Biomedical Engineering and Bioengineering Commons^™

Direct Numerical Simulation Of Turbulent Katabatic Slope Flows With An Immersed-Boundary Method, Clancy Umphrey, Ray Deleon, Inanc Senocak

Mechanical and Biomedical Engineering Faculty Publications and Presentations

We investigate a Cartesian-mesh immersed-boundary formulation within an incompressible flow solver to simulate laminar and turbulent katabatic slope flows. As a proof-of-concept study, we consider four different immersed-boundary reconstruction schemes for imposing a Neumann-type boundary condition on the buoyancy field. Prandtl’s laminar solution is used to demonstrate the second-order accuracy of the numerical solutions globally. Direct numerical simulation of a turbulent katabatic flow is then performed to investigate the applicability of the proposed schemes in the turbulent regime by analyzing both first- and second-order statistics of turbulence. First-order statistics show that turbulent katabatic flow simulations are noticeably sensitive to the …

Sex Differences And The Effects Of Exercise Training On Functional Vasodilation Following Arterial Occlusion In The Balb/C Mouse Spinotrapezius, Britta Nelson

Master's Theses

Peripheral arterial occlusive disease (PAOD) often presents as intermittent claudication, which may be caused by impaired vasodilation. Impairment of resistance vessels may contribute to the pathogenesis of PAOD, and explain the poor correlation between resting blood flow and limb function. Collateral function following arterial occlusion is not well defined, however collaterals and arterialized collateral capillaries (ACCs) in male and female animal models exhibit impaired vasodilation following arterial occlusion, which can potentially be improved with exercise training. Furthermore, resistance vessels in the ischemic tree and stem are likely involved in the pathogenesis of PAOD, however the relative importance of each is …

Damage-Free Peripheral Nerve Stimulation By 12-Ns Pulsed Electric Field, Maura Casciola, Shu Xiao, Andrei G. Pakhomov

Bioelectrics Publications

Modern technologies enable deep tissue focusing of nanosecond pulsed electric field (nsPEF) for non-invasive nerve and muscle stimulation. However, it is not known if PEF orders of magnitude shorter than the activation time of voltage-gated sodium channels (VGSC) would evoke action potentials (APs). One plausible scenario requires the loss of membrane integrity (electroporation) and resulting depolarization as an intermediate step. We report, for the first time, that the excitation of a peripheral nerve can be accomplished by 12-ns PEF without electroporation. 12-ns stimuli at 4.1-11 kV (3.3-8.8 kV/cm) evoked APs similarly to conventional stimuli (100-250 mus, 1-5 V, 103-515 V/m), …

Influence Of Fibroblasts On Functional Arteriogenesis In A Murine Chronic Hindlimb Ischemia Model, Ashli A. Santos

Biomedical Engineering

Peripheral arterial occlusive disease (PAOD) occurs when there is a narrowing or blockage – usually a buildup of plaque - within the arteries that reduces blood flow to tissues which can chronic ischemia. As with most diseases, early detection and proactive treatment are important to maximize prognosis. Exercise effectively treats PAOD, but due to ischemic pain in the limbs, or intermittent claudication (IC), exercise can become painful and difficult. Due to the buildup of plaque, occlusions create an ischemic environment that changes the pressure distribution in collateral networks and increases the shear stress in transverse collaterals. Those two responses signal …

Controllable Moderate Heating Enhances The Therapeutic Efficacy Of Irreversible Electroporation For Pancreatic Cancer, Chelsea M. Edelblute, James Hornef, Niculina I. Burcus, Thomas Norman, Stephen J. Beebe, Karl Schoenbach, Richard Heller, Chunqi Jiang, Sigi Guo

