Engineering Commons^™

Synthesising Life-Sciences And Control Engineering: An Outline Survey And A Practical Example, Aidan O'Dwyer

Conference papers

There is an increasing interest in life science related areas in the electrical and control engineering community [1]. One manifestation of this interest is the development of interdisciplinary programmes, such as the B.Sc. in Medical Physics and Bioengineering, offered by the Dublin Institute of Technology from September 2005. A significant amount of research work in control engineering has focused on aspects of human physiological system, for example blood glucose regulation [2], cardiovascular modelling and control [3], and limb control [4]. There is an increasing emphasis on interdisciplinary research; in recognition of this, the Institute of Electrical Engineers (IEE) has starting …

Motivating Rehabilitation By Distorting Reality, James L. Patton, Yejun Wei, Chris Scharver, Robert V. Kenyon, Robert A. Scheidt

Biomedical Engineering Faculty Research and Publications

We have found, through a series of recent experiments, encouraging evidence that the neuro-motor system is motivated to change motor patterns when exposed to visuo-motor tasks. We have also shown that the learning of these tasks can be heightened with forces and/or visual distortions that appropriately manipulate the error. This process does not require intense concentration and it is often considered a game. We describe the next generation of robotic large-workspace, three dimensional haptics/graphics systems for rehabilitation

Design Of Near-Optimal Waveforms For Chest And Abdominal Compression And Decompression In Cpr Using Computer-Simulated Evolution, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Publications

Objective: To discover design principles underlying the optimal waveforms for external chest and abdominal compression and decompression during cardiac arrest and CPR. Method: A 14-compartment mathematical model of the human cardiopulmonary system is used to test successive generations of randomly mutated external compression waveforms during cardiac arrest and resuscitation. Mutated waveforms that produced superior mean perfusion pressure became parents for the next generation. Selection was based upon either systemic perfusion pressure (SPP=thoracic aortic minus right atrial pressure) or upon coronary perfusion pressure (CPP=thoracic aortic pressure minus myocardial wall pressure). After simulations of 64,414 individual CPR episodes, 40 highly evolved waveforms …

A New Biomechanical Head Injury Criterion, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Publications

This paper presents a new analysis of the physics of closed head injury caused by intense acceleration of the head. At rest a 1 cm gap filled with cerebrospinal fluid (CSF) separates the human brain from the skull. During impact whole head acceleration induces artificial gravity within the skull. Because its density differs slightly from that of CSF, the brain accelerates, strikes the inner aspect of the rigid skull, and undergoes viscoelastic deformation. Analytical methods for a lumped parameter model of the brain predict internal brain motions that correlate well with published high-speed photographic studies. The same methods predict a …

Regulation Of Dna Replication Initiation By Histone Acetylation And The Dna Unwinding Element Binding Protein Due-B, Michael George Kemp

Browse all Theses and Dissertations

Duplication of the genome during S phase of the mitotic cell cycle begins at thousands of sites along chromosomes termed origins of replication. Although many of the essential protein components catalyzing events at these sites are known and are conserved throughout eukaryotes, the likelihood or efficiency of initiation of DNA synthesis at any given genomic site is expected to be influenced by other novel factors, including aspects of chromatin and DNA structure.

Here I show that increased histone H4 acetylation at replication origin loci occurs after treatment with the histone deacetylase inhibitor TSA and coincides with a loss of specific …

Methodology For Quantifying Biomechanical Bone Movement Of Transtibial Amputations, Johanna C. Bell

Browse all Theses and Dissertations

A controversy has long existed about an alternate below knee amputation procedure that may be more beneficial than the traditional transtibial amputation. The proponents of this alternate procedure that stabilizes the distal tibia and fibula claim it reduces excessive movement of the fibula relative to the tibia that occurs with common movements, such as walking. The purpose of this study is to develop a methodology for quantifying excessive movement of the fibula bone relative to the tibia bone in traditional below the knee amputations. The methodology will measure the movement and rotation of the fibula relative to the tibia. These …

Circular Ultrasound Compounding By Designed Matrix Weighting, Gregory Bashford, Jonathan Morse

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Spatial compounding is an imaging technique that aims to improve image contrast by combining partially decorrelated images acquired at different angles or positions. In conventional spatial compounding, data sets are combined with equal weighting. Here, we describe an alternative method of reconstruction using algorithms which weight the data based on a “quality” matrix. The quality matrix is derived from beam-forming characteristics. For each data set, the reliability of the data is assumed to vary spatially. By compounding the data based on the quality matrix, a complete image is formed. Here, we describe the construction of a rotational translation stage and …

