Biomedical Engineering and Bioengineering Commons^™

Experimental Terahertz Imaging And Spectroscopy Of Ex-Vivo Breast Cancer Tissue, Tyler C. Bowman

Graduate Theses and Dissertations

This thesis presents experimental results of terahertz imaging and spectroscopy techniques to analyze excised breast cancer tissue. The pulsed terahertz system at the University of Arkansas was used to assess formalin-fixed, paraffin-embedded breast cancer tissue obtained from 22, 40, and 46 year old patients. The tissue for this research was sliced to relatively thin sections of 10 μm thick and mounted on glass slides. Terahertz reflection time and frequency domain images of the breast cancer tissue were then obtained and compared to histopathology slides from the same patient. Results showed good correlation between the reflection images and histopathology slides for …

Nerve Fiber Diameter Measurements Using Hematoxylin And Eosin Staining And Brightfield Microscopy To Assess The Novel Method Of Characterizing Peripheral Nerve Fiber Distributions By Group Delay, Jorge Arturo Vazquez

Master's Theses

Peripheral neuropathies are a set of common diseases that affect the peripheral nervous system, causing damage to vital connections between various parts of the body and the brain and spinal cord. Different clinical conditions are known to selectively impact various size nerve fibers, which often makes it difficult to diagnose which peripheral neuropathy a patient might have. The nerve conduction velocity diagnostic test provides clinically useful information in the diagnosis of some peripheral neuropathies. This method is advantageous because it tends to be minimally invasive yet it provides valuable diagnostic information. However, this test does not determine characteristics of peripheral …

Potential For Photoacoustic Imaging Of Neonatal Brain, Pantea Tavakolian

Electronic Thesis and Dissertation Repository

Photoacoustic imaging is a hybrid imaging technique that combines many of the merits of both optical and ultrasound imaging. Photoacoustic imaging (PAI) has been hypothesized as a technique for imaging neonatal brain. However, PAI of the brain is more challenging than traditional methods (e.g. near infrared spectroscopy) due to the presence of the skull layer. To evaluate the potential limits the skull places on 3D PAI of the neonatal brain, we constructed a neonatal skull phantom (~1.52-mm thick) with a mixture of epoxy and titanium dioxide powder that provided acoustic insertion loss (1-5MHz) similar to human infant skull bone. The …

Application Of Limited Mixing In The Hele-Shaw Geometry In Fabrication Of Janus Hydrogels, Md Mahmudur Rahman

Md Mahmudur Rahman

It is widely accepted that cells behave differently responding to the stiffness of their extracellular matrix (ECM). Such observations were made by culturing cells on hydrogel substrates of tunable stiffness. However, it was recently proposed that cells may sense how strongly they are tethered to ECM, not the local stiffness of ECM. To investigate both hypotheses, we developed a method to fabricate Janus polyacrylamide (PAAM) gels. We squeeze two drops of different concentrations in the Hele-Shaw geometry to generate radial Stokes flow. When the drops coalesce, limited mixing occurs at the interface due to the narrow confinement, and diffusion normal …

Frontal White Matter Integrity In Adults With Down Syndrome With And Without Dementia, David K. Powell, Allison Caban-Holt, Greg A. Jicha, William C. Robertson, Roberta Davis, Brian T. Gold, Frederick A. Schmitt, Elizabeth Head

Magnetic Resonance Imaging and Spectroscopy Center Faculty Publications

Adults with Down syndrome (DS) are at high risk for developing Alzheimer's disease after the age of 40 years. To detect white matter (WM) changes in the brain linked to dementia, fractional anisotropy (FA) from diffusion tensor imaging was used. We hypothesized that adults with DS without dementia (DS n = 10), DS with dementia (DSAD n = 10) and age matched non-DS subjects (CTL n = 10) would show differential levels of FA and an association with scores from the Brief Praxis Test and the Severe Impairment Battery. WM integrity differences in DS compared with CTL were found predominantly …

Image-Based Registration Methods For Quantification And Compensation Of Prostate Motion During Trans-Rectal Ultrasound (Trus)-Guided Biopsy, Tharindu De Silva

