimally-invasive NADH fluorescence lifetime measurement in vivo. Volumetric muscle loss (VML) injuries were …

4d Epr Oximetry Imaging For 4d Bioprinting And Tissue Engineering, Sajad Sarvari

Graduate Theses, Dissertations, and Problem Reports (ETD)

Bioprinting, akin to 3D printing, employs cell-laden hydrogels such as GelMA (Gelatine Methacrylate) and Alginate instead of plastic or resin to create biological structures. The printing process followed by subsequent tissue maturation is known as 4D bioprinting, where the fourth dimension is time. Ensuring adequate and consistent oxygen, O2, supply within 3D bioprint volume over the entire maturation period process is crucial, as even transient hypoxia can impact cellular behavior and phenotypes. However, printing of fully developed vasculature remains an unresolved technical challenge. Several approaches to chemically (peroxides) or biologically (photosynthesis) generate oxygen during bioprint maturation have been proposed. However, …

Changes In Psychiatric Diagnosis Associated With Sars-Cov-2 Infection And Predicting The Development Of New Psychiatric Illness In Covid Patients By Using Machine Learning Approach: A Study Using The Us National Covid Cohort Collaborative (N3c), Asif Rahman

Graduate Theses, Dissertations, and Problem Reports (ETD)

The enduring impact of COVID-19 extends beyond acute illness, with potential long-term psychiatric consequences raising significant concern among healthcare professionals and researchers alike. Emerging evidence suggests a multifaceted relationship between COVID-19 and the development of different psychiatric illnesses like Schizophrenia Spectrum and Psychotic Disorders (SSPD), Depression, Bipolar disorder, Personality disorder, Trauma, and a range of other mental health conditions. Considering these emerging connections, our study endeavors to rigorously assess the associations between COVID-19 and various psychiatric illnesses while simultaneously employing machine learning techniques to predict the development of new psychiatric disorders in individuals affected by the virus. Leveraging the extensive …

Continuous, Platform Purification Of Viral Products Using Aqueous Two-Phase Extraction, Natalie M. Nold

Dissertations, Master's Theses and Master's Reports

Cell and gene therapies, a ground-breaking class of drugs that can heal genetic diseases and cure cancer, often have treatment costs over $1 million. Most cell and gene therapies are delivered using virus-based delivery vectors, which are incredibly expensive to manufacture. Liquid chromatography is the favored method of viral vector purification since it is easily scalable and can be functionalized to purify by biospecificity, charge, hydrophobicity, or size. However, chromatography-based purification processes are highly expensive and usually only recover 20-50% of the viral vectors. There is currently no platform purification strategy for viral vectors due to differences in their surface …

Computational Analysis Of Vascular Aneurysms, Seyedmostafa Rezaeitaleshmahalleh

Dissertations, Master's Theses and Master's Reports

Vascular aneurysms, such as intracranial aneurysms (IAs) and abdominal aortic aneurysms (AAAs), pose significant health risks, particularly upon rupture. Disturbed hemodynamics, characterized by swirling flow patterns, can lead to cellular and structural changes that disrupt normal physiological processes and contribute to destructive vascular remodeling. Integrating hemodynamic analysis into clinical assessments of aneurysms has become crucial, especially through patient-specific computational fluid dynamics (CFD) simulations based on medical imaging. However, the complexity of CFD tools presents challenges in model creation and post-simulation analysis, limiting their accessibility to clinicians.
This project aimed to advance aneurysm management by exploring the role of intraluminal thrombus …

Energy Content Of Acorns Of Shinnery Oak (Quercus Havardii) In The Diet Of Scaled Quail (Callipepla Squamata) In Southeastern New Mexico, J.L. Hunt, M.E. Grilliot, T.L. Best, D. Lozano-Lopez, E.R. Neilson, I.C. Castillo