Bioelectrics Publications

Irreversible electroporation (IRE) as a non-thermal tumor ablation technology has been studied for the treatment of pancreatic carcinoma and has shown a significant survival benefit. We discovered that moderate heating (MH) at 43°C for 1-2 minutes significantly enhanced ex vivo IRE tumor ablation of Pan02 cells by 5.67-fold at 750 V/cm and by 1.67-fold at 1500 V/cm. This amount of heating alone did not cause cell death. An integrated IRE system with controllable laser heating and tumor impedance monitoring was developed to treat mouse ectopic pancreatic cancer. With this novel IRE system, we were able to heat and maintain the …

An Automated Workflow For Quantifying Rna Transcripts In Individual Cells In Large Data-Sets, Matthew C. Pharris, Tzu-Ching Wu, Xinping Chen, Xu Wang, David M. Umulis, Vikki M. Weake, Tamara L. Kinzer-Ursem

Weldon School of Biomedical Engineering Faculty Publications

Advanced molecular probing techniques such as single molecule fluorescence in situ hybridization (smFISH) or RNAscope can be used to assess the quantity and spatial location of mRNA transcripts within cells. Quantifying mRNA expression in large image sets usually involves automated counting of fluorescent spots. Though conventional spot counting algorithms may suffice, they often lack high-throughput capacity and accuracy in cases of crowded signal or excessive noise. Automatic identification of cells and processing of many images is still a challenge. We have developed a method to perform automatic cell boundary identification while providing quantitative data about mRNA transcript levels across many …

Identifying And Reducing Variability, Improving Scaffold Morphology, And Investigating Alternative Materials For The Blood Vessel Mimic Lab Electrospinning Process, Evan M. Dowey

Master's Theses

The work of the Cal Poly Tissue Engineering Lab is primarily focused on the fabrication, characterization, and improvement of “Blood Vessel Mimics” (BVMs), tissue engineered constructs used to evaluate cellular response to vascular medical devices. Currently, cells are grown onto fibrous, porous tubes made using an in-house electrospinning process from PLGA, a biocompatible co-polymer. The adhesion and proliferation of cells in a BVM is reliant on the micro-scale structure of the PLGA scaffold, and as such it is of great importance for the electrospinning process to consistently produce scaffolds of similar morphologies. Additionally, it has been shown that cell proliferation …

Delayed Hypersensitivity To Nanosecond Pulsed Electric Field In Electroporated Cells, Sarah D. Jensen, Vera A. Khorokhorina, Claudia Muratori, Andrei G. Pakhomov, Olga N. Pakhomova

Bioelectrics Publications

We demonstrate that conditioning of mammalian cells by electroporation with nanosecond pulsed electric field (nsPEF) facilitates their response to the next nsPEF treatment. The experiments were designed to unambiguously separate the electroporation-induced sensitization and desensitization effects. Electroporation was achieved by bursts of 300-ns, 9 kV/cm pulses (50 Hz, n = 3–100) and quantified by propidium dye uptake within 11 min after the nsPEF exposure. We observed either sensitization to nsPEF or no change (when the conditioning was either too weak or too intense, or when the wait time after conditioning was too short). Within studied limits, conditioning never caused desensitization. …

A Spectral Ct Method To Directly Estimate Basis Material Maps From Experimental Photon-Counting Data, Tal Gilat Schmidt, Rina Foygel Barber, Emil Y. Sidky

Biomedical Engineering Faculty Research and Publications

The proposed spectral CT method solves the constrained one-step spectral CT reconstruction (cOSSCIR) optimization problem to estimate basis material maps while modeling the nonlinear X-ray detection process and enforcing convex constraints on the basis map images. In order to apply the optimization-based reconstruction approach to experimental data, the presented method empirically estimates the effective energy-window spectra using a calibration procedure. The amplitudes of the estimated spectra were further optimized as part of the reconstruction process to reduce ring artifacts. A validation approach was developed to select constraint parameters. The proposed spectral CT method was evaluated through simulations and experiments with …

Mutagenesis Of Human Alpha-Galactosidase A For The Treatment Of Fabry Disease, Erin Stokes