Variable Upper And Lower Crop Water Stress Index Baselines For Corn And Soybean, J. O. Payero, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Upper and lower crop water stress index (CWSI) baselines adaptable to different environments and times of day are needed to facilitate irrigation scheduling with infrared thermometers. The objective of this study was to develop dynamic upper and lower CWSI baselines for corn and soybean. Ten-minute averages of canopy temperatures from corn and soybean plots at four levels of soil water depletion were measured at North Platte, Nebraska, during the 2004 growing season. Other variables such as solar radiation (R_s), air temperature (T_a), relative humidity (RH), wind speed (u), and plant canopy height (h) were …

Use Of Time Domain Reflectometry For Continuous Monitoring Of Nitrate-Nitrogen In Soil And Water, J. O. Payero, David D. Tarkalson, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Nitrate-Nitrogen (NO₃-N) losses to ground and surface water are an environmental and agronomic concern in modern crop production systems in the Central Great Plains. Monitoring techniques for nitrogen use in agricultural production are needed to increase crop yield, optimize nitrogen use, and reduce NO₃-N leaching. Time domain reflectometry (TDR) could potentially be calibrated to continuously measure NO₃-N in soil and water. The objectives of this study were to: (1) evaluate the effect of different factors affecting the response of the bulk electrical conductivity (ECb) sensed by TDR, (2) compare the sensitivity and differences between …

Land Application Of Manure For Beneficial Reuse, L. M. Risse, M. L. Cabrera, A. J. Franzluebbers, J. W. Gaskin, John E. Gilley, R. Killorn, D. E. Radcliffe, W. E. Tollner, H. Zhang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The concentration of animal production systems has increased efficiency and improved overall economic return for animal producers. This concentration, along with the advent of commercial fertilizers, has led to a change in the way animal producers view manure. Manure, once valued as a resource by farmers, is now treated as a waste. Air and water quality concerns that arise primarily from the under-utilization or inefficient use of manure contribute to these changing views. However, when properly used, manure is a resource and should be regulated as such. In the United States, the USDA/EPA Unified National Strategy for Animal Feeding Operations …

Properties Of Chitosan Films As A Function Of Ph And Solvent Type, Ki Myong Kim, Jeong Hwa Son, Sung-Koo Kim, Curtis L. Weller, Milford Hanna

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Two different deacetylated chitosans were dissolved in formic, acetic, lactic, or propionic acid to prepare chitosan films. The pH values of the film-forming solutions were adjusted to 3, 4, and 5. Water vapor permeability (WVP), tensile strength (TS), elongation (E), and total soluble matter (TSM) were significantly (P < 0.05) affected by acid type, pH, and degree of deacetylation (DA). Low DA (LDA) chitosan films had lower WVP and TSM, higher TS compared with high DA (HDA) chitosan films. The E values were not affected by DA. As pH increased, WVP and TSM of chitosan films tended to increase while TS decreased significantly (P < 0.05). Chitosan films with acetic and propionic acid solvents had low WVP and TSM and high TS, while films with lactic acid solvent had high E and TSM and the lowest TS. Fourier-transform infrared showed peak shifting in the spectra with different solvents and at different pH values. Chitosan films with lactic acid solvent showed a peak shift to a lower frequency range. The NH3+ band was absent in the pH 5.0 chitosan film spectra.

Modeling Of Transport Phenomena And Melting Kinetics Of Starch In A Co-Rotating Twin-Screw Extruder, Lijun Wang, David D. Jones, Curtis L. Weller, Milford Hanna

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A mathematical model was developed to simulate fluid flow, heat transfer, and melting kinetics of starch in a co-rotating intermeshing twin-screw extruder (TSE). The partial differential equations governing the transport phenomena of the biomaterial in the extruder were solved by a finite element scheme. For validating the model, the predicted product pressure, bulk temperature at the entrance of the die, and minimum residence time of the biomaterial in the extruder were compared with experimental data. Standard errors of product pressure, bulk temperature at the die entrance, and minimum residence time were about 8.8, 2.8, and 17.3%. Simulations were carried out …

Impact Of Tillage And Placement Of Terbufos Insecticide Runoff, Mitiku Mamo, William L. Kranz, Elaine R. Douskey, Shripat T. Kamble, John F. Witkowski

