Biomedical Engineering and Bioengineering Commons^™

The Highly Similar Arabidopsis Homologs Of Trithorax Atx1 And Atx2 Encode Proteins With Divergent Biochemical Functions, Abdelaty Saleh, Raul Alvarez-Venegas, Mehtap Yilmaz, Oahn-Le, Guichuan Hou, Monther Sadder, Ayed Al-Abdallat, Yuannan Xia, Guoqinq Lu, Istvan Ladunga, Zoya Avramova

Nebraska Center for Biotechnology: Faculty and Staff Publications

Gene duplication followed by functional specialization is a potent force in the evolution of biological diversity. A comparative study of two highly conserved duplicated genes, ARABIDOPSIS TRITHORAX-LIKE PROTEIN1 (ATX1) and ATX2, revealed features of both partial redundancy and of functional divergence. Although structurally similar, their regulatory sequences have diverged, resulting in distinct temporal and spatial patterns of expression of the ATX1 and ATX2 genes. We found that ATX2 methylates only a limited fraction of nucleosomes and that ATX1 and ATX2 influence the expression of largely nonoverlapping gene sets. Even when coregulating shared targets, ATX1 and ATX2 may employ different …

Orthogonal Cutting Of Bone, Donal Mccrohan

Theses

The cutting of bone has been undertaken for many centuries. Research in this area is contnually progressing to achieve an efficient cutting action while reducing recovery time and rauma to the patient.

Orthogonal cutting is defined where the cutting edge of the tool is set in a position that is perpendicular to the direction of relative work or tool motion. The failure mechanisms involved in the cutting of bone, their direct relationships to cutting tool geometry and cutting direction for orthogonal cutting are not accurately defined or quantified. A study of the orthogonal cutting behaviour of bone initiated in the …

Balance Performance Measurment In A Phase Shifted Feedback Environment, Craig Alan Hoovler

Theses and Dissertations

Commercial technologies for the objective assessment of balance exist in clinical settings. Training requires integration of sensory information to produce a coordinated motor response related to balance. These systems have had measurable phase delays of up to 250ms in the visual feedback provided to the patient. This provokes an unnatural response, requiring prediction from the subject. The proposed research investigates the impact of visual feedback phase delays on the performance of weight shift tracking tasks in a population of individuals with no known balance deficits.Visual feedback delays were investigated by simulating popular balance training software which utilizes force plates to …

Detailed Characterization Of The Mouse Embryonic Stem Cell Transcriptome Reveals Novel Genes And Intergenic Splicing Associated With Pluripotency, Galih Kunarso, Kee-Yew Wong, Lawrence W. Stanton, Leonard Lipovich

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Transcriptional control of embryonic stem (ES) cell pluripotency has been a subject of intense study. Transcriptional regulators including Oct4 (Oct3/4 index), Sox2 and Nanog are fundamental for maintaining the undifferentiated state. However, the ES cell transcriptome is not limited to their targets, and exhibits considerable complexity when assayed with microarray, MPSS, cDNA/EST sequencing, and SAGE technologies. To identify novel genes associated with pluripotency, we globally searched for ES transcripts not corresponding to known genes, validated their sequences, determined their expression profiles, and employed RNAi to test their function.

Results

Gene Identification Signature (GIS) analysis, a SAGE derivative distinguished …

Site-Specific Effects Of Pecam-1 On Atherosclerosis In Ldl Receptor-Deficient Mice, Shikha Arora, Brian Boylan, Reema Goel, Benjamin R. Schrank, Barbara Fleming, Rose Ann Fleming, Hiroto Mirura, Peter J. Newman, Robert C. Molthen, Debra K. Newman

Biomedical Engineering Faculty Research and Publications

Objective—Atherosclerosis is a vascular disease that involves lesion formation at sites of disturbed flow under the influence of genetic and environmental factors. Endothelial expression of adhesion molecules that enable infiltration of immune cells is important for lesion development. Platelet/endothelial cell adhesion molecule-1 (PECAM-1; CD31) is an adhesion and signaling receptor expressed by many cells involved in atherosclerotic lesion development. PECAM-1 transduces signals required for proinflammatory adhesion molecule expression at atherosusceptible sites; thus, it is predicted to be proatherosclerotic. PECAM-1 also inhibits inflammatory responses, on which basis it is predicted to be atheroprotective.

