Biomedical Commons^™

Biomarker Identification For Prostate Cancer Using An Efficient Feature Selection Algorithm, Vamsi Krishnam Raju Mantena

Electrical & Computer Engineering Theses & Dissertations

In recent years, there has been an increased interest in using protein mass spectrometry to identify biomarkers that discriminate diseased from healthy individuals. A biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathological processes, or pharmacological responses to a therapeutic intervention. Identifying biomarkers will be an important step towards disease characterization and patient management. One challenge of biomarker identification is how to handle the high dimensional mass spectral data. In this thesis, we applied an efficient feature selection algorithm to mass spectrometry data obtained from prostate tissue samples to identify prostate …

An Approach To Identifying The Biomechanical Differences Between Intercostal Cartilage In Subjects With Pectus Excavatum And Normals In Vivo: Reconstruction And Ct Registration, Zhenzhen Yan

Electrical & Computer Engineering Theses & Dissertations

Pectus excavatum (PE) is a congenital chest wall deformity affecting the ribs and sternum and exhibiting a concave appearance in the anterior chest wall. In this thesis, we describe a study to investigate in vivo differences in the pectus excavatum rib cage and outline steps using normals and pectus patients data in developing models and methods to be used in carrying out the study. We propose methods to develop reconstructed models in order to enable proper registration between data collection points (DCPs) on the 3D CT rib cage model and CT skin surface model and registration between CT surrogate models …

An Efficient Algorithm For Biomarker Identification, Jiang Li, Rick Mckenzie, Lisa Cazares, Richard Drake, John Semmens

Electrical & Computer Engineering Faculty Publications

No abstract provided.

Microfabrication Of An Optical Chamber For Exposing Living Cells To Pulsed Electric Fields, Saleh Sheikh

Electrical & Computer Engineering Theses & Dissertations

I have fabricated a chamber which enables the application of Nanosecond Pulsed Electric Fields (nsPEFs) to living cells while monitoring their real time fluorescence with an inverted microscope. The No. I thickness (150µm nominal) coverslip glass substrate used for fabrication allows the use of high numerical aperture oil immersion objectives for imaging intracellular organelles. Electrodes are fabricated by first evaporating a chromium adhesion layer, followed by a nickel seed layer. Subsequently, an ultra-thick positive photoresist is applied and patterned to create a 30µm thick electroplating mold. The electrodes are then electrodeposited into the mold from a nickel sulfamate plating bath. …

Simulation And Modeling Of Nerve Impulse Propagation And Its Blockage By External Electrical Stimulation, Nidhi Nahar

Electrical & Computer Engineering Theses & Dissertations

The electric nature of biological tissues permits the transmission of signals for information and for control and is, therefore, of vital importance for life. The latest scientific achievements and nanoscale probing techniques now allow scientists to research at the subcellular level by measuring the electric current flows through a single ion channel of the cell membrane with the patch-clamp method. With the latter approach, the effects of electrical stimulation can be quantified, understood, and applied to molecular biology and the development of medical diagnostic and therapeutic methods.

In this thesis, the Hodgkin-Huxley approach for unmyelinated fibers, coupled with a transmission …

Bactericidal Effects Of Cold Plasma Technology On Geobacillus Stearothermophilus And Bacillus Cereus Microorganisms, Angela Dawn Morris

Dental Hygiene Theses & Dissertations

Non-equilibrium atmospheric pressure plasma, also known as cold plasma, is a state of matter that consists of a mix of neutral and charged particles. Plasma generates chemically reactive species and ultraviolet radiation making them useful in decontamination applications (Kong & Laroussi, 2003). Research regarding the inactivation of gram-positive bacteria, such as Bacillus atrophaeus, by cold plasma has been studied by Laroussi et al. (2003); however, there is limited research regarding the germicidal effectiveness of cold plasma on the microorganisms Geobacillus stearothermophilus and Bacillus cereus. The purpose of this study was to determine if cold plasma technology inactivates heat …

Self-Consistent Analyses For Potential Conduction Block In Nerves By An Ultrashort High-Intensity Electric Pulse, R. P. Joshi, A. Mishra, Q. Hu, K. H. Schoenbach, A. Pakhomov

