Biomedical Engineering and Bioengineering Commons^™

A Nonrigid Registration Method For Correcting Brain Deformation Induced By Tumor Resection, Yixun Liu, Chengjun Yao, Fotis Drakopoulos, Jinsong Wu, Liangfu Zhou, Nikos Chrisochoides

Computer Science Faculty Publications

Purpose: This paper presents a nonrigid registration method to align preoperative MRI with intraoperative MRI to compensate for brain deformation during tumor resection. This method extends traditional point-based nonrigid registration in two aspects: (1) allow the input data to be incomplete and (2) simulate the underlying deformation with a heterogeneous biomechanical model.

Methods: The method formulates the registration as a three-variable (point correspondence, deformation field, and resection region) functional minimization problem, in which point correspondence is represented by a fuzzy assign matrix; Deformation field is represented by a piecewise linear function regularized by the strain energy of a heterogeneous biomechanical …

Coupling Graphs, Efficient Algorithms And B-Cell Epitope Prediction, Liang Zhao, Steven C. H. Hoi, Zhenhua Li, Limsoon Wong, Hung Nguyen

Research Collection School Of Computing and Information Systems

Coupling graphs are newly introduced in this paper to meet many application needs particularly in the field of bioinformatics. A coupling graph is a two-layer graph complex, in which each node from one layer of the graph complex has at least one connection with the nodes in the other layer, and vice versa. The coupling graph model is sufficiently powerful to capture strong and inherent associations between subgraph pairs in complicated applications. The focus of this paper is on mining algorithms of frequent coupling subgraphs and bioinformatics application. Although existing frequent subgraph mining algorithms are competent to identify frequent subgraphs …

2013 Fall Engr333 Project Final Report, 2013 Fall Engr333

ENGR 333

During the fall of 2013, the Engineering 333 class was asked the question, “what would it take for Calvin College to operate a biofuel vehicle from campus resources?” The three primary considerations included:

• Determining the optimal biofuel feedstock in terms of availability, transportation, and processing.
• Selecting a biofuel vehicle for conversion or purchase to operate on the selected feedstock.
• Designing the infrastructure and process required for operating the selected biofuel vehicle. The design and research described below proposes an environmentally sustainable and cost-effective method for integrating a biofuel vehicle into Calvin’s existing infrastructure.

2013 Fall Engr333 Student Seminar Presentation, Claire Philippi, Karl Bratt, Mike Houtman, Brandon Koster

ENGR 333

File for student presentation, given by students in the Fall 2013 class of ENGR333.

2013 Fall Engr333 Vehicle Poster, 2013 Fall Engr333

ENGR 333

Waste vegetable oil (WVO) was chosen by the class as the best fuel source for the Calvin Biofuel Vehicle Project. The class then considered vehicle options and selected a lawnmower to be powered by WVO.

2013 Fall Engr333 Fuel And Facilities Poster, 2013 Fall Engr333

ENGR 333

The objective of the project was to answer the question: “What would it take for Calvin College to operate a biofuel vehicle from campus resources.” The class split into 3 teams:

• Fuel/Feedstock
• Facilities/Infrastructure
• Vehicle

Near-Infrared Surface-Enhanced Fluorescence Using Silver Nanoparticles In Solution, Michael D. Furtaw

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Fluorescence spectroscopy is a widely used detection technology in many research and clinical assays. Further improvement to assay sensitivity may enable earlier diagnosis of disease, novel biomarker discovery, and ultimately, improved outcomes of clinical care along with reduction in costs. Near-infrared, surface-enhanced fluorescence (NIR-SEF) is a promising approach to improve assay sensitivity via simultaneous increase in signal with a reduction in background. This dissertation describes research conducted with the overall goal to determine the extent to which fluorescence in solution may be enhanced by altering specific variables involved in the formation of plasmonactive nanostructures of dye-labeled protein and silver nanoparticles …

Formulation Development Of A Polymer-Drug Matrix With A Controlled Release Profile For The Treatment Of Glaucoma, Eric W. Tsoi

