Biomedical Engineering and Bioengineering Commons^™

Dna Microarray Image Segmentation Using Active Contours Without Edges Method, Shenghua Ni

Doctoral Dissertations

The goal of this dissertation is to build a better segmentation method for DNA microarray image processing. Segmentation is a partitioning process used to separate a spot area from a non-spot area in DNA microarrays. It directly affects the accuracy of gene expression analysis in the data mining process that follows. A number of DNA microarray segmentation methods have been proposed in the area, but even modern segmentation methods seem to have accuracy problems. In this dissertation, I will present a segmentation method based on the Active Contours Without Edges (ACWE) algorithm and apply it to two types of DNA …

Mechanical Properties Of Hydroxyapatite-Zirconia Compacts Sintered By Two Different Sintering Methods, Declan J. Curran, Thomas J. Fleming, Mark R. Towler, Stuart Hampshire

Chemical and Biochemical Engineering Faculty Research & Creative Works

Microwave sintering is traditionally employed to reduce the sintering temperature required to densify powder compacts. The effect of microwave heating on hydroxyapatite (HA)-zirconia (ZrO₂) green bodies has been investigated in order to understand how microwave energy may affect the physical and mechanical properties of the resultant densified composites. Laboratory synthesised nano-sized HA and a commercial nano-sized ZrO₂ powder have been ball milled to create mixtures containing 0-5 wt% ZrO₂ loadings. Compacts were microwave sintered at either 700, 1000 or 1200°C with a 1 h hold time. Comparative firings were also performed in a resistive element furnace …

An Investigative Study Into The Relationship Of Bone Morphogenetic Protein Antagonist Expression And Osteocyte Density By Region And Quadrant, Scott C. Mosher

Master's Theses

The role of cytokines and cell behavior and viability with respect to bone remodeling and bone behavior is an exciting area of orthopedic research. The purpose of this study was to investigate the relationships between BMP antagonist expression and osteocyte density, lacunar densities and osteocyte viability in cortical bone. Samples of unloaded tibial bone obtained from six C57Bl/6 mice were immunohistochemically stained for gremlin and noggin expression and also underwent methyl green staining to determine osteocyte presence. Bone sections were divided into four quadrants (cranial, caudal, medial and lateral) and three regions (proximal, mid shaft and distal), followed by analysis …

Modeling The Long Term Effects Of Alendronate On Bone Mass Preservation Of The Femur With Articular Surface And Total Hip Replacements, Trevor J. Hryce

Master's Theses

Calculating femoral bone density changes after hip arthroplasty is of interest to researchers and clinicians for predicting the longevity of the prosthetic implant and the surrounding bone. Recently clinicians have been administering bisphosphonate drugs in an attempt to reduce the bone resorption due to stress shielding caused by these implants. Current strain-adaptive computational models with bisphosphonate treatment don’t predict the long term effects or look at treatment with hip resurfacing implants. The main goal of this study was to create and validate a computer model of the human femur incorporating a bone remodeling algorithm based on biological remodeling processes and …

Effect Of Loading Condition On Traction Coefficient Between Shoes And Artificial Turf Surfaces, Seth M. Kuhlman, Michelle B. Sabick, Ronald Pfeiffer, Benjamin Cooper, Jackie Forhan

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Background. The interaction between a shoe and a turf surface is highly complex and difficult to characterize. Over the three decades since artificial turf was introduced, researchers have attempted to understand the traction caused by the interaction. However, some of the methodologies used for traction measurements have not capitalized on advances in currently available technology for testing and most testing conditions have not simulated realistic physiological loads.

Method of Approach. To assess the effect of test condition on traction results, the newly designed TurfBuster testing device was used to collect traction data on FieldTurf™ brand artificial turf under varying conditions. …

A Non-Rigid Registration Method For Analyzing Myocardial Wall Motion For Cardiac Ct Images, Elizabeth B. Philps

Master's Theses (2009 -)

Cardiac resynchronization therapy (CRT) has a high percentage of non-responders. Successfully locating the optimal location for CRT lead placement on a priori images can increase efficiency in procedural preparation and execution and could potentially increase the rate of CRT responders.

