Engineering Commons^™

Theoretically Proposed Optimal Frequency For Ultrasound Induced Cartilage Restoration, April D. Miller, Anuradha Subramanian, Hendrik J. Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Background: Matching the frequency of the driving force to that of the system’s natural frequency of vibration results in greater amplitude response. Thus we hypothesize that applying ultrasound at the chondrocyte’s resonant frequency will result in greater deformation than applying similar ultrasound power at a frequency outside of the resonant bandwidth. Based on this resonant hypothesis, our group previously confirmed theoretically and experimentally that ultrasound stimulation of suspended chondrocytes at resonance (5 MHz) maximized gene expression of load inducible genes. However, this study was based on suspended chondrocytes. The resonant frequency of a chondrocyte does not only depend on the …

A Comprehensive Dosimetric Study On Switching From A Type-B To A Type-C Dose Algorithm For Modern Lung Sbrt, Christina Zhou, Nathan Bennion, Rongtao Ma, Xiaoying Liang, Shuo Wang, Kristina Zvolanek, Megan Hyun, Xiaobo Li, Sumin Zhou, Weining Zhen, Chi Lin, Andrew Wahl, Dandan Zheng

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Type-C dose algorithms provide more accurate dosimetry for lung SBRT treatment planning. However, because current dosimetric protocols were developed based on conventional algorithms, its applicability for the new generation algorithms needs to be determined. Previous studies on this issue used small sample sizes and reached discordant conclusions. Our study assessed dose calculation of a Type-C algorithm with current dosimetric protocols in a large patient cohort, in order to demonstrate the dosimetric impacts and necessary treatment planning steps of switching from a Type-B to a Type-C dose algorithm for lung SBRT planning.

Methods: Fifty-two lung SBRT patients were included, each …

Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, Seong-Il Eyun

Nebraska Center for Biotechnology: Faculty and Staff Publications

Background: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.

Results: This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of …

Evolutionary History Of Chemosensory-Related Gene Families Across The Arthropoda, Seong-Il Eyun, Ho Young Soh, Marijan Posavi, James B. Munro, Daniel S.T. Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, Harshavardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Eun-Ok Park, Joana C. Silva, Richard A. Gibbs, Stephen Richards, Carol Eunmi Lee

Nebraska Center for Biotechnology: Faculty and Staff Publications

Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also examine hypotheses on which arthropod CRG family is most ancient. Thus, we reconstructed phylogenies of CRGs, including those from new arthropod genomes and transcriptomes, and …

Specimen-Specific Natural, Pathological, And Implanted Knee Mechanics Using Finite Element Modeling, Azhar Akber Ali

Electronic Theses and Dissertations

There is an increasing incidence of knee pain and injury among the population, and increasing demand for higher knee function in total knee replacement designs. As a result, clinicians and implant manufacturers are interested in improving patient outcomes, and evaluation of knee mechanics is essential for better diagnosis and repair of knee pathologies. Common knee pathologies include osteoarthritis (degradation of the articulating surfaces), patellofemoral pain, and cruciate ligament injury and/or rupture. The complex behavior of knee motion presents unique challenges in the diagnosis of knee pathology and restoration of healthy knee function. Quantifying knee mechanics is essential for developing successful …

A Method For Measuring The Attachment Strength Of The Cestode Hymenolepis Diminuta To The Rat Intestine, Wanchuan Xie, Gábor R. Rácz, Benjamin S. Terry, Scott Lyell Gardner

Scott L. Gardner Publications

A unique adaptation of many internal parasites of mammals is their ability to stay in the intestine for extended periods of time and resist the normal peristaltic movements and forces that push and expel material. To better understand parasite adhesion behavior and replicate their attachment method in medical devices, an experiment was designed and performed using the rat tapeworm, Hymenolepis diminuta. The experiment employed a tensile test machine and a digital scale and was designed to calculate the attachment strength of the scolex to the mucosa through the change of the value of the digital scale during the tensile …