Methods and Results—We evaluated herein the effect of …

The Effects Of Chronic Hypoxia And Substance P On The Chemosensitive Response Of Individual Nucleus Tractus Solitarius (Nts) Neurons From Adult Rats, Nicole L. Nichols

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The chemosensitive responses of individual nucleus tractus solitarius (NTS) neurons from neonatal rats have been extensively studied, but few studies have examined the chemosensitive responses of NTS neurons from adult rats. In addition, environmental conditions have been used to mimic respiratory diseases/disorders in rats to study how the cellular responses of individual neurons change to regulate breathing during pathological conditions. Lastly, it has been shown that substance P release increases in response to hypoxia from peripheral afferents that primarily terminate in the caudal NTS. We studied the effect of chronic hypoxia (CHx) and substance P on the response to hypercapnia …

Mechanism Of Nanoparticle And Nanotube-Induced Cell Death, Syed Khaja Sohaebuddin

Bioengineering Theses - Archive

Recent advances in nanotechnology have lead to synthesis of high-quality nanoparticles which exhibit unique physical and chemical properties. The novel properties of these nanoparticles are widely being applied for diagnostic and therapeutic purposes and enable new means of biosensing and targeted drug delivery. However, increasing evidence has suggested that some nanoparticles may cause detrimental effects on cells and tissues. Using titanium oxide (TiO2) nanoparticles (5-10 nm diameter), silicon oxide (SiO2) nanoparticles (30 nm diameter), and multi-walled carbon nanotubes (MWCNTs) of different diameters (<8 nm, 20-30 nm, >50 nm), 0.5-2 µm in length as test subjects, we evaluated the in vitro interaction of these …

Integration Of Hyperspectral Imaging System For Optimized Data Acquisition And Control To Revolutionized Pathology Applications, Dipen Rana

Bioengineering Theses - Archive

Detecting and measuring the interactions and expression levels of tumor markers in a cancerous cell are quintessential in prognosis and management of cancer. These have propagated the need to develop better microscopic imaging techniques to understand the cellular structure and its functional behavior. Pathologist use techniques such immunohistochemistry and in situ hybridization to measure and detect these tumor marker expression levels. Fluorophores are used in these techniques as fluorescent tags to identify the tumor markers. These fluorophores have unique absorption and emission spectrum, making them useful to not only identify but also quantify the concentration levels of these markers. This …

Synthesis And Characterization Of Crosslinked Urethane Doped Polyesters For Vascular Tissue Engineering, Jagannath Dey

Bioengineering Theses - Archive

Traditional crosslinked polyester elastomers are inherently weak, and the strategy of increasing crosslink density to improve their mechanical properties makes them brittle materials. Biodegradable polyurethanes, although strong and elastic, do not fare well in dynamic environments due to the onset of permanent deformation. The design and development of a soft, strong and completely elastic (100% recovery from deformation) material for tissue engineering still remains a challenge. Herein, we report the synthesis and evaluation of a new class of biodegradable elastomers, crosslinked polyurethane-doped polyesters (CUPEs), which is able to satisfy the need for soft, strong, and elastic biomaterials. Tensile strength of …

Development Of Novel Multilayered Particles For Drug Delivery And Cell Isolation Applications, Bhanuprasanth Koppolu

Bioengineering Theses - Archive

The objective of this work is to develop multilayered nanoparticles for drug delivery and cell isolation applications. These particles principally consist of three layers; biodegradable polymer, thermo sensitive polymer and magnetic materials. For drug delivery, multilayered nanoparticles (MLNP) consisting of a magnetic core and two encompassing shells made up of temperature sensitive polymer, poly (N-isopropylacrylamide) (PNIPAAm), and biodegradable polymer, poly(D, L lactide-co-glycolide) (PLGA), were developed for targeted and controlled drug delivery. The PNIPAAm layer was immobilized onto magnetic nanoparticles (MNPs) via a silane coupling agent, Vinyltrimethoxysilane (VTMS), and free radical polymerization. These particles were then encapsulated with PLGA using a …

Novel Redox And Dna-Dependent Conformational Changes In Human Ku, A Dna-Double Strand Break Repair Protein, Jason Alexander Lehman

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Ionizing radiation (IR) and radiomimetic drugs used in cancer chemotherapy cause DNA double-strand breaks which are repaired by the nonhomologous end joining (NHEJ) pathway. Ku is a heterodimeric protein comprised of 70 and 80 kDa subunits and recognizes free DNA ends. Once Ku is bound to DNA, it binds to the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and forms a heterotrimeric DNA-PK complex for repair and damage signaling.