Department of Agricultural and Biological Systems Engineering: Faculty Publications

On a national scale, the damage caused by corn rootworm (Diabrotica virgifera virgifera LeConte), can cause economic loss of up to $650 million annually. To limit these losses, corn producers apply terbufos insecticide to approximately 11% of all corn acres at a time when there is a high probability of intense precipitation. When combined with low vegetative cover and disturbed soil surfaces, there is a high potential for terbufos transport into surface water bodies. Increased public concern for environmental contamination from the use of agricultural chemicals has prompted many crop growers to look for crop production practices that minimize …

A Mathematical Model For The Validation Of Safe Air-Blast Chilling Of Cooked Hams, L. J. Wang, A Amézquita, Curtis L. Weller

Department of Agricultural and Biological Systems Engineering: Faculty Publications

An integrated mathematical model of heat transfer and temperature-dependent bacterial growth was developed to validate the safety of cooked hams during air-blast chilling. Heat transfer through a cooked ham was mathematically modeled and analyzed with a finite element method. Response of bacteria to temperatures was quantitatively described using predictive microbiology. The cumulative effect of temperature history on the bacterial growth was taken into account in the model. For chilling cooked hams from 71°C to 10°C, the maximum error between the predicted and experimental core temperature was within 2.2°C, and the deviation between the predicted and measured total weight losses was …

Resistance To Fracture Of Two All-Ceramic Crown Materials Following Endodontic Access, Kelly Copps Wood, David W. Berzins, Qing Luo, Geoffrey A. Thompson, Jeffrey M. Toth, William W. Nagy

Biomedical Engineering Faculty Research and Publications

Statement of problem

There is currently no protocol for managing endodontic access openings for all-ceramic crowns. A direct restorative material is generally used to repair the access opening, rendering a repaired crown as the definitive restoration. This endodontic procedure, however, may weaken the restoration or initiate microcracks that may propagate, resulting in premature failure of the restoration.

Purpose

The purpose of this in vitro study was to evaluate how an endodontic access opening prepared through an all-ceramic crown altered the structural integrity of the ceramic, and the effect of a repair of this access on the load to failure of …

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 …

Evaluation Of Prototype Cell Delivery Catheters Using Agarose Gel And Cell Culture Experiments, Sagar Panse

Theses and Dissertations

Neurodegenerative diseases and brain tumors affect millions of patients worldwide and are associated with significant morbidity and mortality. The blood brain barrier constitutes a major obstacle to delivery of therapeutic agents administered systemically for treating these disorders. Intracranial drug delivery provides a novel way of bypassing the blood brain barrier and achieving high concentration of therapeutic agents in the brain while avoiding systemic side effects. However damage to tissues during insertion of catheters, release of air in the brain and consequent backtracking of dye are some disadvantages with this mode of treatment. We evaluated prototype cell delivery catheters (each with …

Hmg-Coa Reductase Inhibitors Act Synergistically With Ucn-01 Through Ras Inhibition, Payal Khanna

Theses and Dissertations

The primary objective of this study is to elucidate the mechanism by which the reagent UCN-01 induces apoptosis when administered to leukemia cells along with HmG-CoA reductase inhibitors, mainly the statins. In this study, we demonstrated that exposure of leukemia cell lines to lovastatin (20 uM, 18 hours) and UCN-01 (100 nM, 18 hours) resulted in mitochondria dysfunction, procaspase 3 and 9 cleavage, and PAW degradation along with marked cytochrome C release and apoptosis. Although similar molecular mechanisms have not yet been confirmed in other cancers, our hypothesis holds that enhanced apoptotic effects of UCN-01 are due in part to …

Design And Validation Of A Full Contact Gait Simulator For The Cadaveric Lower Extremity, Joseph Michael Iaquinto

Theses and Dissertations

The projects goal was to create a device to simulate full contact gait in the cadaveric lower extremity. The Contact Gait Simulation System loads specific muscles to recreate anatomical dorsi and plantar flexion of the ankle under axial loading. A system of pneumatic load generation was connected a LabVIEW virtual instrument (VI), which controlled the application of these loads. The loads were roughly based off literature cited EMG data, and further modified from feedback. In addition to controlling the load system, the VI also coordinates external sensor timing. Along with this simulator, software was developed specifically for analyzing pressure data …

Detection, Identification And Classification Of Suck, Swallow And Breathing Activity In Premature Infants During Bottle-Feeding, Fedra Adnani