Influence Of Fibroblasts On Metastatic Cancer Cell Drug Resistance In A 3d Microfluidic Cell Array, Elizabeth C. Benoy

Dissertations and Theses

Modeling an accurate depiction of the tumor microenvironment, (TME), is essential to observe the effect external factors might have on the tumor in vivo. In cancer therapy specifically, the outcomes of clinical treatments are heavily dependent on drug testing methods despite the cytotoxic effects these methods might have on the patient. Our lab has previously developed a three layered microfluidic cell array (3D μFCA) to reconstruct the relevantly spatial configuration of tumor and microvasculature found in vivo in order to develop a more efficient tool of high throughput drug discovery and screening. In this study, we optimized this device to …

Design Development And Performance Study Of A Novel Assistive Device For Mobility Of Toddlers And Children With Visual Impairments, Joowon Jun

Dissertations and Theses

Being able to see allows mankind tremendous access to learn about the world, and because so much learning comes visually, children with visual impairments are delayed in developing range of skills: learning own languages, doing activities, socializing with peers, and etc. While children with vision can do virtually all the activities and tasks for granted, children with visual impairment require different types of tools or materials to do same tasks most of time. Amongst all the disadvantages that children with visual impairment have, one of the most critical disadvantageous area that visual impairment brings to toddler is learning to walk. …

Automatic Optimum Atlas Selection For Multi-Atlas Image Segmentation Using Joint Label Fusion, Kofi Agyeman

Dissertations and Theses

Multi-atlas image segmentation using label fusion is one of the most accurate state of the art image segmentation techniques available for biomedical imaging applications. Motivated to achieve higher image segmentation accuracy, reduce computational costs and a continuously increasing atlas data size, a robust framework for optimum selection of atlases for label fusion is vital. Although believed not to be critical for weighted label fusion techniques by some works (Sabuncu, M. R. et al., 2010, [1]), others have shown that appropriate atlas selection has several merits and can improve multi-atlas image segmentation accuracy (Aljabar et al., 2009, [2], Van de Velde …

Multi-Scale Assessment Of Bone Mechanics And The Mineral Phase Of Intramuscular Bone Of Atlantic Herring Fish, Svetlana Zeveleva

Dissertations and Theses

Bone tissue is a complex composite structure made up of a soft organic phase consisting of collagen I and non-collagenous proteins, and a hard inorganic phase consisting of mineral nanoplatelets. Given it’s compositional properties, bone is a unique stiff, tough, and strong biomaterial, making it exceptionally difficult to synthesize ex vivo. While the complete hierarchical structure may change with age and population, the basic building block components of mineralized collagen fibrils, are preserved. This study uses a model of intramuscular bone of the Atlantic herring fish, which present a simple structure, and no process of remodeling.

A multi-scale approach …

Regulation Of The Expression And Activity Of Extracellular Signal-Regulated Kinase 3 (Erk3), Lobna Elkhadragy

Browse all Theses and Dissertations

Mitogen-activated protein kinases (MAPKs) are Ser/Thr kinases that regulate diverse cellular processes. Extracellular signal-regulated kinase 3 (ERK3) is an atypical MAPK that has recently gained interest for its roles in cancer. ERK3 promotes cancer cell migration, invasion and drug resistance, and its expression is upregulated in multiple cancers. However, little is known about the molecular mechanisms that regulate ERK3’s expression and kinase activity. Here, we have identified the oncogenic polycomb group protein BMI1 as a positive regulator of ERK3 level in cancer cells. Mechanistically, BMI1 upregulates ERK3 expression by inhibiting the expression of the tumor suppressor microRNA (miRNA) let-7i, which …

Glycolytic Metabolism And Pregnancy Parameters In The Murine Placenta, Renee Elizabeth Albers

