Engineering Commons^™

Quantifying Variation Across 16s Rrna Gene Sequencing Runs In Human Microbiome Studies, Andrew J. Hoisington, Christopher E. Stamper, Joseph C. Ellis, Christopher A. Lowry, Lisa A. Brenner

Faculty Publications

Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures. Sequencing was performed in the same center across 18 different runs. The simplified mock community showed limitations in accuracy, while precision (e.g., technical variation) was robust …

Left Ventricle Function And Post-Transcriptional Events With Exercise Training In Pigs, Stephanie L. Samani, Shayne C. Barlow, Lisa A. Freeburg, Traci L. Jones, Marlee Poole, Mark A. Sarzynski, Michael R. Zile, Tarek Shazly, Francis G. Spinale

Faculty Publications

Background

Standardized exercise protocols have been shown to improve overall cardiovascular fitness, but direct effects on left ventricular (LV) function, particularly diastolic function and relation to post-transcriptional molecular pathways (microRNAs (miRs)) are poorly understood. This project tested the central hypothesis that adaptive LV remodeling resulting from a large animal exercise training protocol, would be directly associated with specific miRs responsible for regulating pathways relevant to LV myocardial stiffness and geometry.

Methods and results

Pigs (n = 9; 25 Kg) underwent a 4 week exercise training protocol (10 degrees elevation, 2.5 mph, 10 min, 5 days/week) whereby LV chamber stiffness (KC) …

Editorial For Gels 6th Anniversary Special Issue, Esmaiel Jabbari, Gulden Camci-Unal

Faculty Publications

Note: In lieu of an abstract, this is an excerpt from the first page.

This Special Issue celebrates many outstanding quality papers published in Gels over the past six years since its first issue was published in 2015 [...]

Antiviral Polymers: A Review, Ali Akbari, Ashkan Bigham, Vahid Rahimkhoei, Sina Sharifi, Esmaiel Jabbari

Faculty Publications

Polymers, due to their high molecular weight, tunable architecture, functionality, and buffering effect for endosomal escape, possess unique properties as a carrier or prophylactic agent in preventing pandemic outbreak of new viruses. Polymers are used as a carrier to reduce the minimum required dose, bioavailability, and therapeutic effectiveness of antiviral agents. Polymers are also used as multifunctional nanomaterials to, directly or indirectly, inhibit viral infections. Multifunctional polymers can interact directly with envelope glycoproteins on the viral surface to block fusion and entry of the virus in the host cell. Polymers can indirectly mobilize the immune system by activating macrophages and …

Biomechanical And Psychological Predictors Of Failure In The Air Force Physical Fitness Test, Jeffrey Turner, Brent T. Langhals, Torrey J. Wagner

Faculty Publications

Physical fitness is a pillar of U.S. Air Force (USAF) readiness and ensures that Airmen can fulfill their assigned mission and be fit to deploy in any environment. The USAF assesses the fitness of service members on a periodic basis, and discharge can result from failed assessments. In this study, a 21-feature dataset was analyzed related to 223 active-duty Airmen who participated in a comprehensive mental and social health survey, body composition assessment, and physical performance battery. Graphical analysis revealed pass/fail trends related to body composition and obesity. Logistic regression and limited-capacity neural network algorithms were then applied to predict …

Decellularized Articular Cartilage Microgels As Microcarriers For Expansion Of Mesenchymal Stem Cells, Esmaiel Jabbari, Azadeh Sepahvandi

Faculty Publications

Conventional microcarriers used for expansion of human mesenchymal stem cells (hMSCs) require detachment and separation of the cells from the carrier prior to use in clinical applications for regeneration of articular cartilage, and the carrier can cause undesirable phenotypic changes in the expanded cells. This work describes a novel approach to expand hMSCs on biomimetic carriers based on adult or fetal decellularized bovine articular cartilage that supports tissue regeneration without the need to detach the expanded cells from the carrier. In this approach, the fetal or adult bovine articular cartilage was minced, decellularized, freeze-dried, ground, and sieved to produce articular …