Bioelectrics Publications

Simulation studies are presented that probe the possibility of using high-field (>100kV ∕ cm), short-duration (∼50ns) electrical pulses for nonthermal and reversible cessation of biological electrical signaling pathways. This would have obvious applications in neurophysiology, clinical research, neuromuscular stimulation therapies, and even nonlethal bioweapons development. The concept is based on the creation of a sufficiently high density of pores on the nerve membrane by an electric pulse. This modulates membrane conductance and presents an effective "electrical short" to an incident voltage wave traveling across a nerve. Net blocking of action potential propagation can then result. A continuum approach based …

The Effects Of Ultrashort Pulsed Electric Fields On The Fluorescent Molecule Bodipy Fl C5 Ceramide, Rachael Sara Shevin

Electrical & Computer Engineering Theses & Dissertations

Nanosecond pulsed electric fields are able to manipulate internal cell organelles by taking advantage of the small but finite time required for charge to establish across a capacitive barrier. Pulsed electric fields also affect macromolecular structures such as enzymes and proteins. Application of a single nanosecond pulsed electric field decreases the fluorescence of a commercially available biological dye Bodipy FL C₅ Ceramide, used to observe the Golgi apparatus of living cells. The effect is seen when the fluorophore is exposed to an electric field both in vitro and when incorporated into the Golgi of a living Jurkat cell. Observation …

Temporal Calcium Response Of Jurkat Cells To Nanosecond Pulsed Electric Fields, Shaka Shakar Scarlett

Electrical & Computer Engineering Theses & Dissertations

Nanosecond pulsed electric fields (nsPEF) of megavolt per meter field strengths can interact with subcellular structures [1] and consequently trigger a variety of biological events. The exposure can induce apoptosis, as well as an array of differential "sub-lethal effects." One of the most sensitive and immediate responses is the increase in intracellular calcium concentration in pulsed cells [2], [3][4].We investigated the response of Jurkat cells (a human leukemic cell line) to nsPEFs of 60 ns duration and field strengths from 25 tol00 kV/cm. The development of the induced calcium response in individual cells was studied by spinning-disc confocal microscopy with …

Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome Structure At 1.5 A˚ And Cytochrome Interaction With Metal Complexes, Mrunalini Pattarkine, J J. Tanner, C A. Bottoms, Y H. Lee, Judy D. Wall

Faculty Works

The structure of the type I tetraheme cytochrome c3 from Desulfovibrio desulfuricans G20 was determined to 1.5 A˚ by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determined from oxidized crystals soaked in sodium molybdate. Only small structural shifts were obtained with metal binding, consistent with the remarkable structural stability of this protein. In vitro experiments with pure cytochrome showed that molybdate could oxidize the reduced cytochrome, although not as rapidly as U(VI) present as uranyl acetate. Alterations in the overall conformation and thermostability of the metal-oxidized protein were investigated …

Wavelet Analysis In Virtual Colonoscopy, Sharon Greenblum, Jiang Li, Adam Huang, Ronald M. Summers, Armando Manduca (Ed.), Amir A. Amini (Ed.)

Electrical & Computer Engineering Faculty Publications

The computed tomographic colonography (CTC) computer aided detection (CAD) program is a new method in development to detect colon polyps in virtual colonoscopy. While high sensitivity is consistently achieved, additional features are desired to increase specificity. In this paper, a wavelet analysis was applied to CTCCAD outputs in an attempt to filter out false positive detections. 52 CTCCAD detection images were obtained using a screen capture application. 26 of these images were real polyps, confirmed by optical colonoscopy and 26 were false positive detections. A discrete wavelet transform of each image was computed with the MATLAB wavelet toolbox using the …

Hybrid Committee Classifier For A Computerized Colonic Polyp Detection System, Jiang Li, Jianhua Yao, Nicholas Petrick, Ronald M. Summers, Amy K. Hara, Joseph M. Reinhardt (Ed.), Josien P.W. Pluim (Ed.)