Electronic Thesis and Dissertation Repository

Prostate biopsy is the clinical standard for cancer diagnosis and is typically performed under two-dimensional (2D) transrectal ultrasound (TRUS) for needle guidance. Unfortunately, most early stage prostate cancers are not visible on ultrasound and the procedure suffers from high false negative rates due to the lack of visible targets. Fusion of pre-biopsy MRI to 3D TRUS for targeted biopsy could improve cancer detection rates and volume of tumor sampled. In MRI-TRUS fusion biopsy systems, patient or prostate motion during the procedure causes misalignments in the MR targets mapped to the live 2D TRUS images, limiting the targeting accuracy of the …

Uncertainty Quantification Driven Predictive Multi-Scale Model For Synthesis Of Mycotoxins, Sourav Banerjee, Gabriel A. Terejanu, Anindya Chanda

Faculty Publications

Many toxic molds synthesize and release an array of poisons, termed mycotoxins that have an enormous impact on human health, agriculture and economy [1]. These molds contaminate our buildings, indoor air and crops, cause life threatening human and animal diseases and reduce agricultural output [2]. In order to design appropriate approaches to minimize the detrimental effects of these fungi, it is essential to develop diagnostic methodologies that can rapidly and accurately determine based on fungal strains and their growth patterns, the extent of mycotoxin mediated damage caused to the environment.Here we developed a novel multi-scale predictive mathematical model that could …

Developent Of A Phospholipid Encapsulation Process For Quantum Dots To Be Used In Biologic Applications, Logan Grimes

Master's Theses

The American Cancer Society predicts that 1,665,540 people will be diagnosed with cancer, and 585,720 people will die from cancer in 2014. One of the most common types of cancer in the United States is skin cancer. Melanoma alone is predicted to account for 10,000 of the cancer related deaths in 2014. As a highly mobile and aggressive form of cancer, melanoma is difficult to fight once it has metastasized through the body. Early detection in such varieties of cancer is critical in improving survival rates in afflicted patients. Present methods of detection rely on visual examination of suspicious regions …

Smooth Muscle Cell Organization In The Stem Region Of The Gracilis Collateral Circulation, Amanda Krall

Biomedical Engineering

Many patients who suffer from the ischemic Peripheral Arterial Occlusive Disease (PAOD) experience intermittent claudication, which can be attributed to impaired vasodilation. Collateral vessels are the primary site of resistance to blood flow downstream; therefore maximizing vasodilation in collaterals is crucial for efficient circulation. Collaterals function as natural bypasses around the occluded arteries and the increase in flow into these vessels causes them to outwardly remodel into conduit vessels. However, functional vasodilation in the stem region of collateral vessels is impaired at day 7 following femoral ligation, which can be attributed to smooth muscle cell malfunction. However, the increase in …

Extraction Of Intrinsic Fluorescence From Single Fiber Fluorescence Measurements On A Turbid Medium: Experimental Validation, U. A. Gamm, C. L. Hoy, F. Van Leeuwen - Van Zaane, H. J. C. M. Sterenborg, S. C. Kanick, D J. Robinson, A. Amelink

Dartmouth Scholarship

Abstract

The detailed mechanisms associated with the influence of scattering and absorption properties on the fluorescence intensity sampled by a single optical fiber have recently been elucidated based on Monte Carlo simulated data. Here we develop an experimental single fiber fluorescence (SFF) spectroscopy setup and validate the Monte Carlo data and semi-empirical model equation that describes the SFF signal as a function of scattering. We present a calibration procedure that corrects the SFF signal for all system-related, wavelength dependent transmission efficiencies to yield an absolute value of intrinsic fluorescence. The validity of the Monte Carlo data and semi-empirical model is …

Nasopharyngeal Method For Selective Brain Cooling And Development Of A Time-Resolved Near-Infrared Technique To Monitor Brain Temperature And Oxidation Status During Hypothermia, Mohammad Fazel Bakhsheshi

Electronic Thesis and Dissertation Repository

Mild hypothermia at 32-35^oC (HT) has been shown to be neuroprotective for neurological emergencies following severe head trauma, cardiac arrest and neonatal asphyxia. However, HT has not been widely deployed in clinical settings because: firstly, cooling the whole body below 33-34°C can induce severe complications; therefore, applying HT selectively to the brain could minimize adverse effects by maintaining core body temperature at normal level. Secondly, development of an effective and easy to implement selective brain cooling (SBC) technique, which can quickly induce brain hypothermia while avoiding complications from whole body cooling, remains a challenge. In this thesis, we …

Modeling, Analysis, And Control Of A Mobile Robot For In Vivo Fluoroscopy Of Human Joints During Natural Movements, Matthew A. Young