Nanoparticles For Targeted Drug Delivery To Cancer Stem Cells: A Review Of Recent Advances, Yavuz Nuri Ertas, Keyvan Abedi Dorcheh, Ali Akbari, Esmaiel Jabbari

Faculty Publications

Cancer stem cells (CSCs) are a subpopulation of cells that can initiate, self-renew, and sustain tumor growth. CSCs are responsible for tumor metastasis, recurrence, and drug resistance in cancer therapy. CSCs reside within a niche maintained by multiple unique factors in the microenvironment. These factors include hypoxia, excessive levels of angiogenesis, a change of mitochondrial activity from aerobic aspiration to aerobic glycolysis, an upregulated expression of CSC biomarkers and stem cell signaling, and an elevated synthesis of the cytochromes P450 family of enzymes responsible for drug clearance. Antibodies and ligands targeting the unique factors that maintain the niche are utilized …

3-D Fabry–Pérot Cavities Sculpted On Fiber Tips Using A Multiphoton Polymerization Process, Jonathan W. Smith, Jeremiah C. Williams, Joseph S. Suelzer, Nicholas G. Usechak, Hengky Chandrahalim

Faculty Publications

This paper presents 3-D Fabry–Pérot (FP) cavities fabricated directly onto cleaved ends of low-loss optical fibers by a two-photon polymerization (2PP) process. This fabrication technique is quick, simple, and inexpensive compared to planar microfabrication processes, which enables rapid prototyping and the ability to adapt to new requirements. These devices also utilize true 3-D design freedom, facilitating the realization of microscale optical elements with challenging geometries. Three different device types were fabricated and evaluated: an unreleased single-cavity device, a released dual-cavity device, and a released hemispherical mirror dual-cavity device. Each iteration improved the quality of the FP cavity's reflection spectrum. The …

Machine Intelligence For Nerve Conduit Design And Production, Caleb E. Stewart, Chin Fung Kelvin Kan, Brody R. Stewart, Henry W. Sanicola Iii, Jangwook P. Jung, Olawale A. R. Sulaiman, Dadong Wang

Faculty Publications

Nerve guidance conduits (NGCs) have emerged from recent advances within tissue engineering as a promising alternative to autografts for peripheral nerve repair. NGCs are tubular structures with engineered biomaterials, which guide axonal regeneration from the injured proximal nerve to the distal stump. NGC design can synergistically combine multiple properties to enhance proliferation of stem and neuronal cells, improve nerve migration, attenuate inflammation and reduce scar tissue formation. The aim of most laboratories fabricating NGCs is the development of an automated process that incorporates patient-specific features and complex tissue blueprints (e.g. neurovascular conduit) that serve as the basis for more complicated …

Thermoresponsive Nanogels Based On Different Polymeric Moieties For Biomedical Applications, Sobhan Ghaeini-Hesaroeiye, Hossein Razmi Bagtash, Soheil Boddohi, Ebrahim Vasheghani-Farahani, Esmaiel Jabbari

Faculty Publications

Nanogels, or nanostructured hydrogels, are one of the most interesting materials in biomedical engineering. Nanogels are widely used in medical applications, such as in cancer therapy, targeted delivery of proteins, genes and DNAs, and scaffolds in tissue regeneration. One salient feature of nanogels is their tunable responsiveness to external stimuli. In this review, thermosensitive nanogels are discussed, with a focus on moieties in their chemical structure which are responsible for thermosensitivity. These thermosensitive moieties can be classified into four groups, namely, polymers bearing amide groups, ether groups, vinyl ether groups and hydrophilic polymers bearing hydrophobic groups. These novel thermoresponsive nanogels …

Thermoresponsive Nanogels Based On Different Polymeric Moieties For Biomedical Applications, Sobhan Ghaeini-Hesaroeiye, Hossein Razmi Bagtash, Soheil Boddohi, Ebrahim Vasheghani-Farahani, Esmaiel Jabbari