Registration has been used in the past to assess the motion of medical images. Specifically, one method of non-rigid registration has been utilized to assess the motion of left ventricular MR cardiac images. As CT imaging is often performed as part of resynchronization treatment planning and is a fast and accessible means of imaging, extending this registration method to assessing …

Bi-Planar Postural Stability Model: Fitting Parameters To Patient Data Automatically, Andrew Michael Sovol

Master's Theses (2009 -)

Studies of children with cerebral palsy (CP) have shown that maintaining control of posture in quiet standing is often difficult. Physical therapy and assistive devices, both with or without surgery, may be employed in an effort to improve postural stability. Assessing the effectiveness of such interventions is important for healthcare providers and their patients. A previously created bi-planar model of posture control has been further developed as a method of assessment. This MATLAB and Simulink model has successfully replicated experimental results for typical adults and children, as well as children with CP across three different test conditions: eyes open, eyes …

Upper Extremity Kinetics During Lofstrand Crutch-Assisted Gait In Children, Neha Bhagchandani

Master's Theses (2009 -)

Complete biomechanical analysis helps evaluate the motion during various gait patterns for the upper and lower extremities. Extensive studies have been performed to evaluate unassisted gait patterns, but very little has been accomplished for studying assisted motion. Children with pathologies such as osteogenesis imperfecta, spinal cord injury, and cerebral palsy use assistive devices such as anterior and posterior walkers, canes, Lofstrand and axillary crutches for ambulation purposes.

Statistics show that there are currently about 566,000 crutch users in the United States. The long-term crutch users in this population can suffer various upper limb pathologies associated with extensive upper extremity (UE) …

Sensitivity Of Motor Adaptation To The Statistical Properties Of An Environmental Load, Timothy Michael Haswell

Master's Theses (2009 -)

Linear, limited-memory models capture many important features of adaptive motor performance during reaching, stepping and pointing. A recent study in our lab found that a model fitted to data obtained from subjects reaching against elastic loads which varied from trial-to-trial later failed to fit the steady-state response behavior of subjects exposed to deterministic, step changes in load. Does motor adaptation depend on statistical properties of the environment (eg. mean load strength and variability)? Neurologically intact volunteers (n=14) made 6 blocks of 100 planar, ballistic, 10cm, out-and-back reaching movements against spring-like loads having equilibrium positions at the hand's starting point. View …

Finite Element Analysis And Modeling Of A .38 Lead Round Nose Ballistic Gelatin Test, Danielle Datoc

Master's Theses

Firearms are present in two-thirds of United States households. As of 2003, roughly 500,000 projectile wounds occur annually in the United States. This costs an estimated 2.3 billion dollars of medical spending. The best treatment of gunshot wounds relies heavily on experience, but even with experience the unpredictable nature of ballistics can make treatment difficult.

Wound ballistics studies the injury pattern of a particular bullet. Ballistic gelatin tests are used to analyze this pattern. A block of 10 or 20% ballistic gelatin is set and a bullet is fired through the block. Key characteristics of the wound profile seen in …

Human Osteoblast Proliferation In Culture Following A Nanosecond Pulsed Electric Field (Nspef), Leonard Joseph Carinci Jr.

Biological Sciences Theses & Dissertations

Osteoblasts are mononucleate bone forming cells responsible for the deposition of new bone. Application of mechanical stress on bone reveals its ability to produce and release electric potentials across the cell membrane called piezoelectricity. The electric potentials produced in response to mechanical stress may have a direct correlation on osseous cells and the signaling pathways that regulate proliferation. Nanosecond pulsed electric fields (nsPEFs) are high intensity, ultrashort pulses which have the ability to maintain the integrity of the cell membrane by avoiding traditional electroporation. We delivered 8 nsPEFs (0.5 Hz) of a 25 kV/cm or 35 kV/cm electric field strength …

Uncertainty In Indirect Land Use Change Emissions In The Life Cycle Of Biofuels: Implications For Legislation, Adam Liska

Adam Liska Papers

Current EPA life cycle analysis (LCA) of greenhouse gas (GHG) emissions from corn-ethanol will be the foundation for regulations for advanced biofuels. It appears regulatory policies that include emissions from indirect land use change (and other indirect emissions) in the biofuel life cycle are moving faster than the underlying science; there is no comparable scientific study that approaches the complexity in methods currently used by the EPA. There is substantial uncertainty in quantifying direct and indirect emissions from fuels, as evidenced by conflicting results from state and federal regulators and from within the scientific community. If indirect emissions from land …

Design And Development Of An Enzyme-Linked Biosensor For Detection And Quantification Of Phosphate Species, Serkan Akar

FIU Electronic Theses and Dissertations

The objective of this study is to design and development of an enzyme-linked biosensor for detection and quantification of phosphate species. Various concentrations of phosphate species were tested and completed for this study.

