Biomedical Engineering and Bioengineering Commons^™

Molecular Dynamics At Constant Pressure: Allowing The System To Control Volume Fluctuations Via A "Shell" Particle, Mark J. Uline, David S. Corti

Faculty Publications

Since most experimental observations are performed at constant temperature and pressure, the isothermal-isobaric (NPT) ensemble has been widely used in molecular simulations. Nevertheless, the NPT ensemble has only recently been placed on a rigorous foundation. The proper formulation of the NPT ensemble requires a "shell" particle to uniquely identify the volume of the system, thereby avoiding the redundant counting of configurations. Here, we review our recent work in incorporating a shell particle into molecular dynamics simulation algorithms to generate the correct NPT ensemble averages. Unlike previous methods, a piston of unknown mass is no longer needed to control the response …

Computational Optogenetics: Empirically-Derived Voltage- And Light-Sensitive Channelrhodopsin-2 Model, John C. Williams, Jianjin Xu, Zhongju Lu, Aleksandra Klimas, Xuxin Chen, Christina M. Ambrosi, Ira S. Cohen, Emilia Entcheva

Department of Biomedical Engineering Faculty Publications

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silicoprediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, …

2013 Fall Engr333 Project Assignment, Matthew K. Heun

ENGR 333

The Fall 2013 ENGR333 project focused on production and use of biofuels at Calvin University.

I asked the students “What would it take for Calvin College to operate a biofuel vehicle from campus resources?”

Customer

The customer for this project was Calvin’s Physical Plant director Phil Beezhold.

Design Optimization Of An Above-Knee Prosthesis With Energy Regeneration, Taylor Barto, Holly Warner, Rick Rarick, Dan Simon

Undergraduate Research Posters 2013

Above-knee amputees who use a prosthetic leg typically have to compensate for its shortcomings with unnatural hip motions. This compensation eventually leads to adverse health issues such as arthritis. We propose an active prosthesis to improve performance. The motor in our prosthetic knee allows the patient to move his hip normally, thus reducing the possibility of ancillary health issues. To improve the efficiency of the prosthesis, we use the braking phase of the prosthesis to regenerate energy. By storing energy in a supercapacitor during braking, the prosthesis lasts longer between each charge than it would without regenerative braking. We are …

Adaptation Of Scenedesmus Dimorphus To Brackish Water, Dustin Bowden, Joanne M. Belovich

Undergraduate Research Posters 2013

Microalgae is a promising biofuel feedstock for replacement of conventional transportation fuels. Microalgae does not require arable land for cultivation, and the biofuel production rate per acre of land is an order of magnitude greater than that needed for crop-based production methods. Though microalgae to biofuel processes are attractive, none have proven commercially successful due to the high costs of algae dewatering. Moreover, the scarcity of fresh water in many parts of the world prevents development of this process because of competition with drinking water supplies. Our lab has developed an efficient dewatering method using an inclined gravity settler. It …

Towards A More Robust Lower Neck Compressive Injury Tolerance - An Approach Combining Multiple Test Methodologies, Daniel Toomey, King H. Yang, N Yoganadan, F A. Pintar, C A. Van Ee

Biomedical Engineering Faculty Research Publications

Objective.The compressive tolerance of the cervical spine has traditionally been reported in terms of axial force at failure. Previous studies suggest that axial compressive force at failure is particularly sensitive to the alignment of the cervical vertebra and the end conditions of the test methodology used. The present study was designed to develop a methodology to combine the data of previous experiments into a diverse dataset utilizing multiple test methods to allow for the evaluation of the robustness of current and proposed eccentricity based injury criteria.

Methods. Data was combined from two studies composed of dynamic experiments including whole …

Why Is Ca3 More Vulnerable Than Ca1 In Experimental Models Of Controlled Cortical Impact-Induced Brain Injury?, Haojie Mao, Benjamin S. Elkin, Vinay V. Genthikatti, Barclay Morrison Iii, King H. Yang

Biomedical Engineering Faculty Research Publications

One interesting finding of controlled cortical impact (CCI) experiments is that the CA3 region of the hippocampus, which is positioned further from the impact than the CA1 region, is reported as being more injured. The current literature has suggested a positive correlation between brain tissue stretch and neuronal cell loss. However, it is counterintuitive to assume that CA3 is stretched more during CCI injury. Recent mechanical studies of the brain have reported on a level of spatial heterogeneity not previously appreciated—the finding that CA1 was significantly stiffer than all other regions tested and that CA3 was one of the most …

All-Optical Photoacoustic Detection Of Absorbers In Tissue Phantoms, Jami Johnson, Michelle Sabick, Kasper Vanwijk