Faculty Publications

Nanogels, or nanostructured hydrogels, are one of the most interesting materials in biomedical engineering. Nanogels are widely used in medical applications, such as in cancer therapy, targeted delivery of proteins, genes and DNAs, and scaffolds in tissue regeneration. One salient feature of nanogels is their tunable responsiveness to external stimuli. In this review, thermosensitive nanogels are discussed, with a focus on moieties in their chemical structure which are responsible for thermosensitivity. These thermosensitive moieties can be classified into four groups, namely, polymers bearing amide groups, ether groups, vinyl ether groups and hydrophilic polymers bearing hydrophobic groups. These novel thermoresponsive nanogels …

Carbon-Based Artificial Sei Layers For Aqueous Lithium-Ion Battery Anodes, Usha Subramanya, Charleston Chua, Victor Gin He Leong, Ryan Robinson, Gwenlyn Cruz Cabiltes, Prakirti Singh, Bonnie Yip, Anuja Bokare, Folarin Erogbogbo, Dahyun Oh

Faculty Publications

Replacing flammable organic electrolytes with aqueous electrolytes in lithium-ion batteries (LIB) can greatly enhance the safety of next-generation energy storage systems. With the extended electrochemical stability window of electrolytes, 'water-in-salt' (WIS) electrolytes containing LIB presented significant performance improvements. However, the solubility limits of lithium salts in water restrain the extent of kinetic protection offered by the high salt concentration. Here, we report design strategies of anode structure to improve the cycle life of LIB with WIS electrolytes. We introduced partially graphitic protective carbon layers on anode particles using a versatile coating method. This protective layer not only improved charge transfer …

Microwave-Assisted And One-Step Synthesis Of Peg Passivated Fluorescent Carbon Dots From Gelatin As An Efficient Nanocarrier For Methotrexate Delivery, Nasser Arsalani, Parinaz Nezhad-Mokhtari, Esmaiel Jabbari

Faculty Publications

A green and simple process for preparing the polyethylene glycol passivated fluorescent carbon dots (CDs-PEG) have been studied by a microwave pyrolysis method, using gelatin and PEG as starting materials. This method is very effective for development of carbon-based quantum dots from gelatin with high quantum yield (QY). The synthesized CDs-PEG were found to emit blue photoluminescence (PL) with a maximum QY of 34%. At the following research, we investigated the effect of the presence of PEG on PL intensity, and the result showed that CDs-PEG becomes stronger PL properties than pure CDs from gelatin. The synthesized CDs-PEG were characterized …

Bio-Inspired Sensing And Actuating Architectures For Feedback Control Of Civil Structures, Courtney A. Peckens, I. Cook, C. Fogg

Faculty Publications

Civil structures, such as buildings and bridges, are constantly at risk of failure due to external environmental loads, such as earthquakes or strong winds. To minimize the effects of these loads, active feedback control systems have been proposed but such systems still face numerous challenges which impede their widespread adoption. In order to overcome many of these challenges, inspiration can be drawn from the signal processing and actuating techniques employed by the biological central nervous system to develop a bio-inspired control algorithm. In this study the front-end, signal processing techniques employed by biological sensory systems, and in particular the mammalian …

Reactive Ion Plasma Modification Of Poly(Vinyl‐Alcohol) Increases Primary Endothelial Cell Affinity And Reduces Thrombogenicity, Patrick Jurney, Deirdre Anderson, Grace Pohan, Evelyn Yim, Monica Hinds

Faculty Publications

Bulk material properties and luminal surface interaction with blood determine the clinical viability of vascular grafts, and reducing intimal hyperplasia is necessary to improve their long‐term patency. Here, the authors report that the surface of a biocompatible hydrogel material, poly(vinyl alcohol) (PVA) can be altered by exposing it to reactive ion plasma (RIP) in order to increase primary endothelial cell attachment. The power and the carrier gas of the RIP treatment are varied and the resultant surface nitrogen, water contact angle, as well as the ability of the RIP‐treated surfaces to support primary endothelial colony forming cells is characterized. Additionally, …

A Model Of Motor And Sensory Axon Activation In The Median Nerve Using Surface Electrical Stimulation, Jessica L. Gaines, Kathleen E. Finn, Julia P. Slopsema, Lane A. Heyboer, Katharine H. Polasek