Dissertations, Theses, and Capstone Projects

Fabry disease is an X-linked lysosomal storage disorder caused by the deficiency of the enzyme, α-galactosidase A, which results in the accumulation of the lipid substrate. This accumulation results in obstruction of blood flow in patients and early demise at approximately 40-60 years of age. There is currently only one FDA approved treatment (Fabrazyme) classified as an enzyme replacement therapy. However, approximately 88% of patients experience a severe immune response that, rarely, can be fatal and is a huge cost burden at average $250,000 a year per patient. The structure of α-galactosidase A has been previously determined to be a …

Spatial And Temporal Deformation Pattern Of The Brain From Blunt Trauma, Abdus Ali

Theses

It is widely accepted that under extreme loadings the soft tissue of the brain will deform inside the skull, creating large amounts of both stress and strain on the tissue. This can result in a focal injury, or in the case of acceleration and deceleration, diffuse injuries. Any attempt at understanding the underlying mechanisms and effects of TBI, have to start by focusing on what is actually occurring within the brain. The objective of this experiment is to record differences in the spatial and temporal patterns of deformation within the brain during blunt trauma when changing impact parameters. A linear …

Subject And Group Level Changes And Comparison In Functional Connectivity Under Low Vs. High Cognitively Demanding Naturalistic Viewing Conditions Using Fmri, Rakibul Hafiz

Theses

Resting State fMRI is used extensively for analysing brain regions. fMRI is also used to determine task induced activations from cerebral networks. This study involves both rest and task activation data and implements statistical methods applied on Blood Oxygenation Level Dependent (BOLD) signals. The conventional task based designs are very specific and may not reflect day to day activities. The two task conditions in this study are watching a movie called INSCAPE with low cognitive load and segments of contextual Hollywood movies under continuous and natural conditions.

The aim is to investigate individual and group level Functional Connectivity changes between …

Interaction Of Voluntary Activity And Functional Electrical Stimulation In The Upper Extremity As A Method For Short-Term Alteration Of Corticospinal Excitability And Force Control, Katherine Maia Gerton

Theses

Repetitive movement training (RMT) is a well-established method for rehabilitating functional movement. However, many stroke survivors are not able to participate in RMT for the necessary duration to produce results due to rapid muscle fatigue or inability to perform the desired movement at all. Often, functional electrical stimulation (FES) is applied passively, as a rehabilitative therapy, to stroke subjects who are unable to participate in RMT. The effects of voluntary contraction and FES are not well understood for the upper extremity following a stroke. This experiment was designed to elucidate the mechanisms of functional and neurophysiological changes associated with combining …

High Resolution Imaging Of The Mitral Valve In The Natural State With 7 Tesla Mri, Sam E. Stephens, Serguei Liachenko, Neil B. Ingels, Jonathan F. Wenk, Morten O. Jensen

Mechanical Engineering Faculty Publications

Imaging techniques of the mitral valve have improved tremendously during the last decade, but challenges persist. The delicate changes in annulus shape and papillary muscle position throughout the cardiac cycle have significant impact on the stress distribution in the leaflets and chords, thus preservation of anatomically accurate positioning is critical. The aim of this study was to develop an in vitro method and apparatus for obtaining high-resolution 3D MRI images of porcine mitral valves in both the diastolic and systolic configurations with physiologically appropriate annular shape, papillary muscle positions and orientations, specific to the heart from which the valve was …

The Subject Librarian Newsletter, Engineering And Computer Science, Fall 2017, Buenaventura "Ven" Basco

Libraries' Newsletters

No abstract provided.