Electrical & Computer Engineering Faculty Publications

We present a hybrid committee classifier for computer-aided detection (CAD) of colonic polyps in CT colonography (CTC). The classifier involved an ensemble of support vector machines (SVM) and neural networks (NN) for classification, a progressive search algorithm for selecting a set of features used by the SVMs and a floating search algorithm for selecting features used by the NNs. A total of 102 quantitative features were calculated for each polyp candidate found by a prototype CAD system. 3 features were selected for each of 7 SVM classifiers which were then combined to form a committee of SVMs classifier. Similarly, features …

Simulations Of Nanopore Formation And Phosphatidylserine Externalization In Lipid Membranes Subjected To A High-Intensity, Ultrashort Electric Pulse, Q. Hu, R. P. Joshi, K. H. Schoenbach

Bioelectrics Publications

A combined MD simulator and time dependent Laplace solver are used to analyze the electrically driven phosphatidylserine externalization process in cells. Time dependent details of nanopore formation at cell membranes in response to a high-intensity (100kV∕cm), ultrashort (10ns) electric pulse are also probed. Our results show that nanosized pores could typically be formed within about 5ns. These predictions are in very good agreement with recent experimental data. It is also demonstrated that defect formation and PS externalization in membranes should begin on the anode side. Finally, the simulations confirm that PS externalization is a nanopore facilitated event, rather than the …

A System For Monitoring Pressures And Spinal Curvature In Spinally Injured People Immobilised On A Spinal Raft, Ruairí De Fréin, Eoin Flinn, Ted Burke

Articles

We present a system designed to study the pressure at various ‘hot spots’ on the back of the body and the deformation of the spine experienced by a patient when strapped to a spinal board, and the potential alleviation of both by the addition of an inflatable “spinal raft” (or other similar device). In measuring pressure we devised a system of air-filled sacks interfaced with a PC. Each sack, placed under a particular key point on the body, is inflated until its faces just begin to separate and a switch thereby opens. The pressure reading is then captured and displayed …

Implementation Of Gy-Eq For Deterministic Effects Limitation In Shield Design, John W. Wilson, Myung-Hee Y. Kim, Giovanni De Angelis, Francis A. Cucinotta, Nobuaki Yoshizawa, Francis F. Badavi

Mathematics & Statistics Faculty Publications

The NCRP has recently defined RBE values and a new quantity (Gy-Eq) for use in estimation of deterministic effects in space shielding and operations. The NCRP's RBE for neutrons is left ambiguous and not fully defined. In the present report we will suggest a complete definition of neutron RBE consistent with the NCRP recommendations and evaluate attenuation properties of deterministic effects (Gy-Eq) in comparison with other dosimetric quantities.

Studies On The Formation Of Dna-Cationic Lipid Composite Films And Dna Hybridization In The Composites, Murali Sastry, Vidya Ramakrishnan, Mrunalini Pattarkine, Krishna N. Ganesh

Faculty Works

The formation of composite films of double-stranded DNA and cationic lipid molecules (octadecylamine, ODA) and the hybridization of complementary single-stranded DNA molecules in such composite films are demonstrated. The immobilization of DNA is accomplished by simple immersion of a thermally evaporated ODA film in the DNA solution at close to physiological pH. The entrapment of the DNA molecules in the cationic lipid film is dominated by attractive electrostatic interaction between the negatively charged phosphate backbone of the DNA molecules and the protonated amine molecules in the thermally evaporated film and has been quantified using quartz crystal microgravimetry (QCM). Fluorescence studies …

Cationic Surfactant Mediated Hybridization And Hydrophobization Of Dna Molecules At The Liquid/Liquid Interface And Their Phase Transfer, Murali Sastry, Ashavani Kumar, Mrunalini Pattarkine, Vidya Ramakrishnan, Krishna N. Ganesh

Faculty Works

Hybridization of complementary oligonucleotides mediated by a cationic surfactant at the water/hexane interface leads to hydrophobic, double-helical DNA which may be readily phase transferred to the organic phase and cast into thin films on solid substrates.

A Noninvasive Test For Vesico-Ureteric Reflux In Children, R. A. Mevorach, B. Cilento, S. Zahorian, C. Badgett, R. Walker, A. Atala, S. Iannello, M. Meyer

Electrical & Computer Engineering Faculty Publications

Objective To report the development and testing of a device for the noninvasive diagnosis of vesico‐ureteric reflux (VUR) which avoids the need for urethral catheterization (currently required to reliably determine the presence of VUR), and which thus avoids the anxiety of parents and patients that causes many families to refuse such evaluation.