Master's Theses

Glaucoma is the leading cause of blindness in the United States accounting for 9-12% of all cases of blindness. Currently, the front line treatment for glaucoma are prostaglandins that may have to be taken up to several times a day. Even with proper treatment, roughly 11% of the patients using the treatment are non-compliant and lose their vision. In this project, ForSight Laboratories has developed a pharmaceutical drug delivering implant with the capability of sustaining long-term release of a prostaglandin as a new way to treat the condition. This project reports the product development of a polymer drug matrix with …

Modeling And Control Of Nanoparticle Bloodstream Concentration For Cancer Therapies, Scarlett S. Bracey

Doctoral Dissertations

Currently, the most commonly used treatments for cancerous tumors (chemotherapy, radiation, etc.) have almost no method of monitoring the administration of the treatment for adverse effects in real time. Without any real time feedback or control, treatment becomes a "guess and check" method with no way of predicting the effects of the drugs based on the actual bioavailability to the patient's body. One particular drug may be effective for one patient, yet provide no benefit to another. Doctors and scientists do not routinely attempt to quantifiably explain this discrepancy. In this work, mathematical modeling and analysis techniques are joined together …

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.

Polysaccharide-Based Nanocarriers For Improved Drug Delivery, Nan Zhang

Dissertations - ALL

The field of drug delivery has provided a solution to the limited efficacy and high toxicity of many drugs. Nano-sized drug carriers are popular because their size allows for selective accumulation in the diseased area. Polysaccharides are non-toxic and biodegradable natural polymers that can serve as the basis for these nano-sized carriers. Polysialic acid (PSA) is such a polysaccharide with strong hydrophilicity that may reduce uptake by the reticuloendothelial system and prolong drug circulation. In this study, we developed PSA-based nanocarriers, specifically micelles and nanoparticles, for improved drug delivery with improved efficacy and minimized toxicity. PSA-based micelle systems were developed …

Protein Loop Length Estimation From Medium Resolution Cryoem Images, Andrew R. Mcknight

Computer Science Theses & Dissertations

In the post-genomic era, proteomics research presents a new frontier in life science. Proteins play roles in virtually every biological process, and understanding their atomic structures is the key to unraveling how they carry out their work. Compared to the over half million protein sequences in UniProt, only around 25,000 unique sequences have been atomically modeled and deposited to PDB (Protein Databank). Cryoelectron Microscopy (cryoEM) is an important biophysical technique that produces 3D subnanometer resolution images of molecules not amenable to past approaches like x-ray crystallography or nuclear magnetic resonance. De novo modeling is becoming a promising approach to derive …

Spatiotemporal Fluorescent Detection Measurements Using Embedded Waveguide Sensors, Mark C. Harrison, Andrea M. Armani

Engineering Faculty Articles and Research

Integrated waveguide biosensors, when combined with fluorescent labeling, have significantly impacted the field of biodetection. While there are numerous types of waveguide sensors, the fundamental excitation method is fairly consistent: the evanescent field of the waveguide excites a fluorophore whose emission is detected, either directly via imaging or indirectly via a decrease in power transfer. Recently, a sensor device was demonstrated which is able to back-couple the emitted light into the waveguide, allowing the signal to be detected directly. However, this previous work focused on the development of an empirical model, leaving many theoretical questions unanswered. Additionally, the results from …

Study Of Immobilizing Cadmium Selenide Quantum Dots In Selected Polymers For Application In Peroxyoxalate Chemiluminescence Flow Injection Analysis, Christopher S. Moore

Electronic Theses and Dissertations

Two batches of CdSe QDs with different sizes were synthesized for immobilizing in polyisoprene (PI), polymethylmethacrylate (PMMA), and low-density polyethylene (LDPE). The combinations of QDs and polymer substrates were evaluated for their analytical fit-for-use in applicable immunoassays. Hydrogen peroxide standards were injected into the flow injection analyzer (FIA) constructed to simulate enzyme-generated hydrogen peroxide reacting with bis-(2,4,6-trichlorophenyl) oxalate.