We have analyzed the Ku protein using multiple biochemical techniques and uncovered a novel reversible redox change (Andrews, Lehman and Turchi, (2006) JBC 281(19):13596-603). From this data, we hypothesized that a redox-dependent …

Performance Analysis Of Quantitative Bone Measurement With Spiral, Multi-Detector Ct Scanners, Shruti Gupta

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The measure of bone strength and fracture risk assessment is based primarily on bone mineral density (BMD). Computed tomography (CT), a frequently used radiographic technique that provides cross-sectional images, can be used for BMD quantification. Called quantitative computed tomography (QCT), it determines true volumetric density and also differentiates between trabecular and cortical bone. As a result, QCT improves the ability to detect early changes in trabecular BMD accurately and precisely.

The introduction of helical CT for quantitative analysis introduces new complexities. Even though using multi-detector helical CT for BMD assessment is being suggested, a detailed analysis of its validity is …

A New Paradigm For Human Resuscitation Research Using Intelligent Devices, Charles F. Babbs, Andre E. Kemeny, Weilun Quan, Gary Freeman

Weldon School of Biomedical Engineering Faculty Publications

Objectives: To develop new methods for studying correlations between the performance and outcome of resuscitation efforts in real-world clinical settings using data recorded by automatic devices such as automatic external defibrillators (AEDs), and to explore effects of shock timing and chest compression depth in the field. Methods: In 695 records of AED use in the pre-hospital setting, continuous compression data were recorded using AEDs capable of measuring sternal motion during compressions, together with timing of delivered shocks and the electrocardiogram. In patients who received at least one shock, putative return of spontaneous circulation (P-ROSC) was defined as a regular, narrow …

Il-21 Limits Peripheral Lymphocyte Numbers Through T Cell Homeostatic Mechanisms., Shrimati Datta, Nora E. Sarvetnick

Journal Articles: Regenerative Medicine

BACKGROUND: IL-21, a member of the common gamma-chain utilizing family of cytokines, participates in immune and inflammatory processes. In addition, the cytokine has been linked to autoimmunity in humans and rodents.

METHODOLOGY/PRINCIPAL FINDINGS: To investigate the mechanism whereby IL-21 affects the immune system, we investigated its role in T cell homeostasis and autoimmunity in both non-autoimmune C57BL/6 and autoimmune NOD mice. Our data indicate that IL-21R knockout C57BL/6 and NOD mice show increased size of their lymphocyte population and decreased homeostatic proliferation. In addition, our experimental results demonstrate that IL-21 inhibits T cell survival. These data suggest that IL-21 acts …

Histogram-Based Template Matching Object Detection In Images With Varying Brightness And Contrast, Christina Da-Wann Schrider

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Our challenge was to develop a semi-automatic target detection algorithm to aid human operators in locating potential targets within images. In contrast to currently available methods, our approach is relatively insensitive to image brightness, image contrast and object orientation. Working on overlapping image blocks, we used a sliding difference method of histogram matching. Incrementally sliding the histograms of the known object template and the image region of interest (ROI) together, the sum of absolute histogram differences was calculated. The minimum of the resultant array was stored in the corresponding spatial position of a response surface matrix. Local minima of the …

Biomechanical Evaluation Of Locked And Non-Locked Constructs Under Axial And Torsion Loading, Vinit A. Patel

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Locking compression plates are proven to be safe for use in open reduction and internal fixation (ORIF). The ORIF is a procedure performed to treat fractures. It has various combination of holes, the system provides more options for clinicians to use either locking screw or non-locking screws. This thesis investigates and determines the best construct with special locking and non-locking screws under both axial and torsion loading. Twenty femur constructs were assembled with 2 cm osteotomy gap between femur shaft and condyle, bridged with 4.5 mm - 10 holes condyle plates. Femurs were divided in to 4 groups according to …