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Visualizing and characterizing vascular structures is important for many areas of health care, from accessing difficult veins and arteries for laboratory testing, to diagnosis and treatment of cardiovascular disease. Photoacoustic (PA) imaging, one of the fastest growing fields of biomedical imaging, is well suited for this task. PA imaging is based on the photoacoustic effect, which starts with a pulsed laser source incident on biological tissue. If the wavelength of the source matches an absorption wavelength of a chromophore within the tissue, a portion of the pulse energy is absorbed by the chromophore and converted into heat. A subsequent increase …

Comparison Of A Sio2-Cao-Zno-Sro Glass Polyalkenoate Cement To Commercial Dental Materials: Ion Release, Biocompatibility And Antibacterial Properties, A. W. Wren, A. Coughlan, M. M. Hall, M. J. German, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Ion Release and biocompatibility of a CaO-SrO-ZnO-SiO₂ (BT 101) based glass polyalkenoate cement (GPC) was compared against commercial GPCs, Fuji IX and Ketac Molar. The radiopacity (R) was similar for each material, 2.0-2.8. Ion release was evaluated on each material over 1, 7, 30 and 90 days. BT 101 release included Ca (23 mg/L), Sr (23 mg/L) Zn (13 mg/L), Si (203 mg/L). Fuji IX release includes Ca (0.7 mg/L), Al (3 mg/L) Si (26 mg/L), Na (60 mg/L) and P (0.5 mg/L) while Ketac Molar release includes Ca (1 mg/L), Al (0.6 mg/L) Si (23 mg/L), Na (76 …

Automated Methods To Determine Electrospun Fiber Alignment And Diameter Using The Radon Transform, Nicholas J. Schaub, Sean J. Kirkpatrick, Ryan J. Gilbert

Chemical and Biochemical Engineering Faculty Research & Creative Works

Recent evidence demonstrates the ability to change cell function by altering the physical properties of electro spun scaffolds, but many studies still do not characterize electro spun fiber alignment and diameter. To aid in the reporting of these crucial properties, we demonstrate two methods of quantifying electro spun fiber alignment with one method capable of determining electro spun fiber diameter. The first method assesses fiber alignment in a scanning electron microscopy image using the Radon Transform (RT) to calculate the entropy of the fibers in the image. The RT entropy method was more sensitive than a commonly used Fast Fourier …

An Analysis Of Eliminating Electroosmotic Flow In A Microfluidic Pdms Chip, Cecile D. Redington

Master's Theses

The goal of this project is to eliminate electroosmotic flow (EOF) in a microfluidic chip. EOF is a naturally occurring phenomenon at the fluid-surface interface in microfluidic chips when an electric field is applied across the fluid. When isoelectric focusing (IEF) is carried out to separate proteins based on their surface charge, the analytes must remain in the separation chamber, and not migrate to adjacent features in the microfluidic chip, which happens with EOF.

For this project, a microfluidic chip was designed and commissioned to be photolithographically transferred onto a Si wafer. A PDMS component was then casted on the …

Changes In Hemodynamic Responses In Chronic Stroke Survivors Do Not Affect Fmri Signal Detection In A Block Experimental Design, Nutta-On Promjunyakul, Brian D. Schmit, Sheila Schindler-Ivens

Physical Therapy Faculty Research and Publications

The use of canonical functions to model BOLD-fMRI data in people post-stroke may lead to inaccurate descriptions of task-related brain activity. The purpose of this study was to determine whether the spatiotemporal profile of hemodynamic responses (HDRs) obtained from stroke survivors during an event-related experiment could be used to develop individualized HDR functions that would enhance BOLD-fMRI signal detection in block experiments. Our long term goal was to use this information to develop individualized HDR functions for stroke survivors that could be used to analyze brain activity associated with locomotor-like movements. We also aimed to examine the reproducibility of HDRs …

Force Sensing Surgical Scissor Blades Using Fibre Bragg Grating Sensors, Dean Callaghan

Doctoral

This thesis considers the development and analysis of unique sensorised surgical scissor blades for application in minimally invasive robotic surgery (MIRS). The lack of haptic (force and tactile) feedback to the user is currently an unresolved issue with modern MIRS systems. This thesis presents details on smart sensing scissor blades which enable the measurement of instrument-tissue interaction forces for the purpose of force reflection and tissue property identification. A review of current literature established that there exists a need for small compact, biocompatible, sterilisable and robust sensors which meet the demands of current MIRS instruments. Therefore, the sensorised blades exploit …

Novel Paradigms For Visual Field Mapping With Functional Magnetic Resonance Imaging, Yan Ma

Dissertations (1934 -)

The overall goal of this study is to evaluate the existing, and develop new visual field mapping paradigms, which consist of visual stimulation scheme, post-processing and displaying tools using fMRI for both research and clinical applications.