Linear correlations between hydrogen peroxide and chemilumenscent intensities yielded regression values greater than 0.9750 for hydrogen peroxide concentrations between 1.0 x 10^-4 M and 1.0 x 10^-1 M. The developed technique’s LOD was approximately 10 ppm. Variability of the prepared …

A Gamos Plug-In For Geant4 Based Monte Carlo Simulation Of Radiation-Induced Light Transport In Biological Media, Adam K. Glaser, Stephen C. Kanick, Rongxiao Zhang, Pedro Arce, Brian W. Pogue

Dartmouth Scholarship

We describe a tissue optics plug-in that interfaces with the GEANT4/GAMOS Monte Carlo (MC) architecture, providing a means of simulating radiation-induced light transport in biological media for the first time. Specifically, we focus on the simulation of light transport due to the Čerenkov effect (light emission from charged particle's traveling faster than the local speed of light in a given medium), a phenomenon which requires accurate modeling of both the high energy particle and subsequent optical photon transport, a dynamic coupled process that is not well-described by any current MC framework. The results of validation simulations show excellent agreement with …

An Investigation And Analysis Of The Vestibulo-Ocular Reflex In A Vibration Environment, Daniel J. Uribe

Theses and Dissertations

Forty years of innovations have greatly improved Helmet-Mounted Displays (HMDs) and their integration into military systems. However, a significant issue with HMDs is the effect of vibration and the associated Vestibulo-Ocular Reflex (VOR). When a human’s head is subject to low-frequency vibration, the VOR stabilizes the eye with respect to objects in the external environment. However, this response is inappropriate in HMDs as the display moves with the user’s head and the VOR blurs the image as it is projected on the human retina. Current compensation techniques suggest increasing the size of displayed graphics or text to compensate for the …

Picture Of A Chelate In Exchange: The Crystal Structure Of Nahodotma, A 'Semi'-Hydrated Chelate, Katherine M. Payne, Edward J. Valente, Silvio Aime, Mauro Botta, Mark Woods

Chemistry Faculty Publications and Presentations

Crystallography generally only provides static structural information. This can render it an ineffective technique for probing dynamic solution state processes. A crystal of HoDOTMA affords unique structures that effectively represent that of a lanthanide tetra-acetate chelate mid-way through the water exchange process.

Nonlinear Granger Causality And Its Application In Decoding Of Human Reaching Intentions, Mengting Liu

Doctoral Dissertations

Multi-electrode recording is a key technology that allows the brain mechanisms of decision making, cognition, and their breakdown in diseases to be studied from a network perspective. As the hypotheses concerning the role of neural interactions in cognitive paradigms become increasingly more elaborate, the ability to evaluate the direction of neural interactions in neural networks holds the key to distinguishing their functional significance.

Granger Causality (GC) is used to detect the directional influence of signals between multiple locations. To extract the nonlinear directional flow, GC was completed through a nonlinear predictive approach using radial basis functions (RBF). Furthermore, to obtain …

New Microarray Image Segmentation Using Segmentation Based Contours Method, Yuan Cheng

Doctoral Dissertations

The goal of the research developed in this dissertation is to develop a more accurate segmentation method for Affymetrix microarray images. The Affymetrix microarray biotechnologies have become increasingly important in the biomedical research field. Affymetrix microarray images are widely used in disease diagnostics and disease control. They are capable of monitoring the expression levels of thousands of genes simultaneously. Hence, scientists can get a deep understanding on genomic regulation, interaction and expression by using such tools.