Doctoral Dissertations

In this dissertation, the modeling, analysis and control of a multi-degree of freedom (mdof) robotic fluoroscope was investigated. A prototype robotic fluoroscope exists, and consists of a 3 dof mobile platform with two 2 dof Cartesian manipulators mounted symmetrically on opposite sides of the platform. One Cartesian manipulator positions the x-ray generator and the other Cartesian manipulator positions the x-ray imaging device. The robotic fluoroscope is used to x-ray skeletal joints of interest of human subjects performing natural movement activities. In order to collect the data, the Cartesian manipulators must keep the x-ray generation and imaging devices accurately aligned while …

Oriented Collagen And Applications Of Waveguide Evanescent Field Scattering (Wefs) Microscopy, Qamrun Nahar

Electronic Thesis and Dissertation Repository

In this thesis, Waveguide Evanescent Field Scattering (WEFS) microscopy is developed as a non-invasive, label-free live cell imaging technique. This new high-contrast imaging can be employed to study the first hundred nanometers from the surface as it utilizes the evanescent field of a waveguide as the illumination source. Previously, waveguide evanescent field fluorescence (WEFF) microscopy was developed as a fluorescence imaging technique comparable to the total internal reflection fluorescent (TIRF) microscopy. Both the WEFF and WEFS technique utilizes the same fundamental concepts except in WEFS microscopy imaging is accomplished without the application of any fluorescent labeling. In this work, bacterial …

Application Of Limited Mixing In The Hele-Shaw Geometry In Fabrication Of Janus Hydrogels, Md Mahmudur Rahman

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

It is widely accepted that cells behave differently responding to the stiffness of their extracellular matrix (ECM). Such observations were made by culturing cells on hydrogel substrates of tunable stiffness. However, it was recently proposed that cells may sense how strongly they are tethered to ECM, not the local stiffness of ECM. To investigate both hypotheses, we developed a method to fabricate Janus polyacrylamide (PAAM) gels. We squeeze two drops of different concentrations in the Hele-Shaw geometry to generate radial Stokes flow. When the drops coalesce, limited mixing occurs at the interface due to the narrow confinement, and diffusion normal …

Material Differences In Equine Cortical And Trabecular Bone, Ryan B. Allen

Master's Theses

A greater understanding of bone materials would be beneficial in creating more accurate computer models and in the making of biomedical products involving bone. This study set out to determine whether cortical and trabecular bone are two separate materials, or whether they are the same material with a variance in porosity. To answer this question, samples were taken from different sections of the equine metacarpus, underwent densitometry analysis and were statistically analyzed. The majority of results suggest that the material is the same between varying densities of bone and thus the same between cortical and trabecular bone. These particular results …

Quantitative Relaxometry And Diffusion Mri For Lateralization In Mts And Non-Mts Temporal Lobe Epilepsy., Ali R Khan, Maged Goubran, Sandrine De Ribaupierre, Robert R Hammond, Jorge G Burneo, Andrew G Parrent, Terry M Peters

Robarts Imaging Publications

We developed novel methodology for investigating the use of quantitative relaxometry (T1 and T2) and diffusion tensor imaging (DTI) for lateralization in temporal lobe epilepsy. Patients with mesial temporal sclerosis confirmed by pathology (N=8) and non-MTS unilateral temporal lobe epilepsy (N=6) were compared against healthy controls (N=19) using voxel-based analysis restricted to the anterior temporal lobes, and laterality indices for each MRI metric (T1, T2, fractional anisotropy (FA), mean diffusivity, axial and radial diffusivities) were computed based on the proportion of significant voxels on each side. The diffusivity metrics were the most lateralizing MRI metrics in MTS and non-MTS subsets, …

Utilizing Fast Spin Echo Mri To Reduce Image Artifacts And Improve Implant/Tissue Interface Detection In Refractory Parkinson’S Patients With Deep Brain Stimulators, Subhendra N. Sarkar, Pooja R. Sarkar, Efstathios Papavassiliou, Rafael Rojas

Publications and Research

Introduction. In medically refractory Parkinson’s disease (PD) deep-brain stimulation (DBS) is an effective therapeutic tool. Postimplantation MRI is important in assessing tissue damage and DBS lead placement accuracy. We wanted to identify which MRI sequence can detectDBS leads with smallest artifactual signal void, allowing better tissue/electrode edge conspicuity.