Faculty Publications

Surface electrical stimulation has the potential to be a powerful and non-invasive treatment for a variety of medical conditions but currently it is difficult to obtain consistent evoked responses. A viable clinical system must be able to adapt to variations in individuals to produce repeatable results. To more fully study the effect of these variations without performing exhaustive testing on human subjects, a system of computer models was created to predict motor and sensory axon activation in the median nerve due to surface electrical stimulation at the elbow. An anatomically-based finite element model of the arm was built to accurately …

Natural Sensations Evoked In Distal Extremities Using Surface Electrical Stimulation, Julia P. Slopsema, John M. Boss, Lane A. Heyboer, Carson M. Tobias, Brooke P. Draggoo, Kathleen E. Finn, Payton J. Hoff, Katharine H. Polasek

Faculty Publications

Background: Electrical stimulation is increasingly relevant in a variety of medical treatments. In this study, surface electrical stimulation was evaluated as a method to non-invasively target a neural function, specifically natural sensation in the distal limbs.

Method: Electrodes were placed over the median and ulnar nerves at the elbow and the common peroneal and lateral sural cutaneous nerves at the knee. Strength-duration curves for sensation were compared between nerves. The location, modality, and intensity of each sensation were also analyzed. In an effort to evoke natural sensations, several patterned waveforms were evaluated.

Results: Distal sensation was obtained in all but …

Biotemplating Pores With Size And Shape Diversity For Li-Oxygen Battery Cathodes, Dahyun Oh, Cagla Ozgit-Akgun, Esin Akca, Leslie Thompson, Loza Tadesse, Ho-Cheol Kim, Gökhan Demirci, Robert Miller

Faculty Publications

Synthetic porogens provide an easy way to create porous structures, but their usage is limited due to synthetic difficulties, process complexities and prohibitive costs. Here we investigate the use of bacteria, sustainable and naturally abundant materials, as a pore template. The bacteria require no chemical synthesis, come in variable sizes and shapes, degrade easier and are approximately a million times cheaper than conventional porogens. We fabricate free standing porous multiwalled carbon nanotube (MWCNT) films using cultured, harmless bacteria as porogens, and demonstrate substantial Li-oxygen battery performance improvement by porosity control. Pore volume as well as shape in the cathodes were …

Imaging Right Ventricular Function To Predict Outcome In Pulmonary Arterial Hypertension, Alessandro Bellofiore, Melanie Brewis, Rebecca Vanderpool, Naomi Chesler, Martin Johnson, Robert Naeije, Andrew Peacock

Faculty Publications

Right ventricular (RV) function is a major determinant of outcome in pulmonary arterial hypertension (PAH). However, uncertainty persists about the optimal method of evaluation.MethodsWe measured RV end-systolic and end-diastolic volumes (ESV and EDV) using cardiac magnetic resonance imaging and RV pressures during right heart catheterization in 140 incident PAH patients and 22 controls. A maximum RV pressure (Pmax) was calculated from the nonlinear extrapolations of early and late systolic portions of the RV pressure curve. The gold standard measure of RV function adaptation to afterload, or RV–arterial coupling (Ees/Ea) was estimated by the stroke volume (SV)/ESV ratio (volume method) or …

Reduced Haemodynamic Coupling And Exercise Are Associated With Vascular Stiffening In Pulmonary Arterial Hypertension, Alessandro Bellofiore, Eric Dinges, Robert Naeije, Hamorabi Mkrdichian, Lauren Beussink-Nelson, Melissa Bailey, Michael Cuttica, Ranya Sweis, James Runo, Jon Keevil, Christopher Francois, Sanjiv Shah, Naomi Chesler

Faculty Publications

Inadequate right ventricular (RV) and pulmonary arterial (PA) functional responses to exercise are important yet poorly understood features of pulmonary arterial hypertension (PAH). This study combined invasive catheterisation with echocardiography to assess RV afterload, RV function and ventricular–vascular coupling in subjects with PAH.