Theses and Dissertations

Prematurity, especially if extreme, is one of the leading causes of problems and/or death after delivery. Among all the problems encountered by premature infants, feeding difficulties are very common. Many premature infants are fed intravenously at first, and they progress to milk feedings provided by a tube passed into the stomach. At around 34 weeks of gestation, premature infants should be able to breastfeed or take a bottle. At the same time such premature infants are usually faced with difficulty making the transition from tube-feeding to full oral feeding. In this study three physiological measurements of premature infants including sucking, …

Computational Modeling To Predict Mechanical Function Of Joints: Validations And Applications Of Lower Leg Simulations, Peter C. Liacouras

Theses and Dissertations

Computational models of musculoskeletal joints and limbs can provide useful information about joint mechanics. Validated models can be used as a predictive device for understanding joint function and serve as a clinical tool for predicting the outcome of surgical procedures. A new computational modeling approach was developed for simulating joint kinematics that are dictated by bone/joint anatomy, ligamentous constraints, and applied loading.Three-dimensional computational models of the lower leg were created. Model development involved generating three-dimensional surfaces from CT images, followed by importing these surfaces into SolidWorks and COSMOSMotion. ThroughSolidWorks and COSMOSMotion, each bone surface was created into a solid object …

Recent Trends In Robot-Assisted Therapy Environments To Improve Real-Life Functional Performance After Stroke, Michelle J. Johnson

Biomedical Engineering Faculty Research and Publications

Upper and lower limb robotic tools for neuro-rehabilitation are effective in reducing motor impairment but they are limited in their ability to improve real world function. There is a need to improve functional outcomes after robot-assisted therapy. Improvements in the effectiveness of these environments may be achieved by incorporating into their design and control strategies important elements key to inducing motor learning and cerebral plasticity such as mass-practice, feedback, task-engagement, and complex problem solving.

This special issue presents nine articles. Novel strategies covered in this issue encourage more natural movements through the use of virtual reality and real objects and …

Polyetheretherketone As A Biomaterial For Spinal Applications, Jeffrey M. Toth, Mei Wang, Bradley T. Estes, Jeffrey L. Scifert, Howard B. Seim, A. Simon Turner

Biomedical Engineering Faculty Research and Publications

Threaded lumbar interbody spinal fusion devices (TIBFD) made from titanium have been reported to be 90% effective for single-level lumbar interbody fusion, although radiographic determination of fusion has been intensely debated in the literature. Using blinded radiographic, biomechanic, histologic, and statistical measures, we evaluated a radiolucent polyetheretherketone (PEEK)-threaded interbody fusion device packed with autograft or rhBMP-2 on an absorbable collagen sponge in 13 sheep at 6 months. Radiographic fusion, increased spinal level biomechanical stiffness, and histologic fusion were demonstrated for the PEEK cages filled with autograft or rhBMP-2 on a collagen sponge. No device degradation or wear debris was observed. …

A Simple, Inexpensive, And Effective Light- Carrying Laryngoscopic Blade For Orotracheal Intubation Of Rats, Robert C. Molthen

Biomedical Engineering Faculty Research and Publications

The research paradigm of using large laboratory animals, in which oroendotracheal intubations are relatively easy, is shifting toward the use of small animals, such as rodents, in which oropharyngeal access is limited, the arytenoid cartilage cycles are faster, and the glottis is much smaller. The considerable growth recently seen in preclinical imaging studies is accompanied by an increased number of rats and mice requiring in vivo intubation for airway management. Tracheal access is important for ventilation, administration of inhaled anesthetics, instillation of drugs or imaging agents, and maintenance of airway patency to reduce mortality during and after operations. I fashioned …

Preparative Synthesis Of Dtdp-L-Rhamnose Through Combined Enzymatic Pathways, Young Bok Abraham Kang, Yung-Hun Yang, Kwang-Won Lee, Sun-Gu Lee, Jae Kyung Sohng, Hei Chan Lee, Kwangkyoung Liou, Byung-Gee Kim