Phosphate is one of the vital nutrients for all living organisms. Phosphate compounds can be found in nature (e.g., water sediments), and they often exist in aninorganic form. The amount of phosphates in the environment strongly influences the operations of living organisms. Excess amount of phosphate in the environment causes eutrophication which in turn causes oxygen deficit for the other living organisms. Fish die and degradation of …

Antimicrobial And Antioxidant Activities Of Essential Oil And Methanol Extract Of Jasminum Sambac From Djibouti, Fatou Abdoul-Latif, Prosper Edou, François Eba, Nabil Mohamed, Adwa Ali, Samatar Djama, Louis-Clément Obame, Mamoudou Hama Dicko

Pr. Mamoudou H. DICKO, PhD

The essential oil of jasminum sambac from Djibouti was subjected to screening for their possible antioxidant activity by two complementary test systems, namely DPPH free radical scavenging and beta-carotene-linoleic acid assays. Butylated hydroxytoluene (BHT) was used as positive control in both test systems. In the DPPH test system, the IC50 value of essential oil and methanol extract were respectively 7.43 and 2.30 μg/ml. In the beta-carotene-linoleic acid system, oxidation was effectively inhibited by Jasminum sambac, the RAA value of essential oil and methanol extract were respectively 96.6 and 93.9%. When compared to BHT, the essential oil and methanol extract had …

A Linear Finite Element Acoustic Fluid-Structure Model Of Ultrasonic Angioplasty In Vivo, Mark Wylie, Garrett Mcguinness, Graham Gavin

Articles

The delivery of high-power ultrasonic energy via small diameter wire waveguides represents a new alternative therapy for the treatment of chronic totally occluded arteries (CTOs). This type of energy manifests itself as a mechanical vibration at the distal-tip of the waveguide with amplitudes of vibration up to 60 µm and at frequencies of 20- 50 kHz. Disruption of diseased tissue is reported to be a result of direct mechanical ablation, cavitation, pressure components and acoustic streaming and that ablation was only evident above the cavitation threshold. This work presents a linear finite element acoustic fluid-structure model of an ultrasonic angioplasty …

Development Of A Novel Noise Delivery System For Jp-8 Ototoxicity Studies, John E. Stubbs

Theses and Dissertations

Numerous chemicals with ototoxic properties may cause hearing loss directly, potentiate noise-induced hearing loss, or produce additive effects. Of interest to the US Air Force are studies showing ototoxic effects of JP-8 jet fuel and its hydrocarbon constituents. The Naval Health Research Center (NHRC) at Wright-Patterson AFB, Ohio, in conjunction with the USAF, is studying the ototoxic effects of JP-8 in rats. The study requires a white noise source that is one octave band wide, centered at 8 kHz frequency, delivered from outside of exposure chambers. Sound pressure levels must be within ± 2 dB at all exposure points within …

Isolated Cellulose Synthase Promoter Regions, Chandrashekhar P. Joshi

Michigan Tech Patents

The invention relates to methods of inducing expression of coding sequences including cellulose synthase coding sequences in transgenic plants using promoters of cellulose synthase genes from Populus plant species and transgenic plants produced by the methods.

Age-Related Mineralization Heterogeneity In Human Femoral Cortical Bone, Timothy L. Norman, X. Chen

Engineering and Computer Science Faculty Presentations

No abstract provided.

Viscoelastic Effects Of Unreamed Intramedullary Nailing, G. Noble, Timothy L. Norman

Engineering and Computer Science Faculty Presentations

No abstract provided.