Journal of the Arkansas Academy of Science

Shinnery oak (Quercus havardii) is a deciduous, low-growing shrubby tree that is a dominant plant in large areas of grassland in western Oklahoma, the Texas Panhandle, and eastern New Mexico. Acorns of the plant are important food items for many wildlife species, including scaled quail (Callipepla squamata), mourning doves (Zenaida macroura), and endangered lesser prairie-chickens (Tympanuchus pallidicinctus). We analyzed the energy content of acorns of shinnery oak obtained from the crops of scaled quail collected from plains-mesa sand-scrub in Lea and Eddy counties, New Mexico. Acorns were removed from crops and dried for 48 hours at 60°C to remove moisture …

Volar V-Y Advancement Flaps In Reconstructing Fingertip Injuries, Sawsan Abiad

BAU Journal - Science and Technology

Fingertip injuries with exposed bones and joints require immediate or early closure for the preservation of function and avoidance of complications. The ideal procedure should maintain the length of the finger and cover the defect with non-tender, well-padded skin with normal sensation. The aim of this study was to evaluate the role of the different types of volar V-Y advancement flaps in reconstructing and resurfacing injuries of the fingertips at different levels and angles. Thirty patients (N=30) sustaining fingertip injuries of variable etiology and lost components, type III & IV according to Allen’s classification were divided into two groups (n=15) …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Foreword From Editor - 14th Edition, Yandi Andri Yatmo

ASEAN Journal of Community Engagement

This edition of AJCE brings together discussions on the various roles and effectiveness of research and community engagement programs in strengthening local identity, developing skills, and enhancing quality of life towards a resilient society. Expanding such roles, this issue consists of four research articles, one review article, and three case-based articles. The authors of this edition emerge from the background of language, engineering, economy, policy, education, and health, providing different outlooks and methods in overseeing the processes of community-related programs.

Systematic Development Of Ionizable Lipid Nanoparticles For Placental Mrna Delivery Using A Design Of Experiments Approach, Rachel E. Young, Katherine Nelson, Samuel I. Hofbauer, Tara Vijayakumar, Mohamad-Gabriel Alameh, Drew Weissman, Charalampos Papachristou, Jason P Gleghorn, Rachel S. Riley

Henry M. Rowan College of Engineering Departmental Research

Ionizable lipid nanoparticles (LNPs) have gained attention as mRNA delivery platforms for vaccination against COVID-19 and for protein replacement therapies. LNPs enhance mRNA stability, circulation time, cellular uptake, and preferential delivery to specific tissues compared to mRNA with no carrier platform. However, LNPs are only in the beginning stages of development for safe and effective mRNA delivery to the placenta to treat placental dysfunction. Here, we develop LNPs that enable high levels of mRNA delivery to trophoblasts in vitro and to the placenta in vivo with no toxicity. We conducted a Design of Experiments to explore how LNP composition, including …

Combined Risk Based Inspection And Fault Tree Analysis For Repetitive 3-Phase Line Piping Leakage At West Java Offshore Topside Facility, Dona Yuliati, Akhmad Herman Yuwono, D. Rizal Asral, Donanta Dhaneswara

Journal of Materials Exploration and Findings

Hydrocarbon releases might result in serious consequences in various aspects. In addition to the contribution to environmental pollution, repetitive leakages need high repair costs. This study aim is to minimize potential repetitive leakage for other typical 3-phase piping systems. We conducted the risk assessment by adopting Risk Based Inspection (RBI) API 581 to identify risk level, calculating piping lifetime, recommended inspection plan and mitigations. The most relevant root causes can be obtained through quantitative Fault Tree Analysis (FTA). Observation and investigation was taken from eight 3-phase piping systems that experienced repetitive leakages. It has been found that the risk level …

Nitrogen Gas Quenching Pressure Effect On Bs S155 Alloy Steel In Vacuum Furnace, Agus Mulyadi Hasanudin, Eddy Sumarno Siradj

Journal of Materials Exploration and Findings

The production of metal and alloy products requires the use of heat treatment, when during the heat treatment process, quenching is a crucial step. The quenching medium can be anything from water, a salt bath, oil, air and gas. In a vacuum furnace, pressurized gas, most frequently nitrogen (N₂) gas, serves as one of the quenching mediums. One of the drawbacks of the quenching process is the distortion and dimensional change of the parts. This paper aims to investigate the influence of nitrogen gas quenching pressure on the distortion and dimensional change of aerospace actuator gear planet parts …