Patients and methods Fifty‐four children (49 girls and five boys, mean age 7.2 years, range 4–14) previously evaluated as having VUR volunteered to participate; no child was symptomatic at the time of the study. Refluxing units were known to be present by voiding cysto‐urethrography (within 1 year, mean …

Hybridization Of Dna By Sequential Immobilization Of Oligonucleotides At The Air-Water Interface, Murali Sastry, Vidya Ramakrishnan, Mrunalini Pattarkine, Anand Gole, K. N. Ganesh

Faculty Works

The hybridization of DNA by sequential electrostatic and hydrogen-bonding immobilization of single-stranded complementary oligonucleotides at the air-water interface with cationic Langmuir monolayers is demonstrated. The complexation of the single-stranded DNA molecules with octadecylamine (ODA) Langmuir monolayers was followed in time by monitoring the pressure-area isotherms. A large (and slow) expansion of the ODA monolayer was observed during each stage of complexation in the following sequence: primary single-stranded DNA followed by complementary single-stranded DNA followed by the intercalator, ethidium bromide. Langmuir-Blodgett (LB) films of the ODA-DNA complex were formed on different substrates and characterized using quartz-crystal microgravimetry (QCM), Fourier transform infrared …

Electromyography (Emg) Signal Classification By Artificial Neural Networks, Behnam Dashtipour

Electrical & Computer Engineering Theses & Dissertations

EMG signal processing is one of the active fields of biomedical signal processing. One unanswered question is how to determine whether a muscle is fatigued by analyzing the EMG signal. Fatigue detection could be useful in several different practical situations. There are several studies which show there are differences between EMG signal features before fatigue and after fatigue. Generally studies are based on an analytical analysis of the EMG signal instead of a quantitative analysis. In all previous studies in EMG signal processing for fatigue/nonfatigue detection, the result is that there exist some differences between the EMG signal before muscle …

Anion Induced Blue To Purple Transition In Bacteriorhodopsin, Mrunalini Pattarkine, Anil K. Singh

Faculty Works

Purple membrane (PM, λ" role="presentation">λmax" role="presentation">max 570 nm) of H. halobium on treatment with sulphuric acid changes its colour to blue (λ" role="presentation">λmax" role="presentation">max 608 nm). The purple chromophore can be regenerated from the blue chromophore by exogeneous addition of anions such as CI−" role="presentation">− and HPO42−" role="presentation">2−4. Chloride ion is found to be more effective than the dibasic phosphate ion in regenerating the purple chromophore. Nevertheless, one thing common to the anion regeneration is that both CI−" role="presentation">− and HPO42−" role="presentation">2−4 show marked pH effect. At pH 1.0 the efficiency of …

Biofeedback Gait Training Auditory Vs. Visual Techniques, Timothy D. Hiemenz

Electrical & Computer Engineering Theses & Dissertations

Training lower extremity amputees to walk normally is quite a difficult task. Amputees must wear a prosthesis so they can walk at all. This allows them some mobility, but their walking pattern may be unnatural. If their gait is temporally asymmetric, they need to exert more energy to move about. This research was initiated to help lower extremity amputees to walk more efficiently using biofeedback gait training. Two types of feedback were developed and tested to determine which method gave the most understandable feedback, validating its use in a clinical setting.

A normal gait cycle uses the lower limbs to …

Optimization Of Cryopreservation Protocols For Cardiovascular Tissue, Jianfei Hu

Theses and Dissertations in Biomedical Sciences

The purpose of this research was to determine the effects of cryopreservation on the physical, biochemical and cellular aspects of heart valve tissue. The present study demonstrated that radiolabeled proline accumulation provides a quantitative estimate of total cellular metabolic viability. Radiolabeled inulin was demonstrated to be a useful marker for extracellular tissue space. Assessment of metabolic viability of the cellular population of leaflet tissue as a function of procurement and processing revealed that proline accumulation declined with increasing warm and cold ischemic times. Amphotericin B and streptomycin were toxic to the cells. Cefoxitin, lincomycin, polymyxin B, vancomycin and penicillin had …

Development And Characterization Of Monoclonal Antisperm Antibodies: Potential For Contraception, Dilrowshan H. Haque

Theses and Dissertations in Biomedical Sciences

There is an expressed need to develop a greater variety of safe contraceptive methods which would find acceptance worldwide, particularly in developing countries. Immunization against spermatozoa might be such a method as judged by the accumulated evidence from studies on human females and in a number of female animal species.

Two extraction techniques were used for sperm membrane antigen isolation. The first technique involved NP-40 detergent for antigen extraction from human motile sperm and the second technique employed homogenized human testis for antigen extraction. Using these immunogens, sperm membrane-specific monoclonal antibodies (MAbs) were developed. When these antisperm MAbs were subjected …