Height Adjustment In Assessing Dual Energy X-Ray Absorptiometry Measurements Of Bone Mass And Density In Children, Babette S. Zemel, Mary B. Leonard, Andrea Kelly, Joan M. Lappe, Vicente Gilsanz, Sharon Oberfield, Soroosh Mahboubi, John A. Shepherd, Thomas N. Hangartner, Margaret M. Frederick, Karen K. Winer, Heidi J. Kalkwarf

Biomedical, Industrial & Human Factors Engineering Faculty Publications

Context: In children, bone mineral content (BMC) and bone mineral density (BMD) measurements by dual-energy x-ray absorptiometry (DXA) are affected by height status. No consensus exists on how to adjust BMC or BMD (BMC/BMD) measurements for short or tall stature.

Objective: The aim of this study was to compare various methods to adjust BMC/BMD for height in healthy children.

Design: Data from the Bone Mineral Density in Childhood Study (BMDCS) were used to develop adjustment methods that were validated using an independent cross-sectional sample of healthy children from the Reference Data Project (RDP).

Setting: We conducted the study in five …

Mitochondrial Matrix K+ Flux Independent Of Large-Conductance Ca2+-Activated K+ Channel Opening, Mohammed Aldakkak, David F. Stowe, Qunli Cheng, Wai-Meng Kwok, Amadou K.S. Camara

Biomedical Engineering Faculty Research and Publications

Large-conductance Ca²⁺-activated K⁺ channels (BK_Ca) in the inner mitochondrial membrane may play a role in protecting against cardiac ischemia-reperfusion injury. NS1619 (30 μM), an activator of BK_Ca channels, was shown to increase respiration and to stimulate reactive oxygen species generation in isolated cardiac mitochondria energized with succinate. Here, we tested effects of NS1619 to alter matrix K⁺, H⁺, and swelling in mitochondria isolated from guinea pig hearts. We found that 30 μM NS1619 did not change matrix K⁺, H⁺, and swelling, but that 50 and 100 …

Homotopy Perturbation Algorithm Using Laplace Transformation, Mohammad Madani, Mahdi Fathizade

Mohammad Madani

In this paper, a combinatory method of the Laplace transform and the homotopy perturbation method is proposed to solve non-homogeneous partial differential equations with variable coefficients. The obtained approximate solutions are compared with exact solutions and those obtained by other analytical methods, showing reliability of the present method.

One-Pot Enzymatic Synthesis Of Deoxy-Thymidine-Diphosphate (Tdp)-2-Deoxy-∝-D-Glucose Using Phosphomannomutase, Yung-Hum Yang, Young Bok (Abraham) Kang, Dae-Hee Kim, Tek-Hyung Lee, Sung-Hee Park, Kwangwon Lee, Dongwon Yoo, Kwang-Kyung Liou, Hee-Chan Lee, Jae-Kyung Sohng, Byung-Gee Kim

Faculty Publications - Biomedical, Mechanical, and Civil Engineering

Production of deoxy-thymidine-diphosphate (TDP)-sugars as substrates of glycosyltransferases, has been one of main hurdles for combinatorial antibiotic biosynthesis, which combines sugar moiety with aglycon of various antibiotics. Here, we report the one-pot enzymatic synthesis of TDP-2-deoxy-glucose employing high efficient TMP kinase (TMK; E.C. 2.7.2.12), acetate kinase (ACK; E.C. 2.7.1.21), and TDP-glucose synthase (TGS; E.C. 2.7.7.24) with phosphomannomutase (PMM; E.C. 5.4.2.8). In this study, replacing phosphoglucomutase (PGM; E.C. 5.4.2) by PMM from Escherichia coli gave four times higher specific activity on 2-deoxy-6-phosphate glucose, suggesting that the activity on 2-deoxy-glucose-6-phosphate was mainly affected by PMM activity, not PGM activity. Using an in …

Crystallization Of Community-Acquired Respiratory Distress Syndrome Toxin From Mycoplasma Pneumonia, Olga N. Pakhomova, Alexander B. Taylor, Argentina Becker, Stephen P. Holloway, T. R. Kannan, Joel B. Baseman, P. John Hart

Bioelectrics Publications

Community-acquired respiratory distress syndrome toxin (CARDS TX) is a 591-amino-acid protein with ADP-ribosyltransferase and vacuolating activities that damages the cells lining the respiratory tracts of patients infected with the bacterial pathogen Mycoplasma pneumoniae. Crystals of CARDS TX were grown in space group C2, with unit-cell parameters a = 191.4, b = 107.4, c = 222.1 A, beta = 90.6 degrees. A complete 2.2 A data set was obtained from a single CARDS TX crystal.