The Role Of Colony Morphology And Substratum Inclination On The Distribution Of Eunicella Verrucosa On Shallow Reefs, Luke Thompson

The Plymouth Student Scientist

Eunicella verrucosa plays an important role in shallow reefs, where they produce a complex 'sheet tree' morphology that supports a variety of benthic-dwelling organisms. E. verrucosa is considered 'vulnerable' by the IUCN Red List, which validates the importance of understanding the biotic and abiotic factors influencing the species morphology and survival. This study analyses how horizontal and vertical slope inclinations influence colony morphology. A population of 115 E. verrucosa colonies were observed at Plymouth's inner breakwater fort at 8–13.8m in depth. The influence of inclination on morphology was investigated by observing colony height, encrusting branch diameter and branch complexity for …

A Statistical Analysis Of The Population Of Barbel In The River Teme

The Plymouth Student Scientist

The focus of this project is on the population of barbel (Barbus barbus) living in the River Teme, over a number of years with the objective of examining the fish population size specifically investigating any temporal trend in fish population numbers and, if found, with the further aim of examining any covariates that may be causing the trend. In order to answer these questions, two datasets were investigated and rigorously analysed in order to ascertain whether stocks of barbel are in decline and, if so, to further examine which covariates could be contributing to their depletion. A number of statistical …

Getting Off On The Right Foot: Addressing Severe Lymphedema Through A Novel Shoe Design, Carl R. Russell Iii, Anjollie M. Ramakrishna, Christopher H. Johns Iii, Alana V. Van Wijnen

Purdue Journal of Service-Learning and International Engagement

Engineering Projects in Community Service (EPICS) is a service-learning design program run by the College of Engineering at Purdue University. EPICS teaches students design skills by providing solutions for individuals, communities, and organizations in the surrounding area while mirroring engineering industry standards. Biomedical Engineering is a team within EPICS that strives to serve community partners through biomedical applications. HR is a patient who suffers from severe lymphedema. This condition results in her foot swelling three times its original size and requires her to utilize weekly leg compression therapy. Prescription shoes are slightly adequate. However, they lead to sores and pain …

A Computational Exploration: Docking Analysis Of Compounds From Foeniculum Vulgare As Potential Aromatase Inhibitors For Endometriosis Candidate Therapy, Dwi Anita Suryandari, Puji Sari, Hadi Sunaryo, Khaerunissa Anbar Istiadi

Indonesian Journal of Medical Chemistry and Bioinformatics

Aromatase inhibitors (AI) have controlling symptoms and size of endometriotic implants, making them a promising second-line therapy for endometriosis treatment.pretreatment with letrozole, an AI, combined with leuprolide acetate and resveratrol has been found to improve in vitro fertilization (IVF) outcomes in women mild endometriosis.in this study we screening and analysis of ten phenolic compounds from Foeniculum vulgare using molecular docking with Mcole server.from this results showed that three phenolic trans resveratrol (TR), caempherol coumaril (CC) have low gibbs energy compare with resveratrol (R). The binding modalities of compound TR and compound R were hydrogen-bonding between the hydroxyl and oxygen atom …

Développement D’Un Système De Mesure Pour La Caractérisation Des Traitements Absorbants En Laboratoire, Alain Berry, Olivier Robin, Thomas Dupont, Franck Sgard

Rapports de recherche scientifique

Le bruit constitue une préoccupation de plus en plus importante et généralisée dans le monde. Selon l’Organisation mondiale de la Santé, environ une personne sur quatre dans le monde souffrira de déficience auditive à des degrés divers d’ici à 2050. Dans de nombreux pays et régions du globe, le bruit représente le second facteur environnemental provoquant le plus de dommages sanitaires, et ce derrière la pollution atmosphérique. Sur un volet cognitif ou perceptif, le bruit environnemental peut par exemple perturber le sommeil et gêner l’apprentissage en milieu scolaire. Dans un milieu de travail, il peut perturber la bonne compréhension/perception de …

Air-Jet Bioprinting Of Stem Cell-Encapsulated Alginate Micro-Droplets For Organoid Biomanufacturing, Mirabella B. Stump