Methods. Using an IRB approved protocol 8 advanced PDpatientswere imagedwithinMRconditional safety guidelines at lowRF power (SAR ≤ 0.1 W/kg) in coronal plane at 1.5T by various sequences.The image slices were subjectively evaluated for diagnostic quality and the lead contact diameters were compared to identify a sequence least affected by metallic leads.

Results …

Surface Functionalization And Bioconjugation Of Nanoparticles For Biomedical Applications, Longyan Chen

Electronic Thesis and Dissertation Repository

Colloidal inorganic nanoparticles (NPs) have been attracting considerable interest in biomedicine, from drug and gene delivery to imaging, sensing and diagnostics. It is essential to modify the surface of nanoparticles to have enhanced biocompatibility and functionality for the in vitro and in vivo applications, especially in delivering locally and recognizing biomolecules. Herein, the goal of this research work is to develop advanced NPs with well-tailored surface functionalities and/or bio-functionality for the applications in cell tracking and analytes detection.

In the first project, quantum dots incorporating with gelatin nanoparticles (QDs-GNPs) have been developed for bioimaging applications. Two different approaches have been …

Advances In Optics For Biotechnology, Medicine And Surgery, Maryann Fitzmaurice, Brian W. Pogue, Guillermo J. Tearney, James W. Tunnell

Dartmouth Scholarship

The guest editors introduce a Biomedical Optics Express feature issue that includes contributions from participants at the 2013 conference on Advances in Optics for Biotechnology, Medicine and Surgery XIII.

Sparse Signal Reconstruction From Polychromatic X-Ray Ct Measurements Via Mass Attenuation Discretization, Renliang Gu, Aleksandar Dogandžić

Aleksandar Dogandžić

We propose a method for reconstructing sparse images from polychromatic x-ray computed tomography (ct) measurements via mass attenuation coefficient discretization. The material of the inspected object and the incident spectrum are assumed to be unknown. We rewrite the Lambert-Beer’s law in terms of integral expressions of mass attenuation and discretize the resulting integrals. We then present a penalized constrained least-squares optimization approach forreconstructing the underlying object from log-domain measurements, where an active set approach is employed to estimate incident energy density parameters and the nonnegativity and sparsity of the image density map are imposed using negative-energy and smooth ℓ1-norm penalty …

Stabilization Of Extended Diffuse Optical Spectroscopy Measurements On In Vivo Human Skeletal Muscle During Dynamic Exercise, Brad A. Henry

Theses and Dissertations--Biomedical Engineering

This research investigates various applications of diffuse correlation spectroscopy (DCS) on in-vivo human muscle tissue, both at rest and during dynamic exercise. Previously suspected muscle tissue relative blood flow (rBF) baseline shift during extended measurement with DCS and DCS-Near infrared spectroscopy (NIRS) hybrid optical systems are verified, quantified, and resolved by redesign of optical probe and alteration in optical probe attachment methodology during 40 minute supine bed rest baseline measurements. We then translate previously developed occlusion techniques, whereby rBF and relative oxygen consumption rV̇O₂ are calibrated to initial resting absolute values by use of a venous occlusion (VO) and …

Detection Of Temporal Lobe Epilepsy Using Support Vector Machines In Multi-Parametric Quantitative Mr Imaging., Diego Cantor-Rivera, Ali R Khan, Maged Goubran, Seyed M Mirsattari, Terry M Peters

Robarts Imaging Publications

The detection of MRI abnormalities that can be associated to seizures in the study of temporal lobe epilepsy (TLE) is a challenging task. In many cases, patients with a record of epileptic activity do not present any discernible MRI findings. In this domain, we propose a method that combines quantitative relaxometry and diffusion tensor imaging (DTI) with support vector machines (SVM) aiming to improve TLE detection. The main contribution of this work is two-fold: on one hand, the feature selection process, principal component analysis (PCA) transformations of the feature space, and SVM parameterization are analyzed as factors constituting a classification …

Stationary Wavelet Transform For Under-Sampled Mri Reconstruction., Mohammad H Kayvanrad, A Jonathan Mcleod, John S H Baxter, Charles A Mckenzie, Terry M Peters