We also introduce a novel Affymetrix microarray image simulation model and how the Affymetrix microarray image is simulated by using this model. This simulation …

Distal Placement Of An End-To-Side Bypass Graft Anastomosis: A 3d Computational Study, John Di Cicco, Ayodeji Demuren

Mechanical & Aerospace Engineering Faculty Publications

A three-dimensional (3D) computational fluid dynamics study of shear rates around distal end-to-side anastomoses has been conducted. Three 51% and three 75% cross-sectional area-reduced 6 mm cylinders were modeled each with a bypass cylinder attached at a 30-degree angle at different placements distal to the constriction. Steady, incompressible, Newtonian blood flow was assumed, and the full Reynolds-averaged Navier-Stokes equations, turbulent kinetic energy, and specific dissipation rate equations were solved on a locally structured multiblock mesh with hexahedral elements. Consequently, distal placement of an end-to-side bypass graft anastomosis was found to have an influence on the shear rate magnitudes. For the …

Synthesis And Characterization Of Biodegradable Poly(Vinyl Esters) With Hdac Inhibitory Activity, Kyle Lawrence Horton

Wayne State University Theses

HDAC inhibitors are known to have anti-inflammatory properties. HDAC inhibitors are used in combination with Oct4 to generate induced pluripotent stem cells. I hypothesized that polyesters based on simple aliphatic HDAC inhibitors like valproic acid (VPA) and phenylbutyric acid (PBA) can serve as alternatives to existing polyester biomaterials with improved anti-inflammatory properties and as scaffolds for generation of iPSCs when used in combination with layer-by-layer thin films delivering reprogramming transcription factors. Vinyl ester of phenylbutyric acid (VEPA) and vinyl ester of valproic acid (VEVA) were synthesized from their carboxylic acid precursors using an iridium complex catalyst at yields as high …

Studies Of Functionalized Nanoparticles For Smart Self-Assembly And As Controlled Drug Delivery, Xiaochu Ding

Dissertations, Master's Theses and Master's Reports - Open

This dissertation is related to the studies of functionalized nanoparticles for self-assembly and as controlled drug delivery system. The whole topic is composed of two parts. In the first part, the research was conducted to design and synthesize a new type of ionic peptide-functionalized copolymer conjugates for self-assembly into nanoparticle fibers and 3D scaffolds with the ability of multi-drug loading and governing the release rate of each drug for tissue engineering. The self-assembly study confirmed that such peptide-functionalized amphiphilic copolymers underwent different self-assembly behavior. The bigger nanoparticles were more easily assembled into nanoparticle fibers and 3D scaffolds with larger pore …

Visual Exploration And Information Analytics Of High-Dimensional Medical Images, Darshan Pai

Wayne State University Dissertations

Data visualization has transformed how we analyze increasingly large and complex data sets. Advanced visual tools logically represent data in a way that communicates the most important information inherent within it and culminate the analysis with an insightful conclusion. Automated analysis disciplines - such as data mining, machine learning, and statistics - have traditionally been the most dominant fields for data analysis. It has been complemented with a near-ubiquitous adoption of specialized hardware and software environments that handle the storage, retrieval, and pre- and postprocessing of digital data. The addition of interactive visualization tools allows an active human participant in …

Bacillus Thuringiensis: Transgenic Crops, Julie A. Peterson, John J. Obrycki, James D. Harwood

Department of Entomology: Faculty Publications

Bacillus thuringiensis (Bt) crops, genetically modified to express insecticidal toxins that target key pests of corn, cotton, rice, potato, and other crops, have been rapidly adopted and have become dominant fixtures in agroecosystems throughout the world. Due to the constitutive nature of Bt toxin expression, insecticidal proteins may be found in nearly all plant tissues, presenting multiple sources for Bt toxins to enter the environment, thus creating complex direct and indirect pathways for non-target organisms to be exposed to insecticidal proteins. The environmental impacts of Bt crops have been widely debated, although both benefits and risks do exist. Benefits of …

Design Of A Pretreatment And Enzymatic Saccharification Scheme Of Understory From Managed Pine Forest For A Biochemical-Refinery Platform: The Example Of The Sweetgum Tree, Angele Djioleu