Electronic Theses and Dissertations

Biomanufactured 3D-organoids show promise for modeling and treating various conditions, particularly insulin-dependent diabetes mellitus (type-1 diabetes). Pancreatic islet organoids serve as sustainable sources of insulin-producing β-cells, potentially restoring insulin regulation in patients and providing a long-term solution for diabetes. Hydrogel droplet printing is an emerging technique in regenerative medicine due to its advantageous tunability and biocompatibility; however, challenges of consistency, quality control, and scalability persist. To address these issues, we developed a novel air-jetting based droplet bioprinting system for the generation of monodispersed alginate micro-droplets. The objective of this project was to incorporate human induced pluripotent stem cells (hiPSCs) into …

Paper-Based Ratiometric Sensor Array For Pathogenic Bacterial Species Identification, Aayushi Laliwala

Theses & Dissertations

Bacterial infections are the leading cause of mortality worldwide due to the lack of accurate diagnosis of the pathogens causing infections. Currently, microbiological and molecular techniques are used to identify pathogenic bacteria. However, these techniques have limitations as they are time-consuming, cost-inefficient, and require trained personnel. Therefore, timely and precise identification of pathogenic bacteria is crucial for public safety. Our lab previously synthesized a fluorescent sensor array (3-hydroxyflavone derivatives) encapsulated in hyaluronic acid-based nanoparticles to identify bacterial species and recognize their Gram status. Though promising, this technique was relatively time-consuming and required high sample and volumes.

To overcome these limitations, …

Ai’S Next Frontier — Dermatology? How It May Help Close The Health Gap For Dark-Skinned Patients, Gretchen B. Smail

Capstones

This project examines how engineers are creating artificial intelligence systems to help with dermatology diagnosis. Researchers believe that these systems can help close the health care gap in lower income and Black and brown communities, but dermatologists of color worry that these systems are not being trained to recognize skin conditions on patients of color.

12.04.2023 Orsp Connect, Liz Williamson

ORED Newsletter

Week of December 4, 2023

12.11.2023 Orsp Connect, Liz Williamson

ORED Newsletter

December 11, 2023 Newsletter

Bioactivity And Structural Properties Of Hydroxyapatite On Ti6a|4v And Si(100) Surfaces By Pulsed Laser Deposition, Salizhan Kylchbekov

Masters Theses & Specialist Projects

Although biomedical implant technology is very advanced, there are still caveats in terms of biocompatibility properties because metals are inert to biological processes such as osseointegration, cell growth, and cell adhesion. This results in statistically significant complications and opens rooms for improvements. Among many techniques to improve this problem, coating the metal surface with biologically functional materials has resulted in the best performances. Hydroxyapatite (HAP), Ca_₁₀(PO_₄)_₆(OH)_₂, is the most stable form of calcium phosphates in human body environment and is functional in key processes such as ion exchange, osteoblast (bone cells) formation, …

Combining Adhesive And Nonadhesive Injectable Hydrogels For Intervertebral Disc Repair In An Ovine Discectomy Model., Christopher J Panebianco, Caroline Constant, Andrea J. Vernengo, Dirk Nehrbass, Dominic Gehweiler, Tyler J Distefano, Jesse Martin, David J Alpert, Saad B Chaudhary, Andrew C Hecht, Alan C Seifert, Steven B Nicoll, Sibylle Grad, Stephan Zeiter, James C Iatridis

Henry M. Rowan College of Engineering Departmental Research

BACKGROUND: Intervertebral disc (IVD) disorders (e.g., herniation) directly contribute to back pain, which is a leading cause of global disability. Next-generation treatments for IVD herniation need advanced preclinical testing to evaluate their ability to repair large defects, prevent reherniation, and limit progressive degeneration. This study tested whether experimental, injectable, and nonbioactive biomaterials could slow IVD degeneration in an ovine discectomy model.

METHODS: Ten skeletally mature sheep (4-5.5 years) experienced partial discectomy injury with cruciate-style annulus fibrosus (AF) defects and 0.1 g nucleus pulposus (NP) removal in the L1-L2, L2-L3, and L3-L4 lumbar IVDs. L4-L5 IVDs were Intact controls. IVD injury …