Motion-Control System Of Bench-Top Ct Scanner, Tarpit Kaushikbhai Patel

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Computed Tomography (CT) imaging has found applications in many areas such as diagnostic visualization, quantitative estimation, and therapeutic verification. In this wide range of applications, a CT scanner that can provide the data collection schemes of both second- and third-generation data-collection geometries will be an asset for laboratory research. In this thesis project, we developed a mechanical design and constructed a dual-generation CT scanner that provides flexibility in accommodating a wide range of object sizes with minimum scan time. Using 3-D graphical design software, models of the current second-generation CT scanner and possible solutions for modification were simulated. Based on …

Finite Element Optimization Of Hip Implant Geometrical Parameters To Determine Safe Zones And Resist Dislocation, Himanshu K. Bhatt

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A computational study was performed using finite element analysis (FEA) of three dimensional solid hip implant models. Twelve different hip implant models were designed to investigate the performance of geometrical parameters affecting hip stability. The parameters examined were head diameter, neck diameter, head-to-neck ratio, neck angle and acetabular liner thickness. Component orientations included cup anatomical inclination and cup anteversion, which should be accounted for during total hip implant design as well as in the practice of arthroplasties. A static analysis was performed for all 12 hip designs using stainless steel 316L. von Mises stress, contact stress, contact penetration, and sliding …

Automated Analysis Of Metacarpal Cortical Thickness In Serial Hand Radiographs, Aarti Raheja

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To understand the roles of various genes that influence skeletal bone accumulation and loss, accurate measurement of bone mineralization is needed. However, it is a challenging task to accurately assess bone growth over a person's lifetime. Traditionally, manual analysis of hand radiographs has been used to quantify bone growth, but these measurements are tedious and may be impractical for a large-scale growth study. The aim of this project was to develop a tool to automate the measurement of metacarpal cortical bone thickness in standard hand-wrist radiographs of humans aged 3 months to 70+ years that would be more accurate, precise …

Aging And Sleep Stage Effects On Entropy Of Electroencephalogram Signals, Swetha Vennelaganti

University of Kentucky Master's Theses

The aging brain is characterized by alteration in synaptic contacts, which leads to decline of motor and cognitive functions. These changes are reflected in the age related shifts in power spectrum of electroencephalogram (EEG) signals in both wakefulness and sleep. Various non-linear measures have been used to obtain more insights from EEG analysis compared to the conventional spectral analysis. In our study we used Sample Entropy to quantify regularity of the EEG signal. Because elderly subjects arouse from sleep more often than younger subjects, we hypothesized that Entropy of EEG signals from elderly subjects would be higher than that from …

Pathogen Best Management Practices (Bmps), Richard K. Koelsch

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Management practices targeting pathogens focus on establishing multiple barriers between the pathogen source and water, with each barrier designed to lessen the risk of pathogens. The “Agricultural Environmental Management” program developed at Cornell University for dairy producers in New York watersheds promotes a four-barrier approach.

Alkaline Pretreatment Of Coastal Bermudagrass For Bioethanol Production, Ziyu Wang, Deepak R. Keshwani, Arthur P. Redding, Jay J. Cheng

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Lignocellulosic materials are regarded as an alternative energy source for bioethanol production to reduce our reliance on fossil fuels. Pretreatment is important for improving the enzymatic digestibility of lignocelluloses to increase the yield of fermentable sugars. Alkaline (sodium hydroxide and lime (calcium hydroxide)) pretreatment of coastal bermudagrass for enhanced reducing sugars recovery was investigated in this study. The effect of NaOH pretreatment at 121°C using 1%, 2% and 3% (w/v) NaOH for 15, 30, 60 and 90 minutes was evaluated first. Lower NaOH concentrations (0.5% and 0.75%) and lower temperatures (50, 80 and 100°C) were then examined. Lime (0.1 g …

Nutrient Transport As Affected By Rate Of Overland Flow, John E. Gilley, W. F. Sabatka, B. Eghball, David B. Marx

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Little information is currently available concerning the effects of varying flow rate on nutrient transport by overland flow. The objective of this study was to measure the effects of overland flow rate on nutrient transport following the application of beef cattle or swine manure to plots containing 0, 2, 4, or 8 Mg ha^-1 of corn residue. After addition of residue materials to 0.75 m wide by 2.0 m long plots, beef cattle or swine manure was added and the plots were then either disked or maintained in a no-till condition. Three 30 min simulated rainfall events, separated by …

Narrow Grass Hedge Effects On Nutrient Transport Following Compost Application, John E. Gilley, B. Eghball, David B. Marx