We first directly compared phase mapping and random multifocal mapping paradigms with respect to clinically relevant factors. Multifocal mapping was superior in immunity to noise and was able to accurately decompose the response of single voxels to multiple stimulus locations. In contrast, phase mapping activated more extrastriate visual areas and was more efficient per run in achieving a statistically efficient response in a minimum …

Mechanoadaptation Of Feed Artery Smooth Muscle Cells In The Stem Of The Collateral Circulation, Allison Peck

Biomedical Engineering

Many patients suffering from peripheral arterial occlusive disease (PAOD) experience intermittent claudication, pain during locomotion. Previous studies suggest that this symptom could be explained in part by impaired vasodilation in collateral arteries. In this study, femoral ligation was performed on a murine animal model, stimulating collateral outward remodeling. The mechanism by which a collateral increases its luminal diameter in response to the increase in blood flow following occlusion warrents further investigation due to impaired vasodilation following collateral remodeling. Specifically, resting diameter is elevated in the stem region of the collateral circuit, but this increase in vessel size cannot be explained …

Outer Retinal Structure In Best Vitelliform Macular Dystrophy, David B. Kay, Megan E. Land, Robert F. Cooper, Adam M. Dubis, Pooja Godara, Alfredo Dubra, Joseph Carroll, Kimberly E. Stepien

Biomedical Engineering Faculty Research and Publications

Importance Demonstrating the utility of adaptive optics scanning light ophthalmoscopy (AOSLO) to assess outer retinal structure in Best vitelliform macular dystrophy (BVMD).

Objective To characterize outer retinal structure in BVMD using spectral-domain optical coherence tomography (SD-OCT) and AOSLO.

Design, Setting, and Participants Prospective, observational case series. Four symptomatic members of a family with BVMD with known BEST1 mutation were recruited at the Advanced Ocular Imaging Program research lab at the Medical College of Wisconsin Eye Institute, Milwaukee.

Intervention Thickness of 2 outer retinal layers corresponding to photoreceptor inner and outer segments was measured using SD-OCT. Photoreceptor mosaic AOSLO images within …

How Industry Benefits From Student Design, Jay R. Goldberg

Biomedical Engineering Faculty Research and Publications

No abstract provided.

Ex Vivo Diffusion Tensor Imaging Of Spinal Cord Injury In Rats Of Varying Degrees Of Severity, Michael Jirjis, Shekar N. Kurpad, Brian D. Schmit

Biomedical Engineering Faculty Research and Publications

The aim of this study was to characterize magnetic resonance diffusion tensor imaging (DTI) in proximal regions of the spinal cord following a thoracic spinal cord injury (SCI). Sprague–Dawley rats (n = 40) were administered a control, mild, moderate, or severe contusion injury at the T8 vertebral level. Six direction diffusion weighted images (DWIs) were collected ex vivo along the length of the spinal cord, with an echo/repetition time of 31.6 ms/14 sec and b = 500 sec/mm2. Diffusion metrics were correlated to hindlimb motor function. Significant differences were found for whole cord region of interest (ROI) drawings for fractional …

Hypoxia Preconditioning Increases Survival And Decreases Expression Of Toll-Like Receptor 4 In Pulmonary Artery Endothelial Cells Exposed To Lipopolysaccharide, Irshad Ali, Rahul Nanchal, Fouad Husnain, Said H. Audi, G. Ganesh Konduri, John C. Densmore, Meetha Medhora, Elizabeth R. Jacobs

Biomedical Engineering Faculty Research and Publications

Pulmonary or systemic infections and hypoxemic respiratory failure are among the leading causes of admission to intensive care units, and these conditions frequently exist in sequence or in tandem. Inflammatory responses to infections are reproduced by lipopolysaccharide (LPS) engaging Toll-like receptor 4 (TLR4). Apoptosis is a hallmark of lung injury in sepsis. This study was conducted to determine whether preexposure to LPS or hypoxia modulated the survival of pulmonary artery endothelial cells (PAECs). We also investigated the role TLR4 receptor expression plays in apoptosis due to these conditions. Bovine PAECs were cultured in hypoxic or normoxic environments and treated with …

Synthetic Polymeric Carbohydrates Recognized Toxoplasma Gondii Tachyzoites And Induced Early Phagocytosis By Macrophages, Souzan Hussain Eassa

Theses and Dissertations

Toxoplasmosis is a parasitic disease caused by the intracellular protozoan Toxoplasma gondii your words (T. gondii your words) that affects most types of warm-blooded vertebrate cells. Up to one third of the humans population in the world is chronically infected by this parasite. Human and animals at risk for toxoplasmosis include fetuses, newborns, and immunologically impaired patients. To date, there is no vaccine available and no drug has a successful effective against chronic form of toxoplasmosis. Recent Toxoplasma your words diagnostic methods showed high false positive results and cannot detect the parasite in the early infection stage. Early diagnosis of …