Biomedical Engineering and Bioengineering Commons^™

Substrate-Mediated Gene Delivery For Assessment Of Signal Transduction Pathways In Cancer Cells, Angela K. Pannier, Zain Bengali, Eric A. Ariazi, V. Craig Jordan, Lonnie D Shea

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

Gene delivery has the potential to be used in diagnostic applications, specifically to investigate cellular signal transduction pathways responsible for disease. Analysis of multiple pathways or genes in a parallel format can be achieved using a transfected cell array, a high throughput approach to correlate gene expression with functional cell responses, based on gene delivery from a substrate that supports cell adhesion. Substrate-mediated gene delivery functions by self-assembling DNA with nonviral vectors, resulting in positively charged complexes that can interact with a biomaterial or substrate. Cells cultured on the substrate are exposed to elevated DNA concentrations within the local microenvironment, …

Interaction Of Visual And Proprioceptive Feedback During Adaptation Of Human Reaching Movements, Robert A. Scheidt, Michael A. Conditt, Emanuele L. Secco, Ferdinando A. Mussa-Ivaldi

Biomedical Engineering Faculty Research and Publications

People tend to make straight and smooth hand movements when reaching for an object. These trajectory features are resistant to perturbation, and both proprioceptive as well as visual feedback may guide the adaptive updating of motor commands enforcing this regularity. How is information from the two senses combined to generate a coherent internal representation of how the arm moves? Here we show that eliminating visual feedback of hand-path deviations from the straight-line reach (constraining visual feedback of motion within a virtual, “visual channel”) prevents compensation of initial direction errors induced by perturbations. Because adaptive reduction in direction errors occurred with …

Characterization Of Mismatch Between Behavioral Stimuli And Frmi Data Using The Kalman Filter, Jason Steffener

Dissertations

The advance of blood oxygen level dependent function magnetic resonance imaging, (BOLD fMRI), allows researchers to non-invasively investigate the functioning human brain. The BOLD fMRI response to brief stimuli is called the hemodynamic response function (HRF), which can vary across brain regions and across subjects.

Models of the HRF are used to increase sensitivity of statistical maps; however, they often don't account for spatial and temporal variance. Physiological effects, such as learning, fatigue or habituation, introduce mismatch between statistical models and the data. Methods that use minimal a priori information and track time varying signals are able to show the …

Relationship Between The Autonomic Nervous System And The Recovering Heart Post Exercise Using Heart Rate Variability, Pierre Asselin

Theses

The goal of this thesis is to determine if a relationship exists between the activity of the autonomic nervous system (ANS) and the speed of heart rate recovery post maximal exercise. The parasympathetic branch of the ANS was assessed during rest by obtaining the high frequency (HF) component of the heart rate variability (HRV) frequency spectrum. The recovery time was estimated by fitting an exponential curve to the heart rate post exercise where the exponent was used to calculate the time constant to indicate recovery time. A regression was then performed on the HF and recovery time in order to …

Non-Linear Digital Control Of A Mckibben Muscle System, Surinkumar Patel

Theses

McKibben muscles are pneumatic actuators that have potential application in the rehabilitation of persons with physical impairments. These actuators have been known to exhibit similarities in human musculoskeletal systems. In order to better understand and improve the closed - loop control of these pneumatic muscles, a physical joint model was constructed with an agonist and an antagonist muscle operating under non-linear control. With the use of LabVIEW software, compliant McKibben air muscles and Flock-of-Birds sensor, the author was able to implement and compare a standard bang-bang controller and experimental non-linear digital Proportional (P) controller. The feedback mechanism is based on …

Ambulatory Biopotential Measurement, Lakshmi Chitra Penugonda

Theses

Biopotential signals measure the electrical activity of different parts of the body. Conventional bedside monitors only provide information about the body under restricted conditions. Observation and documentation of biopotential signal during daily activities and the relation to patient symptoms may be important factors for clinical decision-making. Ambulatory monitoring helps to monitor the biopotential signal of a patient in the natural environment. The effective ambulatory system can help a physician to diagnose the patient's abnormality.