What Does The Time Constant Of The Pulmonary Circulation Tell Us About The Progression Of Right Ventricular Dysfunction In Pulmonary Arterial Hypertension?, Alessandro Bellofiore, Z. Wang, Naomi Chesler

Faculty Publications

Compliance (C) and resistance (R) maintain a unique, inverse relationship in the pulmonary circulation, resulting in a constant characteristic time that has been observed in healthy subjects as well as patients with pulmonary arterial hypertension (PAH). However, little is known about the dependence of right ventricular (RV) function on the coupled changes in R and C in the context of this inverse relationship. We hypothesized three simple dependencies of RV ejection fraction (RVEF) on R and C. The first model (linear-R) assumes a linear RVEF-R relation; the second (linear-C) assumes a linear RVEF-C relation; and the third one combines the …

Non-Invasive Right Ventricular Efficiency Using 4d Flow Mri, Alejandro Roldán-Alzate, Scott Grogan, Heidi Kellihan, Alessandro Bellofiore, Naomi Chesler, Oliver Wieben, Christopher Francois

Faculty Publications

Pulmonary arterial hypertension (PH) is a progressive disease of increased resistance to flow through the lungs, leading to right ventricular (RV) failure [1]. MRI is increasingly used to assess right ventricular (RV) function in PH. RV stroke work (SW) based on invasive pressure and volume measurements, is used to assess ventricular work. Determining RV work from MRI could enable a more complete characterization of RV and PA interactions in PH. The purpose of this study was to non-invasively estimate RV work from simultaneously acquired RV volume (VRV) and pulmonary artery flow (QPA) using a 4D flow-sensitive MRI sequence …

Monolithic Optofluidic Ring Resonator Lasers Created By Femtosecond Laser Nanofabrication, Hengky Chandrahalim, Qiushu Chen, Ali A. Said, Mark Dugan, Xudong Fan

Faculty Publications

We designed, fabricated, and characterized a monolithically integrated optofluidic ring resonator laser that is mechanically, thermally, and chemically robust. The entire device, including the ring resonator channel and sample delivery microfluidics, was created in a block of fused-silica glass using a 3-dimensional femtosecond laser writing process. The gain medium, composed of Rhodamine 6G (R6G) dissolved in quinoline, was flowed through the ring resonator. Lasing was achieved at a pump threshold of approximately 15 μJ/mm². Detailed analysis shows that the Q-factor of the optofluidic ring resonator is 3.3 × 10⁴, which is limited by both solvent …

Increasing Label-Free Stem Cell Sorting Capacity To Reach Transplantation-Scale Throughput, Melinda Simon, Ying Li, Janahan Arulmoli, Lisa Mcdonnell, Adnan Akil, Jamison Nourse, Abraham Lee, Lisa Flanagan

Faculty Publications

Dielectrophoresis (DEP) has proven an invaluable tool for the enrichment of populations of stem and progenitor cells owing to its ability to sort cells in a label-free manner and its biological safety. However, DEP separation devices have suffered from a low throughput preventing researchers from undertaking studies requiring large numbers of cells, such as needed for cell transplantation. We developed a microfluidic device designed for the enrichment of stem and progenitor cell populations that sorts cells at a rate of 150,000 cells/h, corresponding to an improvement in the throughput achieved with our previous device designs by over an order of …

The Effect Of Platelet-Rich Plasma (Prp) On Muscle Contusion Healing In A Rat Model., Demetris Delos, Matthew J. Leineweber, Salma Chaudhury, Saif Alzoobaee, Yingxin Gao, Scott Alan Rodeo

Faculty Publications

Background: Current therapy for muscle contusions is usually limited to nonsteroidal anti-inflammatory drugs and/or use of the RICE principle (rest, ice, compression, elevation); thus, other forms of treatment that can potentially accelerate the rate of healing are desirable. Hypotheses: A local injection of platelet-rich plasma (PRP) would lead to accelerated healing rates compared with controls; also, delayed administration of PRP would lead to a blunted response compared with immediate treatment. Study Design: Controlled laboratory study. Methods: Forty-six male Lewis rats each underwent a single blunt, nonpenetrating impact to the gastrocnemius muscle via a drop-mass technique and subsequently received either a …

Uncertainty Quantification Driven Predictive Multi-Scale Model For Synthesis Of Mycotoxins, Sourav Banerjee, Gabriel A. Terejanu, Anindya Chanda