Electrically Mediated Delivery Of Plasmid Dna To The Skin, Using A Multielectrode Array, Richard Heller, Yolmari Criz, Loree C. Heller, Richard A. Gilbert, Mark J. Jaroszeski

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take full advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is a strong candidate to meet this delivery criterion. Electroporation of the skin is a simple, direct, in vivo method to deliver genes for therapy. Previously, delivery to the skin was performed by means of applicators with relatively large distances between electrodes, resulting in significant muscle stimulation and pain. These applicators also had limitations in controlling the directionality of the applied field. …

Controlling Nonviral Gene Delivery Through The Cell-Biomaterial Interface, Beth A. Duensing

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Controlling Nonviral Gene Delivery through the Cell-Biomaterial Interface
Beth Ann Duensing, M.S. University of Nebraska, 2010
Adviser: Angela Pannier

Cell-biomaterial interactions and the corresponding cellular behaviors are poorly understood. Therefore, in this study, the ability of biomaterial surface properties to control nonviral gene delivery was investigated through surface chemistry and protein adsorption and subsequently correlated to cellular behaviors controlled by cell-biomaterial interactions. Self-assembled monolayers (SAMs) of alkanethiols on gold were used as model biomaterials to investigate the effect of surface properties on nonviral gene transfer to cells adhered to these surfaces. SAMs presenting terminal CH₃, OH, COO^{- …}

Ct Energy Weighting In The Presence Of Scatter And Limited Energy Resolution, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Purpose: Energy-resolved CT has the potential to improve the contrast-to-noise ratio(CNR) through optimal weighting of photonsdetected in energy bins. In general, optimal weighting gives higher weight to the lower energy photons that contain the most contrast information. However, low-energy photons are generally most corrupted by scatter and spectrum tailing, an effect caused by the limited energy resolution of the detector. This article first quantifies the effects of spectrum tailing on energy-resolved data, which may also be beneficial for material decomposition applications. Subsequently, the combined effects of energy weighting, spectrum tailing, and scatter are investigated through simulations.

Methods: The study first …

Lipids And Collagen Matrix Restrict The Hydraulic Permeability Within The Porous Compartment Of Adult Cortical Bone, Demin Wen, Caroline Androjna, Amit Vasanji, Joanne M. Belovich, Ronald J. Midura

Chemical & Biomedical Engineering Faculty Publications

In vivo the hydraulic permeability of cortical bone influences the transport of nutrients, waste products and signaling molecules, thus influencing the metabolic functions of osteocytes and osteoblasts. In the current study two hypotheses were tested: the presence of (1) lipids and (2) collagen matrix in the porous compartment of cortical bone restricts its permeability. Our approach was to measure the radial permeability of adult canine cortical bone before and after extracting lipids with acetone-methanol, and before and after digesting collagen with bacterial collagenase. Our results showed that the permeability of adult canine cortical bone was below 4.0 × 10 …

Links With Canada Benefit Dit Prosthesis Research, Colm O'Kane

Articles

Colm O’Kane is a lecturer in the School of Manufacturing and Design Engineering and a member of the DIT Biomedical Device and Assistive Technology Research Group. He is currently engaged in PhD research in the field of knee prosthesis development, focused on developing optimised strategies for partial and total joint replacements used in treatment of osteoarthritis of the knee joint. This article is an account of a research scholarship sponsored by the CHC Helicopter Corporation and awarded by the Ireland Canada University Foundation (ICUF). This foundation awards annual scholarships for research visits between Ireland and Canada with the aspiration of …

St Monitoring On The Programmer For Implantable Cardioverter Devices, Sarina Satya

Master's Theses

Cardiovascular disease is one of the most prevalent causes of death which has a high mortality rate. If identified early and treated appropriately, the mortality in patients with cardiovascular disease can be hugely reduced. For several decades, 12-Lead ECG has been the standard technique used to identify ischemia, and recent studies have shown that intracardiac electrogram has many benefits over external monitoring such as holter. ST Monitoring feature has been added to St. Jude Medical intracardiac cardioverter defibrillators (ICD) to leverage the ECG technology for identifying cardiovascular disease. This algorithm monitors the intracardiac electrogram to detect and report patterns which …