Browse all Theses and Dissertations

The placenta is a complex and essential organ composed largely of fetal-derived cells, including several different trophoblast subtypes that work in unison to support nutrient transport to the fetus during pregnancy. Abnormal placental development can lead to pregnancy-associated disorders that often involve metabolic dysfunction. The scope of dysregulated metabolism during placental development may not be fully representative of the in vivo state in defined culture systems, such as cell lines or isolated primary cells. Thus, assessing metabolic function in intact placental tissue would provide a better assessment of placental metabolism. In this study, we describe a methodology for assaying glycolytic …

Phospholipase D: Key Player In Macrophage-Mediated Inflammation And Resolution, Ramya Ganesan

Browse all Theses and Dissertations

Phospholipase D (PLD) is a cell membrane remodeling and signaling protein implicated in the pathology of chronic inflammation. As PLD is also central to macrophage cell migration, we investigated the molecular basis of PLD's involvement and regulation in macrophage-initiated inflammation (atherosclerosis) and resolution. We have found that PLD is associated with signaling proteins and positively affects cell movement, phagocytosis and NADPH-initiated release of Reactive Oxygen Species (ROS). We found that PLD2 but not PLD1 is important for foam cell formation that causes atherogenesis. We have also found a novel way of inducing macrophage class-switch (polarization) by PLD overexpression. PLD induces …

Proteomic Analysis Of Ischemic Stroke Blood Biomarkers, April Arnold Daubenspeck

Browse all Theses and Dissertations

Stroke is a global burden that claims 6 million lives and permanently disables another 5 million each year. The risk of morbidity and mortality following stroke decreases when early diagnosis and treatment are achieved. However there is no blood test to diagnose ischemic stroke because biomarkers to date have not shown adequate sensitivity and specificity to be adopted into hospital protocols. The overall objective of this dissertation was to identify novel blood protein biomarkers of ischemic stroke. We achieved this by using a number of proteomic and statistical techniques to investigate the differential abundance of proteins in the blood of …

Making Meaning: Shifts In Meaningfulness Across Three Modeling Units, Jeannette Manger

Browse all Theses and Dissertations

Recent reform calls for a more comprehensive approach to science education that positions learners as constructors of knowledge via scientific practices (NRC, 2012; Osborne, 2014). This 'practice turn' shifts from passive science learning to incorporating science actions with epistemic thinking (Duschl & Grandy, 2013; Ford & Forman, 2006; Osborne, 2014; Shouse, Schweingruber, & Duschl, 2007). Teachers are often underprepared in understanding the nuances of scientific practices, and frequently struggle with supporting students in meaningful practice engagement (Abd-El-Khalick & Akerson, 2004; Crawford, 1999; Davis, Petish, & Smithey, 2006; Duschl & Gitomer, 1997). Here, I draw upon the Berland et al. Epistemologies …

Biochemical And Histological Differences Between Costal And Articular Cartilages, Michael W. Stacey

Bioelectrics Publications

Biologically, costal cartilage is an understudied tissue type and much is yet to be learned regarding underlying mechanisms related to form and function, and how these relate to disease states, specifically chest wall deformity. Chest wall deformities have a component of inheritance, implying underlying genetic causes; however the complexity of inheritance suggests multiple genetic components. At our Centre investigations were performed on gene expression of key select genes from costal cartilage removed at surgery of patients with chest wall deformity to show high expression of decorin, a key player in collagen fiber formation and growth. Also, the degree of tissue …

Pet Imaging Of Early Therapeutic Response In Solid Tumors, Stephanie J. Blocker

Wayne State University Dissertations

An important pillar of precision medicine for oncology is the ability to identify patients who respond to treatment early into their therapy. Positron emission tomography (PET) allows physicians and researchers to measure changes in tumor behavior prior to noticeable differences in morphology.

Objective: Determine the utility of multiple tracers for PET in assessing early changes in tumor activity that result from treatment.

Methods: Two tracers for PET were studied. 64Cu-labeled liposomes were used to assess changes in liposome delivery two solid colon tumors early into treatment with bevacizumab (Bev). 18F-FMAU thymidine analog (1-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)thymine), was utilized to detect early response to …

Biom 4110/6110: The Science Of Medicine (Syllabus), Bradford D. Pendley

Biomedical Engineering Syllabi Archive

Course Description: Integration of fundamental principles from physics, chemistry, biology and mathematics, and applications of these principles to solve problems in medicine.