In this project, a low cost and flexible ambulatory biopotential system, compared to the commercially available systems, was designed and tested. Concurrently a software program was …

Analysis Of Acceleration And Deceleration During Cyclic Exercise, Jeena Vadi

Theses

The Cyclic Exercise Protocol is a novel protocol that is designed to create a series of cyclic waves of exercise and recovery. This exercise protocol involves short bursts of exercise lasting for 60 seconds or less followed by a period of complete cardio recovery. This study involves the analysis of the acceleration and the deceleration regions of the cyclic exercise sessions. The objective of this study was to develop an algorithm to quantitatively analyze the acceleration and the deceleration regions of cyclic exercise sessions. The acceleration and the deceleration regions of cycles were split into three segments and each segment …

Applications Of Using The Odor Footprint Tool, Richard R. Stowell, L. Koppolu, Dennis D. Schulte, Richard K. Koelsch

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

The Odor Footprint Tool is a science-based computer resource for use in evaluating the potential odor impact of new and expanded animal production facilities. It was developed to assist livestock producers, their service providers, and county planning and zoning officials in making reasonable decisions while limiting the negative impact of livestock operations on surrounding neighbors and rural communities. The Odor Footprint Tool utilizes an EPA regulatory model (AERMOD), weather databases, new source code, and user input to generate regional odor roses, odor footprints, and directional setback distance curves. Odor roses provide a generic picture of the directionality of …

Using Ems’S To Improve Compliance On Livestock And Poultry Operations, L. Mark Risse, Richard K. Koelsch, Bill Bland, Elizabeth A. Bird, Thomas M. Bass

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

Across the United States and abroad, innovative producers, processors, trade organizations and others in the agricultural sector are exploring the promise of Environmental Management Systems (EMS) to improve their environmental and business performance. An Environmental Management System or EMS helps farmers develop their own, personal strategies for reducing environmental risk on their operations by integrating environmental management considerations into production management decisions. It is a voluntary, flexible approach and is based on a producer's own sense of how best to manage an operation.

Partnerships for Livestock Environmental Management Systems is a 4-year project to explore the potential of livestock Environmental …

Cellulose Utilization By Clostridium Thermocellum: Bioenergetics And Hydrolysis Product Assimilation, Yi-Heng P. Zhang, Lee R. Lynd

Dartmouth Scholarship

The bioenergetics of cellulose utilization by Clostridium thermocellum was investigated. Cell yield and maintenance parameters, Y(X/ATP)True = 16.44 g cell/mol ATP and m = 3.27 mmol ATP/g cell per hour, were obtained from cellobiose-grown chemostats, and it was shown that one ATP is required per glucan transported. Experimentally determined values for G(ATP)P-T (ATP from phosphorolytic beta-glucan cleavage minus ATP for substrate transport, mol ATP/mol hexose) from chemostats fed beta-glucans with degree of polymerization (DP) 2-6 agreed well with the predicted value of (n-2)/n [corrected] (n = mean cellodextrin DP assimilated). A mean G(ATP)(P-T) value of 0.52 +/- 0.06 was calculated …

Validating Surface Energy Balance Fluxes Derived From Airborne Remote Sensing, José Luis Chávez Egüez

Biological Engineering

Remote sensing-derived energy balance components were compared against measured eddy covariance energy balance terms using heat flux source area models to validate the airborne multispectral remote sensing procedure in the estimation of instantaneous and daily evapotranspiration rates.

A procedure was developed to generate raster layers of the footprint weights for weighting/integrating the different components of the energy balance model and obtain meaningful comparisons to similar energy balance terms measured at eddy covariance and/or Bowen ratio stations.

Soil heat flux and surface aerodynamic temperature models were studied in an effort to improve the remote sensing estimation of distributed evapotranspiration rates. Aerial …

Gene Delivery Through Cell Culture Substrate Adsorbed Dna Complexes, Zain Bengali, Angela K. Pannier, Tatiana Segura, Brian C. Anderson, Jae-Hyung Jang, Thomas D. Mustoe, Lonnie D Shea

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Efficient gene delivery is a fundamental goal of biotechnology and has numerous applications in both basic and applied science. Substrate-mediated delivery and reverse transfection enhance gene transfer by increasing the concentration of DNA in the cellular microenvironment through immobilizing a plasmid to a cell culture substrate prior to cell seeding. In this report, we examine gene delivery of plasmids that were complexed with cationic polymers (polyplexes) or lipids (lipoplexes) and subsequently immobilized to cell culture or biomaterial substrates by adsorption. Polyplexes and lipoplexes were adsorbed to either tissue culture polystyrene or serum-adsorbed tissue culture polystyrene. The quantity of DNA immobilized …

Prevention Of Atrophic Nonunion Development By Recombinant Human Bone Morphogenetic Protein-7, Takeshi Makino, David J. Hak, Scott Hazelwood, Shane Curtiss, A. Hari Reddi