Robarts Imaging Publications

In addition to coil sensitivity data (parallel imaging), sparsity constraints are often used as an additional lp-penalty for under-sampled MRI reconstruction (compressed sensing). Penalizing the traditional decimated wavelet transform (DWT) coefficients, however, results in visual pseudo-Gibbs artifacts, some of which are attributed to the lack of translation invariance of the wavelet basis. We show that these artifacts can be greatly reduced by penalizing the translation-invariant stationary wavelet transform (SWT) coefficients. This holds with various additional reconstruction constraints, including coil sensitivity profiles and total variation. Additionally, SWT reconstructions result in lower error values and faster convergence compared to DWT. These concepts …

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 …

Cervical Cancer Histology Image Feature Extraction And Classification, Peng Guo

Masters Theses

"Cervical cancer, the second most common cancer affecting women worldwide and the most common in developing countries can be cured if detected early and treated. Expert pathologists routinely visually examine histology slides for cervix tissue abnormality assessment. In previous research, an automated, localized, fusion-based approach was investigated for classifying squamous epithelium into Normal, CIN1, CIN2, and CIN3 grades of cervical intraepithelial neoplasia (CIN) based on image analysis of 62 digitized histology images obtained through the National Library of Medicine. In this research, CIN grade assessments from two pathologists are analyzed and are used to facilitate atypical cell concentration feature development …

Full-Field Vibrometry By High-Speed Digital Holography For Middle-Ear Mechanics, Ivo Dobrev

Ivo Dobrev

Hearing loss affects approximately 1 in 10 people in the world and this percentage is increasing every year. Some of the most common courses for hearing loss are disorders of the human tympanic membrane (TM or eardrum) and middle-ear. Early detection and diagnosis of hearing loss as well as research and understanding of the hearing process depend on medical and research tools for quantification of the hearing capabilities, including the function of the human TM in the complex acoustic-mechanical transformation of environmental sounds into vibrations of the middle- and the inner-ear.

Current ear exams are assessing the state of the …

Is The 3d Sound-Induced Motion Of The Tympanic Membrane Consistent With Thin-Shell Theory?, Morteza Khaleghi, Cosme Furlong, Jeffrey Tao Cheng, John J. Rosowski

Morteza Khaleghi

The acousto-mechanical-transformer behavior of the tympanic membrane (TM) is determined by its shape and mechanical properties. Holographic studies of 1D vibrations of the TM have been reported by several groups; however, 3D

measurements of TM displacement are few. In this study, we will use full-field-of-view holographic techniques to near simultaneously measure the shape and 3D sound-induced

displacement of cadaveric TMs.

The geometrical constraints imposed by the ear canal make 3D measures of TM displacement in intact ears difficult. However, we can, even in such a confined geometry, measure both a 1D component of sound-induced displacement and

the shape of the …

Xena: An Automated 'Open-Source' 129xe Hyperpolarizer For Clinical Use, Panayiotis Nikolaou, Aaron M. Coffey, Laura L. Walkup, Brogan M. Gust, Nicholas Whiting, Hayley Newton, Iga Muradyan, Mikayel Dabaghyan, Kaili Ranta, Gregory D. Moroz, Matthew S. Rosen, Samuel Patz, Michael J. Barlow, Eduard Y. Chekmenev, Boyd M. Goodson

Nicholas Whiting

Cdi-Type Ii: Collaborative Research: Cyber Enhancement Of Spatial Cognition For The Visually Impaired, Nicholas Giudice

University of Maine Office of Research Administration: Grant Reports

Wayfinding is an essential capability for any person who wishes to have an independent life-style. It requires successful execution of several tasks including navigation and object and place recognition, all of which necessitate accurate assessment of the surrounding environment. For a visually-impaired person these tasks may be exceedingly difficult to accomplish and there are risks associated with failure in any of these. Guide dogs and white canes are widely used for the purpose of navigation and environment sensing, respectively. The former, however, has costly and often prohibitive training requirements, while the latter can only provide cues about obstacles in one's …

Reconstruction Of Patient-Specific Bone Models From X-Ray Radiography, Hatem Amin Abdel Fattah El Dakhakhni

Doctoral Dissertations

The availability of a patient‐specific bone model has become an increasingly invaluable addition to orthopedic case evaluation and planning [1]. Utilized within a wide range of specialized visualization and analysis tools, such models provide unprecedented wealth of bone shape information previously unattainable using traditional radiographic imaging [2]. In this work, a novel bone reconstruction method from two or more x‐ray images is described. This method is superior to previous attempts in terms of accuracy and repeatability. The new technique accurately models the radiological scene in a way that eliminates the need for expensive multi‐planar radiographic imaging systems. It is also …