Biom 3110: Medical Physiology (Syllabus), Bradford D. Pendley

Biomedical Engineering Syllabi Archive

Course Description: Basic principles of human physiology and how these are applied in medicine and biomedical engineering problem and devices; physiological principles using appropriate mathematical and engineering models to construct an understanding of how the body works as an integrated system.

A Computational Study Of Vegf Production By Patterned Retinal Epithelial Cell Colonies As A Model For Neovascular Macular Degeneration, Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis, Nicholas Flann

Biology Faculty Publications

Background: The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) forms of the disease, retinal pigment epithelial (RPE) cells respond to adjacent atrophied regions by secreting vascular endothelial growth factor (VEGF) that in turn recruits new blood vessels which lead to a further reduction in retinal function and vision. In vitro models exist for studying VEGF expression in wet AMD (Vargis et al., Biomaterials 35(13):3999–4004, 2014), but are limited in the patterns of necrotic and intact RPE epithelium they can …

Biomanufacturing Through Igem-An International Student Competition, Asif Rahman, Ryan J. Putman, Neal Hengge, Charles D. Miller

Biological Engineering Faculty Publications

The foundations of synthetic biology are built on molecular biology and genetic engineering. One of the purposes of synthetic biology is to make biology easier to engineer by the creation of standardized biological parts and devices. There are a wide range of potential applications for synthetic biology and a variety of approaches to constructing parts and systems. Undergraduate Science, Technology, Engineering, and Mathematics (STEM) students from around the world apply synthetic biology principles at the annual International Genetically Engineered Machine (iGEM) competition to demonstrate functioning biological systems created from standardized parts. The iGEM competition will continue to add to the …

Qualitative Analysis Of Microbial Dynamics During Anaerobic Digestion Of Microalgal Biomass In A Uasb Reactor, Anna Doloman, Yousef Soboh, Andrew J. Walters, Ronald C. Sims, Charles D. Miller

Biological Engineering Faculty Publications

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the …

Fabrication Of Flexible, Biofunctional Architectures From Silk Proteins, Ramendra K. Pal

Theses and Dissertations

Advances in the biomedical field require functional materials and processes that can lead to devices that are biocompatible, and biodegradable while maintaining high performance and mechanical conformability. In this context, a current shift in focus is towards natural polymers as not only the structural but also functional components of such devices. This poses material-specific functionalization and fabrication related questions in the design and fabrication of such systems. Silk protein biopolymers from the silkworm show tremendous promise in this regard due to intrinsic properties: mechanical performance, optical transparency, biocompatibility, biodegradability, processability, and the ability to entrap and stabilize biomolecules. The unique …

Investigation Of Polymeric Composites For Controlled Drug Release, Hsi-Wei Yeh

Theses and Dissertations

The Electrospray (ES) technique is a promising particle generation method for drug delivery due to its capabilities of producing monodisperse PLGA composite particles with unique configurations and high drug encapsulation efficiency. In the dissertation work, the coaxial dual capillary ES was used to generate drug-loaded core-shell PLGA particles to study the effects of particle filling materials, drug loading locations and particle shell thicknesses on the resultant in vitro release behaviors of the hydrophilic and/ or hydrophobic model drugs. Through release profile characterization of drug-loaded PLGA particles (particle size: 400 nm and 1 μm), it was confirmed that the co-encapsulation of …

Pore-Confined Carriers And Biomolecules In Mesoporous Silica For Biomimetic Separation And Targeting, Shanshan Zhou

Theses and Dissertations--Chemical and Materials Engineering

Selectively permeable biological membranes composed of lipophilic barriers inspire the design of biomimetic carrier-mediated membranes for aqueous solute separation. This work imparts selective permeability to lipid-filled pores of silica thin film composite membranes using carrier molecules that reside in the lipophilic self-assemblies. The lipids confined inside the pores of silica are proven to be a more effective barrier than bilayers formed on the porous surface through vesicle fusion, which is critical for quantifying the function of an immobilized carrier. The ability of a lipophilic carrier embedded in the lipid bilayer to reversibly bind the target solute and transport it through …