Biomedical Engineering

Severe periosteal and soft tissue disruption at the time of fracture may result in the formation of an atrophic nonunion. We have developed a reproducible atrophic nonunion in an animal model. The purpose of this study was to evaluate whether the immediate application of recombinant human BMP-7 to the fracture site could rescue the healing process in this nonunion model. A total of 56 three month old Fisher 344 rats were utilized. A 1.25mm diameter K-wire was inserted into the femur in a retrograde fashion, and a mid-diaphyseal closed transverse fracture was created using a standard three point bending device. …

Simulations Of Transient Membrane Behavior In Cells Subjected To A High-Intensity Ultrashort Electric Pulse, Q. Hu, S. Viswanadham, R. P. Joshi, Karl H. Schoenbach, Stephen J. Beebe, P. F. Blackmore

Bioelectrics Publications

A molecular dynamics (MD) scheme is combined with a distributed circuit model for a self-consistent analysis of the transient membrane response for cells subjected to an ultrashort (nanosecond) high-intensity (approximately 0.01-V/nm spatially averaged field) voltage pulse. The dynamical, stochastic, many-body aspects are treated at the molecular level by resorting to a course-grained representation of the membrane lipid molecules. Coupling the Smoluchowski equation to the distributed electrical model for current flow provides the time-dependent transmembrane fields for the MD simulations. A good match between the simulation results and available experimental data is obtained. Predictions include pore formation times of about 5-6 …

Alterations In Wall Shear Stress Predict Sites Of Neointimal Hyperplasia After Stent Implantation In Rabbit Iliac Arteries, John F. Ladisa, Lars E. Olson, Robert C. Molthen, Douglas Anthony Hettrick, Phillip F. Pratt, Michael D. Hardel, Judy R. Kersten, David C. Warltier, Paul S. Pagel

Biomedical Engineering Faculty Research and Publications

Restenosis resulting from neointimal hyperplasia (NH) limits the effectiveness of intravascular stents. Rates of restenosis vary with stent geometry, but whether stents affect spatial and temporal distributions of wall shear stress (WSS) in vivo is unknown. We tested the hypothesis that alterations in spatial WSS after stent implantation predict sites of NH in rabbit iliac arteries. Antegrade iliac artery stent implantation was performed under angiography, and blood flow was measured before casting 14 or 21 days after implantation. Iliac artery blood flow domains were obtained from three-dimensional microfocal X-ray computed tomography imaging and reconstruction of the arterial casts. Indexes of …

Department Of Biological Systems Engineering Newsletter, Issue 1, April 2005

BSE Department Magazine

Contents:
Welcome: Comments from Department Head
New Lab in BSE
Dr. Martin Serves as BSE Interim Head
Splinter Labs
New Department Head
Hello-Goodbye
Faculty and Staff News
Cliff Hunter Memorial Picnic
Student News
Quarter-scale Tractor Team
Freshmen Eat Cars
Scholarship Recognition
Annual Spring Recognition Banquet
New Graduates
Generous Gifts to Endowments in BSE

Numerical Simulation Of Nanopulse Penetration Of Biological Matter Using The Z -Transform, Shengjun Su

Doctoral Dissertations

Short duration, fast rise time ultra-wide-band (UWB) electromagnetic pulses (“nanopulses”) are generated by numerous electronic devices in use today. Moreover, many novel technologies involving nanopulses are under development and expected to become widely used soon. Study of nanopulse bioeffects is needed to probe their useful range in possible biomedical and biotechnological applications, and to ensure human safety.

Based on the well-known dispersive properties of biological matter and their expression as a summation of terms corresponding to the main polarization mechanisms, the Cole-Cole expression is commonly employed to describe the frequency dependence of the dielectric properties of a tissue. Solving the …

Application Of Self -Assembled Ultrathin Film Coatings To Stabilize Enzyme Encapsulation And Activity In Alginate Microspheres, Rohit Srivastava

Doctoral Dissertations

Alginate-based hydrogels have been used for the encapsulation of a variety of materials, including enzymes, proteins, and cells for a wide range of applications from drug delivery to biosensors and bioreactors. However, due to the high porosity of the matrix, it has been increasingly difficult to retain macromolecules inside the alginate matrix, leading to loss in functionality over time. In an effort to improve the stability for long-term biosensor use, this work investigated layer-by-layer self-assembly as a potential technique to provide a diffusion barrier to an encapsulated macromolecule. Alginate microspheres (∼2–50μm radius) were fabricated using an emulsification technique, and were …

Microencapsulation Techniques Towards Building A Sensor: A Study Of Factors Affecting Enzyme Encapsulation And Stability, Suman R. Nayak