Faculty Publications

Many toxic molds synthesize and release an array of poisons, termed mycotoxins that have an enormous impact on human health, agriculture and economy [1]. These molds contaminate our buildings, indoor air and crops, cause life threatening human and animal diseases and reduce agricultural output [2]. In order to design appropriate approaches to minimize the detrimental effects of these fungi, it is essential to develop diagnostic methodologies that can rapidly and accurately determine based on fungal strains and their growth patterns, the extent of mycotoxin mediated damage caused to the environment.Here we developed a novel multi-scale predictive mathematical model that could …

Averaging Improves Strain Images Of The Biceps Brachii Using Quasi-Static Ultrasound Elastography, Matthew Leineweber, J Westborn, A Cochran, Y Gao, J Choi

Faculty Publications

OBJECTIVE:Quasi-static ultrasound elastography is a technique for measuring tissue deformation (strain) under externally applied loading and can be used to identify the presence of abnormalities. The objective of this study was to demonstrate the efficacy of averaging strain images from repeated compression cycles in mitigating user-induced error using quasi-static ultrasound elastography.METHODS:Freehand compressions were performed with an ultrasound transducer on the biceps brachii of nine participants (five males and four females), as well as with a custom automated compression system. Sets of strain images from the freehand techniques were averaged to create single representative images and compared against strain images from …

Modulation Of Leukocyte Infiltration And Phenotype In Microporous Tissue Engineering Scaffolds Via Vector Induced Il-10 Expression, R. Michael Gower, Ryan M. Boehler, Samira M. Azarin, Christine F. Ricci, Joshua N. Leonard, Lonnie D. Shea

Faculty Publications

Biomaterial scaffolds are central to many tissue engineering strategies as they create a space for tissue growth and provide a support for cell adhesion and migration. However, biomaterial implantation results in unavoidable injury resulting in an inflammatory response, which can impair integration with the host and tissue regeneration. Toward the goal of reducing inflammation, we investigated the hypothesis that a lentiviral gene therapy-based approach to localized and sustained IL-10 expression at a scaffold could modulate the number, relative proportions, and cytokine production of infiltrating leukocyte populations. Flow cytometry was used to quantify infiltration of six leukocyte populations for 21 days …

Biologically Enhanced Cathode Design For Improved Capacity And Cycle Life For Lithium-Oxygen Batteries, Dahyun Oh, Jifa Qi, Yi-Chun Lu, Yong Zhang, Yang Shao-Horn, Angela Belcher

Faculty Publications

Lithium-oxygen batteries have a great potential to enhance the gravimetric energy density of fully packaged batteries by two to three times that of lithium ion cells. Recent studies have focused on finding stable electrolytes to address poor cycling capability and improve practical limitations of current lithium-oxygen batteries. In this study, the catalyst electrode, where discharge products are deposited and decomposed, was investigated as it has a critical role in the operation of rechargeable lithium-oxygen batteries. Here we report the electrode design principle to improve specific capacity and cycling performance of lithium-oxygen batteries by utilizing high-efficiency nanocatalysts assembled by M13 virus …

Mammalian Cells Preferentially Internalize Hydrogel Nanodiscs Over Nanorods And Use Shape-Specific Uptake Mechanisms, Rachit Agarwal, Vikramjit Singh, Patrick Jurney, Li Shi, S. Sreenivasan, Krishnendu Roy

Faculty Publications

Size, surface charge, and material compositions are known to influence cell uptake of nanoparticles. However, the effect of particle geometry, i.e., the interplay between nanoscale shape and size, is less understood. Here we show that when shape is decoupled from volume, charge, and material composition, under typical in vitro conditions, mammalian epithelial and immune cells preferentially internalize disc-shaped, negatively charged hydrophilic nanoparticles of high aspect ratios compared with nanorods and lower aspect-ratio nanodiscs. Endothelial cells also prefer nanodiscs, however those of intermediate aspect ratio. Interestingly, unlike nanospheres, larger-sized hydrogel nanodiscs and nanorods are internalized more efficiently than their smallest counterparts. …