Faculty Publications - Biomedical, Mechanical, and Civil Engineering

dTDP-L-rhamnose, an important precursor of O-antigen, was prepared on a large scale from dTMP by executing an one-pot reaction in which six enzymes are involved. Two enzymes, dTDP-4-keto-6-deoxy-D-glucose 3,5-epimerase and dTDP-4-keto-rhamnose reductase, responsible for the conversion of dTDP-4-keto-6-deoxy- D-glucose to dTDP-L-rhamnose, were isolated from their putative sequences in the genome of Mesorhizobium loti, functionally expressed in Escherichia coli, and their enzymatic activities were identified. The two enzymes were combined with an enzymatic process for dTDP-4- keto-6-deoxy-D-glucose involving TMP kinase, acetate kinase, dTDP-glucose synthase, and dTDP-glucose 4,6- dehydratase, which allowed us to achieve a preparative scale synthesis of dTDP-L-rhamnose using dTMP …

Analysis Of Indentation Loading Of Cortical Bone Using Acoustic Emission Techniques, Ashkan Safari, Ger Reilly, Brendan Mccormack

Conference Papers

In this study, we recorded the number of Acoustic emission (AE) hits and related AE energy during indentation fracture of cortical bone using a PAC PCI-2 card and pico sensor. A threshold value of 43dB was used to filter premature trigger due to background noise. Registered AE hits had more than one count (threshold crossing). Amplifier gain was set at 40dB with a (0.1-1) MHz band pass filter. 8mm cubes of cortical bones were indented in the longitudinal direction at constant crosshead speed of 1 mm min-1 using a large 2D, 50˚ wedge indenter. We hypothesised that signals occurring as …

Characterization Of Gdp-Mannose Pyrophosphorylase From Escherichia Coli O157:H7 Edl933 And Its Broad Substrate Specificity, Yung-Hun Yang, Young Bok (Abraham) Kang, Kwang-Won Lee, Tek-Hyung Lee, Sung-Soo Park, Bum-Yeol Hwang, Byung-Gee Kim

Faculty Publications - Biomedical, Mechanical, and Civil Engineering

GDP-mannose pyrophosphorylase gene (ManC) of Escherichia coli (E. coli) O157 was cloned and expressed as a highly soluble protein in E. coli BL21 (DE3). The enzyme was subsequently purified using hydrophobic and ion exchange chromatographies. ManC showed very broad substrate specificities for four nucleotides and various hexose-1-phosphates, yielding ADP-mannose, CDP-mannose, UDP-mannose, GDP-mannose, GDP-glucose and GDP-2-deoxy-glucose.

Bayer Ag V. Housey Pharmaceuticals: Protection For Biotechnological Research Tools Under Section 271(G) Found Wanting, Matthew Barthalow

The University of New Hampshire Law Review

[Excerpt] "Research tools, a subset of biotechnological inventions protected by process patents, are “tools that scientists use in the laboratory, including cell lines, monoclonal antibodies, reagents, animal models, growth factors, combinatorial chemistry and DNA libraries, clones and cloning tools (such as PCR), methods, laboratory equipment and machines.” Many companies base their business models on the ability to find pharmaceutical products using their proprietary drug discovery research tools. Research tools used for drug discovery ‘include bioinformatic methods for identifying the interaction of certain proteins and their association with disease, methods for confirming protein targets, screening assays to identify molecules active against …

Investigation Of Breast Tumor Hemodynamics By Near Infrared Spectroscopy: Applications To Cancer Therapy Monitoring, Jae Gwan Kim

Bioengineering Dissertations - Archive

Hyperoxic gas interventions using carbogen (95% O2 and 5% CO2) or oxygen has been tried to increase the tumor oxygenation since it will enhance the therapeutic effects on the tumors. Others in the laboratory had previously applied near infrared spectroscopy (NIRS) to monitor the changes in tumor blood oxygenation during hyperoxic gas intervention and found that oxyhemoglobin concentration changes (D[HbO2]) during gas intervention can be fitted by a two-exponential equation containing two time constants. Based on the model, they formed a hypothesis that changes in oxygenated hemoglobin concentration result from well perfused and poorly perfused regions of an animal tumor …

High Resolution Optical Coherence Tomography (Oct) System For Integration With A Multimodal Optical Imaging Workstation, Kapil Bharati Langer

Bioengineering Theses - Archive

Development and construction of a high resolution Optical Coherence Tomography (OCT) system is described. OCT is one of the modalities in an integrated multimode optical imaging workstation built around an inverted Differential Interference Contrast (DIC) microscope in our laboratory, to image cells and tissue samples. The design and construction of the OCT sample path is dictated by its integration to the optical imaging workstation. The OCT system is controlled via a DAC card, interfaced using LabVIEW to the computer. The image of the sample under observation is constructed from the raster scan data acquired by the DAQ. Ti-Sapphire broadband laser …