Doctoral Dissertations

Minimally and non-invasive glucose sensing techniques are instrumental in improving the quality of life of diabetics, point-of-care testing, critical care monitoring, development of new anti-diabetic drugs or therapeutic compounds, and the study of basic physiology. The overall goal of this project was to build a fluorescent glucose sensor by incorporating relevant sensing chemistry within microcapsules. The specific aims for this research were to study various processes used for the fabrication of micro-containers, the use of these for encapsulation purposes, and the application of the encapsulated system towards glucose sensing. The following is a brief description highlighting the key areas of …

Biosensing With Microcantilever-Based Sensors, Xiaodong Yan

Doctoral Dissertations

Microcantilevers provide an ideal platform for biosensors. The micron-sized transducer brings several advantages, such as high sensitivity, small sample quantity for analysis, portability, implantable sensor devices, and the ability to be mass produced and integrated into standard microelectronic processing technologies like complementary metal oxide seminconductors (CMOS).

The objective of this research is to investigate and develop modification methods of microcanitlevers for biosensing applications.

Two microcantilever modification methods were investigated. They are self-assembly monolayer method and layer-by-layer method. A fundamental procedure for modification of microcantilevers using the layer-by-layer approach was developed for the first time in this research. These modification methods …

A Numerical Method For Obtaining An Optimal Temperature Distribution In A 3d Triple-Layered Cylindrical Skin Structure, Le Zhang

Doctoral Dissertations

In recent years, it has been interesting to research hyperthermia combined with radiation and cytotoxic drugs to enhance the killing of tumors. The crucial problem is that when heating the tumor tissues, one needs to keep the surrounding normal tissue below a temperature that will produce harm. Thus, it is important to obtain the temperature field of the entire treatment region. The objective of this dissertation is to develop a numerical model for obtaining an optimal temperature distribution in a 3D triple-layered cylindrical skin structure. To this end, we pre-specify the temperatures to be obtained at the center and perimeter …

Blood Flow Measurements With Magnetic Resonance Phase Velocity Mapping, George P. Chatzimavroudis

Chemical & Biomedical Engineering Faculty Publications

Magnetic resonance (MR) phase velocity mapping (PVM) is a non-invasive technique that can measure the flow velocity in any spatial direction in an imaging slice. This technique has wide application in the clinical field in quantifying blood flow, as well as in non-biomedical areas. This review describes the value and/or potential of MR PVM as a diagnostic/monitoring technique in heart valve regurgitation and in the total cavo-pulmonary connection. A single slice placed in the aortic root can accurately quantify the aortic regurgitant volume. A multi-slice control volume method has high potential for the quantification of the mitral regurgitant volume. …

Segmentation Of Non-Viable Myocardium In Delayed Enhancement Magnetic Resonance Images, Arunark Kolipaka, George P. Chatzimavroudis, Richard D. White, Thomas P. O’Donnell, Randolph M. Setser

Chemical & Biomedical Engineering Faculty Publications

Purpose: To evaluate six algorithms for segmenting non-viable left ventricular (LV) myocardium in delayed enhancement (DE) magnetic resonance imaging (MRI). Methods: Twenty-three patients with known chronic ischemic heart disease underwent DE-MRI. DE images were first manually thresholded using an interactive region-filling tool to isolate non-viable myocardium. Then, six thresholding algorithms, based on the image intensity characteristics of either LV blood pool (BP), viable LV myocardium, or both, were applied to each image. For the Mean−2SD_BP algorithm, thresholds were equal to the mean BP intensity minus twice its standard deviation. For the Mean+2SD_Semi, Mean+3SD_Semi, Mean+2SD_{Auto …}

Identification And Expansion Of Pancreatic Stem/Progenitor Cells., You-Qing Zhang, Marcie Kritzik, Nora Sarvetnick

Journal Articles: Regenerative Medicine

Pancreatic islet transplantation represents an attractive approach for the treatment of diabetes. However, the limited availability of donor islets has largely hampered this approach. In this respect, the use of alternative sources of islets such as the ex vivo expansion and differentiation of functional endocrine cells for treating diabetes has become the major focus of diabetes research. Adult pancreatic stem cells /progenitor cells have yet to be recognized because limited markers exist for their identification. While the pancreas has the capacity to regenerate under certain circumstances, questions where adult pancreatic stem/progenitor cells are localized, how they are regulated, and even …

Method And Device For Removal Of Cryoprotectant From Cryopreserved Biological Cells And Tissues, Dayong Gao, Xiangdong Cui

