Biomedical Commons^™

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 …

The Human Eye Position Control System In A Rehabilitation Setting, Yvonne Nolan, Ted Burke, C. Boylan, Annraoi De Paor

Articles

Our work at Ireland’s National Rehabilitation Hospital involves designing communication systems for people suffering from profound physical disabilities. One such system uses the electro-oculogram, which is an (x,y) system of voltages picked up by pairs of electrodes placed, respectively, above and below and on either side of the eyes. The eyeball has a dc polarisation between cornea and back, arising from the photoreceptor rods and cones in the retina. As the eye rotates, the varying voltages projected onto the electrodes drive a cursor over a mimic keyboard on a computer screen. Symbols are selected with a switching action derived, for …

An Electro-Oculogram Based System For Communication And Control Using Target Position Variation, Ronan Fitzmaurice, Ted Burke, Annraoi De Paor

Conference Papers

In this paper we describe a novel mode of human computer interaction based on gaze tracking using the electro-oculogram (EOG). Despite the relative simplicity of recording this signal, it is often discounted as a reliable method of gaze tracking because of problems arising from changing sensitivity and DC drift. We describe an original technique, Target Position Variation (TPV), which addresses this issue by presenting moving icons which, when followed with the eye, create a corresponding pattern in the EOG signal which can be used to infer the correct gaze position and to compensate for variations in sensitivity.

Selective Field Effects On Intracellular Vacuoles And Vesicle Membranes With Nanosecond Electric Pulses, Ephrem Tekle, Hammou Oubrahim, Sergey M. Dzekunov, Juergen F. Kolb, Karl H. Schoenbach

Bioelectrics Publications

Electric pulses across intact vesicles and cells can lead to transient increase in permeability of their membranes. We studied the integrity of these membranes in response to external electric pulses of high amplitude and submicrosecond duration with a primary aim of achieving selective permeabilization. These effects were examined in two separate model systems comprising of 1), a mixed population of 1,2-di-oleoyl-sn-glycero-3-phosphocholine phospholipid vesicles and in 2), single COS-7 cells, in which large endosomal membrane vacuoles were induced by stimulated endocytosis. It has been shown that large and rapidly varying external electric fields, with pulses shorter than the charging time of …

Creating Clinically Useful In Silico Models Of Intracranial Pressure Dynamics, Wayne W. Wakeland, Joe Fusion, Brahm Goldstein

Complex Systems Faculty Publications and Presentations

To create clinically useful computer simulation models of intracranial pressure (ICP) dynamics by using prospective clinical data to estimate subject-specific physiologic parameters.

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 …

Using Optimization To Calibrate Models Of Intracranial Pressure Dynamics To Patients With Intracranial Hypertension, Wayne W. Wakeland, A. Bulbul, Mateo Aboy, James Mcnames, Brahm Goldstein

Complex Systems Faculty Publications and Presentations

Aim: Automatically calibrate ICP Dynamic model to a specific patients.

Method: Use optimization algorithm to estimate parameter values (ICP, compliances, resistances) that minimize the squared error in predicted ICP.

Results: Estimated parameter values are plausible and improve predicted ICP. Optimization time for 18 minute episode = 2.5 min. for 1 parameter, 10 to 200 min. for multiple simultaneous parameters (too long).

A Comparison Of System Dynamics And Agent-Based Simulationapplied To The Study Of Cellular Receptor Dynamics, Wayne W. Wakeland, Edward J. Gallaher, Louis Macovsky, C. Athena Aktipis

Complex Systems Faculty Publications and Presentations

Cellular receptor dynamics are often analyzed using differential equations, making system dynamics (SD) a candidate methodology. In some cases it may be useful to model the phenomena at the biomolecular level, especially when concentrations and reaction probabilities are low and might lead to unexpected behavior modes. In such cases, agent-based simulation (ABS) may be useful. We show the application of both SD and ABS to simulate non-equilibrium ligand-receptor dynamics over a broad range of concentrations, where the probability of interaction varies from low to very low. Both approaches offer much to the researcher and are complementary. We did not find …

Calibrating An Intracranial Pressure Dynamics Model With Clinical Data - A Progress Report, Wayne W. Wakeland, James Mcnames, Brahm Goldstein