Macrodamage Accumulation Model For A Human Femur, Farah Hamandi, Tarun Goswami

Biomedical, Industrial & Human Factors Engineering Faculty Publications

The objective of this study was to more fully understand the mechanical behavior of bone tissue that is important to find an alternative material to be used as an implant and to develop an accurate model to predict the fracture of the bone. Predicting and preventing bone failure is an important area in orthopaedics. In this paper, the macrodamage accumulation models in the bone tissue have been investigated. Phenomenological models for bone damage have been discussed in detail. In addition, 3D finite element model of the femur prepared from imaging data with both cortical and trabecular structures is delineated using …

Rice Hull Bioreactor For Recirculating Aquaculture, Marlon A. Greensword

LSU Doctoral Dissertations

The engineering of floating media biofilters has been optimized over the years. The backwashing process has made them more energy and water efficient. Likewise, moving bed bioreactors (MBBR) are gaining interest and popularity because they are relatively affordable to build. Yet, developing countries’ aquaculture production remains largely excluded from the advances made in recirculating aquaculture systems (RAS). This discrepancy is partially driven by the high costs of media such plastic beads and Kaldnes (KMT) media, commonly used in MBBR.

This dissertation evaluates the usability and profitability of rice hulls (RH), an abundant by-product in many developing nations, as a sinking …

Rapid Thermocycler System For Rapid Amplification Of Nucleic Acids And Related Methods, Joel R. Termaat, Scott E. Whitney, Hendrik J. Viljoen, Matthew R. Kreifels

Department of Chemical and Biomolecular Engineering: Patents

A thermocycling device and method of operating a thermocycler instrument, the instrument including a sample holder, at least one thermal cycling element, and at least one first and second temperature sensors, for causing the sample holder containing the at least one sample to undergo polymerase chain reaction amplification by repeated cycling between at least a denaturation heating stage and an aunealing cooling stage. The first temperature corresponding with the temperature of the sample holder is monitored using the at least one first temperature sensor, and a second temperature corresponding with the temperature external of the sample holder is monitored using …

Performance Assessment Of Diffuse Optical Spectroscopic Imaging Instruments In A 2-Year Multicenter Breast Cancer Trial, Anais Leproux, Thomas D.O. Sullivan, Albert E. Cerussi, Amanda Durkin, Brian Hill, Nola M. Hylton, Arjun G. Yodh, Stefan A. Carp, David A. Boas, Shudong Jiang, Keith D. Paulsen, Brian W. Pogue, Darren M. Roblyr, Wei T. Yang, Bruce J. Tromberg

Dartmouth Scholarship

We present a framework for characterizing the performance of an experimental imaging technology, diffuse optical spectroscopic imaging (DOSI), in a 2-year multicenter American College of Radiology Imaging Network (ACRIN) breast cancer study (ACRIN-6691). DOSI instruments combine broadband frequency-domain photon migration with time-independent near-infrared (650 to 1000 nm) spectroscopy to measure tissue absorption and reduced scattering spectra and tissue hemoglobin, water, and lipid composition. The goal of ACRIN-6691 was to test the effectiveness of optically derived imaging endpoints in predicting the final pathologic response of neoadjuvant chemotherapy (NAC). Sixty patients were enrolled over a 2-year period at participating sites and received …

Development And Validation For A Mobile Speech-In-Noise Audiometric Task, Tommy Peng

McKelvey School of Engineering Graduate Student Theses & Dissertations

Traditional speech-in-noise hearing tests are performed by clinicians with specialized equipment. Furthermore, these tasks often present contextually weak sentences in background babble, which are poor representations of real-world situations. This study proposes a mobile audiometric task, Semantic Auditory Search, which uses the Android platform to bypass the need for specialized equipment and presents multiple tasks of two competing real-world conversations to estimate the user’s speech-in-noise hearing ability. Through linear regression models built from data of seventy-nine subjects, three Semantic Auditory Search metrics have been shown to have statistically significant (p < 0.05) with medium effects sizes for predicting QuickSIN SNR50. The internal consistency of the task was also high, with a Cronbach’s alpha of 0.88 or more across multiple metrics. In conclusion, this preliminary study suggests that Semantic Auditory Search can accurately and reliably perform as an automated speech-in-noise hearing test. It also has tremendous potential for extension into automated tests of cognitive function, as well.