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The placement of stiff‐stemmed grass hedges on the contour along a hillslope has been shown to decrease nutrient transport in runoff. This study was conducted to measure the effectiveness of a narrow grass hedge in reducing runoff nutrient transport from plots with a range of soil nutrient values. Composted beef cattle manure was applied at dry weights of 0, 68, 105, 142, and 178 Mg ha^-1 to a silty clay loam soil and then incorporated by disking. Soil samples were collected 243 days later for analysis of water‐soluble phosphorus (WSP), Bray and Kurtz No. 1 phosphorus (Bray‐1 P), NO …

Rule-Based Mamdani-Type Fuzzy Modeling Of Skin Permeability, Deepak R. Keshwani, David D. Jones, George E. Meyer, Rhonda M. Brand

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Two Mamdani type fuzzy models (three inputs–one output and two inputs–one output) were developed to predict the permeability of compounds through human skin. The models were derived from multiple data sources including laboratory data, published data bases, published statistical models, and expert opinion. The inputs to the model include information about the compound (molecular weight and octonal–H₂O partition coefficient) and the application temperature. One model included all three parameters as inputs and the other model only included information about the compound. The values for mole molecular weight ranged from 30 to 600 Da. The values for the log …

Performance Evaluation Of Aluminum Test Cell Designed For Determining The Heat Resistance Of Bacterial Spores In Foods, H.-J. Chung, Sohan Birla, Juming Tang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Thermal inactivation kinetic studies are necessary to determine heat resistances of spores in the development of new thermal processes for low-acid shelf-stable products. Most currently available sample holders used in the kinetic studies take long time to reach the target sample temperature, hence fail to provide isothermal condition. In this research, novel aluminum test cells were developed to facilitate easy loading and unloading solid and liquid food samples in a hermetically sealed 1 ml cavity to evaluate the heat resistance of bacterial spores when heated at temperatures above 100 °C. Design of the test cell was governed by minimum come-up …

Construction, Installation, And Performance Of Two Repacked Weighing Lysimeters, José O. Payero, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Weighing lysimeters are the standard method for directly measuring evapotranspiration (ET). This paper discusses the construction, installation, and performance of two (1.52 m × 1.52 m × 2.13-m deep) repacked weighing lysimeters for measuring ET of corn and soybean in West Central Nebraska. The cost of constructing and installing each lysimeter was approximately US $12,500, which could vary depending on the availability and cost of equipment and labor. The resolution of the lysimeters was 0.0001 mV V^-1, which was limited by the data processing and storage resolution of the datalogger. This resolution was equivalent to 0.064 and 0.078 …

Variability Analyses Of Alfalfa-Reference To Grass-Reference Evapotranspiration Ratios In Growing And Dormant Seasons, Suat Irmak, Ayse Kilic, T. A. Howell, Derrel Martin, J. O. Payero, K. S. Copeland

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Alfalfa-reference evapotranspiration (ET_r) values sometimes need to be converted to grass-reference ET (ET_o), or vice versa, to enable crop coefficients developed for one reference surface to be used with the other. However, guidelines to make these conversions are lacking. The objectives of this study were to: (1) develop ET_r to ET_o ratios (K_r values) for different climatic regions for the growing season and nongrowing (dormant) seasons; and (2) determine the seasonal behavior of K_r values between the locations and in the same location for different seasons. Monthly average K_r values …

Analytical Modeling With Decoupled Optimal Control Of Biomechanical Sit -To -Stand Movement, Asif Mahmood Mughal

Theses and Dissertations

Biomechanical movements with multiple degrees of freedom exhibit complex coordination and control mechanisms in the presence of physiological constraints. A human body biomechanical model which can mimic diverse 3D physiological movements is a challenging task. In this study, we develop a mathematical framework to study human sit-to-stand (STS) movement using 2D biomechanical models. This analytical framework models the physiological system for feedback controller design. A 2D 4-segment biomechanical model with optimal feedback controller design provides a motivation to extend this scheme for analytical 3D bipedal modeling. We used a newly developed mathematical modeling toolbox (Maple’s DynaFlexPro) to generate 3D 8-segment …

The Power Of Soil: Using It To Our Advantage, Judith L. Sims, R. Otis

Biological Engineering Faculty Publications

No abstract provided.