Skintronics: Wireless, Skin-Wearable Electronics For Monitoring Of Electrocardiogram, Matthew B. Piper, Woon-Hong Yeo, Yongkuk Lee

UROP Posters

The ECGs I micro-fabricate are designed to be flexible, stretchable and wireless circuits that can be applied to the skin directly. The device is encased in a conformal, silicon-like substrate, that allows the ECG to be attached with the electrodes. Each electrode has been previously measured and verified that it will be correctly placed for an accurate reading. Prototyping this ECG/electrode device allows the user to mount the prototype directly to the patient without having to attach and wire ten other electrodes. This prototype solves the issue that comes about when a doctor, nurse or emergency medical technician must attach …

Design Of A Fine-Needle Aspiration Biopsy Device For Thyroid Nodules, Troy Furst, Christa Spieth, Gunnar Lovhoiden, Michael Spieth

Posters, Presentations, and Papers

While other devices currently exist to assist in FNA biopsies, none remove the repetitive whole wrist or arm movements needed to collect the sample.

Evaluating Outer Segment Length As A Surrogate Measure Of Peak Foveal Cone Density, Melissa A. Wilk, Brandon M. Wilk, Christopher S. Langlo, Robert F. Cooper, Joseph Carroll

Biomedical Engineering Faculty Research and Publications

Adaptive optics (AO) imaging tools enable direct visualization of the cone photoreceptor mosaic, which facilitates quantitative measurements such as cone density. However, in many individuals, low image quality or excessive eye movements precludes making such measures. As foveal cone specialization is associated with both increased density and outer segment (OS) elongation, we sought to examine whether OS length could be used as a surrogate measure of foveal cone density. The retinas of 43 subjects (23 normal and 20 albinism; aged 6–67 years) were examined. Peak foveal cone density was measured using confocal adaptive optics scanning light ophthalmoscopy (AOSLO), and OS …

Diffusion Tensor Imaging Correlates With Short-Term Myelopathy Outcome In Patients With Cervical Spondylotic Myelopathy, Aditya Vedantam, Avinash Rao, Shekar N. Kurpad, Michael B. Jirjis, Gerald Eckardt, Brian D. Schmit, Marjorie C. Wang

Biomedical Engineering Faculty Research and Publications

Objective

To determine if spinal cord diffusion tensor imaging indexes correlate with short-term clinical outcome in patients undergoing elective cervical spine surgery for cervical spondylotic myelopathy (CSM).

Methods

A prospective consecutive cohort study was performed in patients undergoing elective cervical spine surgery for CSM. After obtaining informed consent, patients with CSM underwent preoperative T2-weighted magnetic resonance imaging and diffusion tensor imaging of the cervical spine. Fractional anisotropy (FA) values at the level of maximum cord compression and at the noncompressed C1-2 level were calculated on axial images. We recorded the modified Japanese Orthopaedic Association (mJOA) scale, Neck Disability Index, and …

Structurofunctional Resting-State Networks Correlate With Motor Function In Chronic Stroke, Benjamin Kalinosky, Reivian B. Barillas, Brian D. Schmit

Biomedical Engineering Faculty Research and Publications

Purpose

Motor function and recovery after stroke likely rely directly on the residual anatomical connections in the brain and its resting-state functional connectivity. Both structural and functional properties of cortical networks after stroke are revealed using multimodal magnetic resonance imaging(MRI). Specifically, functional connectivity MRI (fcMRI) can extract functional networks of the brain at rest, while structural connectivity can be estimated from white matter fiber orientations measured with high angular-resolutiondiffusion imaging (HARDI). A model that marries these two techniques may be the key to understanding functional recovery after stroke. In this study, a novel set of voxel-level measures …