Graduate Theses and Dissertations

The possibility of using sweetgum from southern pine dominated forests as a biobased refinery feedstock was investigated. First, a baseline hydrolysis scheme for sweetgum wood and bark was designed. Sweetgum wood and bark were pretreated with 0.98% (v/v) sulfuric acid at 140°C for 30, 40, 50, 60 or 70 min and at 160°C for 30, 40, 50 or 60 min. The water insoluble solid (WIS) fraction was hydrolyzed with a cellulase enzyme cocktail. Results showed that maximum xylose and glucose yields from the wood were 82 and 86%, respectively. Similarly, the respective maximum yields of xylose and glucose from the …

A Watershed Scale Evaluation Of Selected Second Generation Biofeedstocks On Water Quality, Gurdeep Singh

Graduate Theses and Dissertations

This study compares a novel simulation approach to the conventional Soil and Water Assessment Tool (SWAT) modeler's approach for targeting biofuel crop production on marginal lands. In conventional SWAT modeling approach, non-spatial definition of hydrological response units (HRUs) results in the simulation of biofuel crops on both marginal and non-marginal land. This study provides an alternative approach in which a marginal-land raster was integrated into the land use and land cover (LULC) raster in such a way that the land uses were divided into marginal and non-marginal components. This modified LULC was used for model setup which resulted in marginal …

The Design And Testing Of A Solar Autoclave With Broad Spectrum Sterilization Capabilities, Sarah S. Trabia

Honors College Theses

Energy is difficult to come by in developing countries and this interferes with the ability of doctors to provide good healthcare to their patients. Without decent sterilization, patients can become infected and diseases can spread throughout hospitals. This study involves designing a solar autoclave for developing countries that is as efficient as electrical autoclaves. The design is intended to not require any electrical input and to be affordable to those who cannot afford advanced medical equipment. Once the solar autoclave is designed, it will be tested to determine if it can sterilize equipment against a variety of different bacteria, including …

A Novel Microfluidic Enrichment Technique For Carbonylated Proteins, Bryant C. Hollins

Doctoral Dissertations

Proteins are the building blocks of cells in living organisms, and are composed of amino acids. The expression of proteins is regulated by the processes of transcription and translation. Proteins undergo post-translational modifications in order to dictate their role physiologically within a cell.

Not all post-translational modifications are beneficial for the protein or the cell. One type of post-translational modification, called carbonylation, irreversibly places a carbonyl group onto an amino acid residue, most commonly proline, lysine, arginine, and threonine. This modification can have severe consequences physiologically, including loss of solubility, loss of function, and protein aggregation.

Carbonylated proteins have commonly …

Whole-Word Recognition From Articulatory Movements For Silent Speech Interfaces, Jun Wang, Ashok Samal, Jordan R. Green, Frank Rudzicz

Department of Special Education and Communication Disorders: Faculty Publications

Articulation-based silent speech interfaces convert silently produced speech movements into audible words. These systems are still in their experimental stages, but have significant potential for facilitating oral communication in persons with laryngectomy or speech impairments. In this paper, we report the result of a novel, real-time algorithm that recognizes whole-words based on articulatory movements. This approach differs from prior work that has focused primarily on phoneme-level recognition based on articulatory features. On average, our algorithm missed 1.93 words in a sequence of twenty-five words with an average latency of 0.79 seconds for each word prediction using a data set of …

Role Of Glutathione In Lung Retention Of 99mtc-Hexamethylpropyleneamine Oxime In Two Unique Rat Models Of Hyperoxic Lung Injury, Said H. Audi, David L. Roerig, Steven Thomas Haworth, Anne V. Clough

Biomedical Engineering Faculty Research and Publications

Rat exposure to 60% O₂ for 7 days (hyper-60) or to >95% O₂ for 2 days followed by a 24-hour in room air (hyper-95R) confers susceptibility or tolerance, respectively, of the otherwise lethal effects of subsequent exposure to 100% O₂. The objective of this study was to determine if lung retention of the radiopharmaceutical agent ^99mTc-HMPAO (hexamethylpropyleneamine oxime) is differentially altered in hyper-60 and hyper-95R rats. Tissue retention of HMPAO is dependent on intracellular content of the antioxidant glutathione (GSH) and mitochondrial function. HMPAO was injected i.v. in anesthetized rats and planar images were acquired. …