Biomedical Engineering Faculty Patents

Novel methods and devices for removing cryoprotectant from cryoprotectant-containing liquids, and from cells residing therein, are disclosed. In one aspect, the method comprises passing the cryoprotectant-containing liquid through at least one semipermeable hollow fiber membrane contained in a hollow module in a first direction, while passing a liquid which is substantially free of cryoprotectant through the hollow module in a second direction to remove cryoprotectant across a diffusion gradient. In another aspect, a device is described for removing cryoprotectant from a liquid, comprising a hollow module with at least one semipermeable hollow fiber membrane therein for accomplishing such counter-current diffusion …

Automated Migration Analysis Based On Cell Texture: Method & Reliability, Jianfeng Qin, Thomas W. Chittenden, Ling Gao, Justin D D. Pearlman

Dartmouth Scholarship

Background: In this paper, we present and validate a way to measure automatically the extent of cell migration based on automated examination of a series of digital photographs. It was designed specifically to identify the impact of Second Hand Smoke (SHS) on endothelial cell migration but has broader applications. The analysis has two stages: (1) preprocessing of image texture, and (2) migration analysis.

Results: The output is a graphic overlay that indicates the front lines of cell migration superimposed on each original image, with automated reporting of the distance traversed vs. time. Expert preference compares to manual placement of leading …

Effects Of An Impedance Threshold Valve Upon Hemodynamics In Standard Cpr: Studies In A Refined Computational Model, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Publications

An impedance threshold valve (ITV) is a new airway adjunct for resuscitation that permits generation of a small vacuum in the chest during the recoil phase of chest compression. Objectives: To explore in detail the expected magnitude and the hemodynamic mechanisms of circulatory augmentation by an ITV in standard CPR. Method: A 14-compartment mathematical model of the human cardiopulmonary system—upgraded to include applied chest compression force, elastic recoil of the chest wall, anatomic details of the heart and lungs, and the biomechanics of mediastinal compression—is exercised to explore the conditions required for circulatory augmentation by an ITV during various modes …

Circumferential Vascular Deformation After Stent Implantation Alters Wall Shear Stress Evaluated With Time-Dependent 3d Computational Fluid Dynamics Models, John F. Ladisa, Lars E. Olson, Ismail Guler, Douglas Anthony Hettrick, Judy R. Kersten, David C. Warltier, Paul S. Pagel

Biomedical Engineering Faculty Research and Publications

The success of vascular stents in the restoration of blood flow is limited by restenosis. Recent data generated from computational fluid dynamics (CFD) models suggest that stent geometry may cause local alterations in wall shear stress (WSS) that have been associated with neointimal hyperplasia and subsequent restenosis. However, previous CFD studies have ignored histological evidence of vascular straightening between circumferential stent struts. We tested the hypothesis that consideration of stent-induced vascular deformation may more accurately predict alterations in indexes of WSS that may subsequently account for histological findings after stenting. We further tested the hypothesis that the severity of these …

Antegrade Iliac Artery Stent Implantation For The Temporal And Spatial Examination Of Stent-Induced Neointimal Hyperplasia And Alterations In Regional Fluid Dynamics, John F. Ladisa, Heidi T. Meier, Lars E. Olson, Judy R. Kersten, David C. Warltier, Paul S. Pagel

Biomedical Engineering Faculty Research and Publications

Neointimal hyperplasia remains an important problem after stent implantation. Previous investigations examining vascular responses to stent implantation and effects of drugs have used a retrograde deployment approach that may inadvertently alter the local fluid dynamics surrounding the stent. We present a model of antegrade iliac artery stent implantation that facilitates the analysis of stent-induced alterations in neointimal hyperplasia and wall shear stress in vivo. Methods: Stent delivery catheters were inserted through the left carotid artery in anesthetized rabbits (n=37). Catheters were advanced under fluoroscopic guidance to the distal iliac arteries, where the stent was deployed. Hemotoxylin and eosin …

An In Vitro Comparison Of The Rake Angles Between K3 And Profile Endodontic File Systems, David Y. Chow, Sheila E. Stover, James Bahcall, Andris Jaunberzins, Jeffrey M. Toth

Biomedical Engineering Faculty Research and Publications

The purpose of this study was to compare rake angles of the ProFile and K3 file systems. Twenty-five 40/0.06 taper files were obtained for each system. Five files from the same manufacturer were placed perpendicularly into a vial of Epoxicure Resin and left to set for 24 h. The set-ups were removed from the vials and each were sectioned 5 mm from the tip of the files and polished. A photomicrograph was taken of each file with 100× magnification. Five sets of ProFile and five sets of K3 files were processed in this manner. Images were captured digitally, and rake …