Complex Systems Faculty Publications and Presentations

We describe the calibration of a computer model of intracranial pressure (ICP) dynamics to correspond with annotated clinical data taken from a patient being treated for elevated ICP due to a traumatic brain injury. The research protocol employed during treatment includes adjusting the elevation of the head of the bed, adjusting the ventilator settings to induce mild hyperventilation and hypoventilation, and adjusting the height of the cerebrospinal fluid drainage system. The model behavior corresponds to the experimental data quite well in the case of the changing the head of the bed, but less well in the case of changing the …

Stimulation Of Capacitative Calcium Entry In Hl-60 Cells By Nanosecond Pulsed Electric Fields, Jody A. White, Peter F. Blackmore, Karl H. Schoenbach, Stephen J. Beebe

Bioelectrics Publications

Nanosecond pulsed electric fields (nsPEFs) are hypothesized to affect intracellular structures in living cells providing a new means to modulate cell signal transduction mechanisms. The effects of nsPEFs on the release of internal calcium and activation of calcium influx in HL-60 cells were investigated by using real time fluorescent microscopy with Fluo-3 and fluorometry with Fura-2. nsPEFs induced an increase in intracellular calcium levels that was seen in all cells. With pulses of 60 ns duration and electric fields between 4 and 15 kV/cm, intracellular calcium increased 200-700 nM, respectively, above basal levels (similar to100 nM), while the uptake of …

Developing Software For Wound Measurement, Savo Kordic

Theses : Honours

Chronic wounds such as leg ulcers, pressure ulcers and diabetic ulcers affect many thousands of people in Australia. In addition to the costs of these wounds in terms of human suffering, loss of income and resources, there are costs related to the treatment of ulcers. Thus, there is a genuine need to develop an accurate and a fully objective application for wound measurement. The aim of this project was to create software for the measurement of wounds. In achieving this goal, several issues were addressed: an accurate measurement method capable of detecting small changes in an open wound surface area, …

Time Domain Dielectric Spectroscopy Analysis Of Hl-60 Cell Suspensions After Microsecond And Submicrosecond Pulsed Electric Fields, Allen Laurence Garner

Electrical & Computer Engineering Theses & Dissertations

Pulsed electric fields (PEF's) above a certain voltage threshold cause electroporation for microsecond pulses and intracellular effects for submicrosecond pulses. Models describing these effects often depend on the electrical properties of the cell, which are altered by the PEF. Time domain dielectric spectroscopy was used to provide data for these models and to measure changes in the conductivity of HL-60 cell suspensions due to single 50 μs and 10 ns PEF's of the same energy. For 1.1 kV/cm, 50 μs pulses, the conductivity rose within a minute after the pulse and dropped dramatically approximately forty minutes after the pulse. For …

An Investigation Into Non-Verbal Sound-Based Modes Of Human-To-Computer Communication With Rehabilitation Applications, Ted Burke

Conference Papers

During the course of our work in the National Rehabilitation Hospital in Ireland we have encountered patients who, while unable to speak, are capable of making reproducible utterances. We present techniques used to harness such utterances, in addition to whistling, as a means of communication and control. A simple technique for identifying the phonemes /o/ and /s/ (in single-symbol ARPAbet notation) is presented with applications. The use of pitch variation as a means of controlling a continuously variable parameter is described with two applications - a microcontroller based light dimmer switch and a computer program which facilitates mouse pointer control. …

The Effects Of Intense Submicrosecond Electrical Pulses On Cells, Jingdong Deng, Karl H. Schoenbach, E. Stephen Buescher, Pamela S. Hair, Paula M. Fox, Stephen J. Beebe

Bioelectrics Publications

A simple electrical model for living cells predicts an increasing probability for electric field interactions with intracellular substructures of both prokaryotic and eukaryotic cells when the electric pulse duration is reduced into the submicrosecond range. The validity of this hypothesis was verified experimentally by applying electrical pulses (durations 100 μs– 60 ns, electric field intensities 3–150 kV/cm) to Jurkat cells suspended in physiologic buffer containing propidium iodide. Effects on Jurkat cells were assessed by means of temporally resolved fluorescence and light microscopy. For the longest applied pulses, immediate uptake of propidium iodide occurred consistent with electroporation as the cause of …

Modeling Intracranial Fluid Flows And Volumes During Traumatic Brain Injury To Better Understand Pressure Dynamics, Wayne W. Wakeland, James Mcnames, Mateo Aboy, D. Hollemon, Brahm Goldstein

Complex Systems Faculty Publications and Presentations

See additional files below for the Presentation.

We describe a computer model of intracranial pressure (ICP) dynamics that evaluates clinical treatment options for elevated ICP during traumatic brain injury (TBI). The model uses fluid volumes as primary state variables and explicitly models fluid flows as well as the resistance, compliance, and pressure associated with each intra - and extracranial compartment (arteries and arterioles, capillary bed, veins, venous sinus, ventricles, and brain parenchyma). The model evaluates clinical events and therapies such as intra - and extra-parenchymal hemorrhage, cerebral edema, cerebrospinal fluid drainage, mannitol administration, head elevation, and mild hyperventilation. The model …

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies …

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 …

Characterization Of The Biological Activities Of Recombinant Fusion Protein Green Fluorescent Protein/Human Zona Pellucida Protein 3 (Gfp/Hzp3), Zhiyong Lin

Theses and Dissertations in Biomedical Sciences

Despite numerous reports indicating the successful production of bioactive recombinant ZP3, no report has shown the rhZP3 having direct binding activity with human sperm. Recombinant ZP3 generated from our previous study displayed binding activity with human sperm through indirect evidence from hemizona assay (HZA).

This present study focused on the production of recombinant ZP3 with direct binding activity with human sperm. Through the application of a pEGFP expression vector, fusion protein GFP/ZP3 was successfully generated and expressed. The expression of GFP/ZP3 was evidenced by RT-PCR and western blot. The fusion protein was partially purified by Ni-NTA affinity column from cell …

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 …

A Study Of Transconductance Degradation In Hemt Using A Self-Consistent Boltzmann-Poisson-Schrodinger Solver, Rahim Khoie

Electrical & Computer Engineering Faculty Research

A self-consistent Boltzmann-Poisson-Schrödinger Solver is used to study the transconductance degradation in high electron mobility transistor (HEMT), which has extensively been reported by both experimental [1]-[8] and computational [9]-[ 13] researchers. As the gate voltage of a HEMT device is increased, its transconductance increases until it reaches a peak value, beyond which, the transconductance is degraded rather sharply with further increase in applied gate bias. We previously reported a two-subband self-consistent Boltzmann-Poisson- Schrödinger Solver for HEMT. [14] We further incorporated an additional self-consistency by calculating field-dependent, energy-dependent intersubband and intrasubband scattering rates due to ionized impurities and polar optical phonons.[15] …

Thermodynamic Modeling And Analysis Of Human Stress Responses, Satish C. Boregowda

Mechanical & Aerospace Engineering Theses & Dissertations

A novel approach based on the second law of thermodynamics is developed to investigate the psychophysiology and quantify human stress level. Two types of stresses (thermal and mental) are examined. A Unified Stress Response Theory (USRT) is developed under the new proposed field of study called Engineering Psychophysiology. The USRT is used to investigate both thermal and mental stresses from a holistic (human body as a whole) and thermodynamic viewpoint. The original concepts and definitions are established as postulates which form the basis for thermodynamic approach to quantify human stress level. An Objective Thermal Stress Index (OTSI) is developed by …

Time Enough - Consequences Of Human Microchip Implantation, Elaine M. Ramesh

RISK: Health, Safety & Environment (1990-2002)

Dr. Ramesh argues that microchip implantation is both possible and, for some purposes, desirable and suggests that now is the time to consider strategies for preventing potentially grievous intrusion into personal privacy.

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 …

Fetal Heart Rate Detection With A Passive Acoustic Sensor System, Zongyao Zhou

Electrical & Computer Engineering Theses & Dissertations

Research and development is presented of real time signal processing methodologies for the detection of fetal heart tones from noise contaminated signals obtained from passive acoustic sensors. A nonlinear Teager energy operator is utilized for detection of the fetal heart tone event. Autocorrelation and a parallel redundancy correction algorithm derives fetal heart rates. A real time monitoring system is described which records and plots the time history of both the fetal heart rate and the acoustic fetal heart signal. The system is validated in the context of the fetal nonstress test. Comparisons are made with ultrasonic nonstress tests on a …

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 …