Engineering Commons^™

Optical Dosimetry Tools And Monte Carlo Based Methods For Applications In Image Guided Optical Therapy In The Brain, Akshay N Prabhu Verleker

Open Access Dissertations

Purpose: The long-term goal of this research is to determine the feasibility of using near infra-red light to stimulate drug release in metastatic lesions within the brain. In this work, we focused on developing the tools needed to quantify and verify photon fluence distribution in biological tissue. To accomplish this task, an optical dosimetry probe and Monte Carlo based simulation code were fabricated, calibrated and developed to predict light transport in heterogeneous tissue phantoms of the skull and brain. Empirical model (EM) of photon transport using CT images as input were devised to provide real-time calculations capable of being translated …

Tissue Engineering, Alonzo Cook

BYU Research Development Office Research Networking Conference

This research will drive significant advancements in biomedical engineering, addressing critical health issues across cardiovascular repair, neuroscience, vision, renal function, and orthopedics. By developing innovative technologies and therapies, the study aims to improve patient outcomes and quality of life

The Role Of Mechanical Loading In Chondrocyte Signaling Pathways, Qiaoqiao Wan

Open Access Dissertations

Chondrocytes are a predominant cell type present in articular cartilage, whose integrity is jeopardized in joint degenerative diseases such as osteoarthritis (OA). In the chondrocytes of patients with OA, the elevated levels of inflammatory cytokines such as interleukin 1β (IL1β) and tumor necrosis factor α (TNFα) have been reported. These cytokines contribute to degradation of cartilage matrix by increasing activities of proteolytic enzymes. In addition to their contribution to proteolytic enzymes, these cytokines adversely affect anabolic activity of chondrocytes by inhibiting the production of proteoglycans and type II collagen. Therefore, blocking the action of these cytokines is a potential strategy …

Diagnostic Quality Assessment Of Compressed Sensing Accelerated Magnetic Resonance Neuroimaging., Mohammad Kayvanrad, Amy Lin, Rohit Joshi, Jack Chiu, Terry Peters

Robarts Imaging Publications

PURPOSE: To determine the efficacy of compressed sensing (CS) reconstructions for specific clinical magnetic resonance neuroimaging applications beyond more conventional acceleration techniques such as parallel imaging (PI) and low-resolution acquisitions.

MATERIALS AND METHODS: Raw k-space data were acquired from five healthy volunteers on a 3T scanner using a 32-channel head coil using T2 -FLAIR, FIESTA-C, time of flight (TOF), and spoiled gradient echo (SPGR) sequences. In a series of blinded studies, three radiologists independently evaluated CS, PI (GRAPPA), and low-resolution images at up to 5× accelerations. Synthetic T2 -FLAIR images with artificial lesions were used to assess diagnostic accuracy for …

Development Of A Fluidic Mixing Nozzle For 3d Bioprinting, Will Hoggatt

Open Access Theses

3D bioprinting is a relatively new and very promising field that uses conventional 3D printing techniques and adapts them to print biological materials that are suited for use with cells. These bioprinters can be used to print cells encapsulated within biological "ink" (bio-ink) to create and customize complex three-dimensional tissues and organs. Our work has focused on developing a new bioprinter nozzle that addresses critical gaps with present-day bioprinters, namely, the lack of standardized, physiologically-relevant biomaterials, and their one nozzle per composition printing capacity. These shortcomings preclude printing a range of cellular and biomaterial compositions (including gradients of cells and …

Functional Studies Of The Human Telomerase Holoenzyme, Mohammed E. Sayed

Bioengineering Dissertations - Archive

Telomeres are the DNA structures that cap the ends of linear chromosomes. In humans, telomeres are composed of the hexameric repeats TTAGGG. The reverse transcriptase, telomerase maintains the telomeres by adding the TTAGGG repeats to the chromosomes during cell division. In the absence of telomerase, telomere length limits the self-renewal capabilities of cells. Telomerase is expressed in approximately 90% of all human cancers, making it an almost universal therapeutic target as well as an important player in the progression from healthy to cancerous cell. The biophysical studies discussed in this thesis focus on expanding the understanding of the function and …

Intuitive Human Robot Interfaces For Upper Limb Prosthetics, Oguz Yetkin

Bioengineering Dissertations - Archive

Modern robotic prosthetic devices for upper limb amputees promise to alleviate an important disability, but are underutilized due to the inability to properly control them. Specifically, the devices afford more degrees of freedom (DOFs) than are con- trollable by easily decoded biological signals. These devices, such as the DEKA arm, can have as many as 18 DOFs, although six is a more typical number (control of each finger plus thumb rotation). Unfortunately, the use of these devices remains limited by the ability of users to simultaneously control more than one degree of freedom at a time with commercially deployed technology. …

Centimeter-Deep Tissue Fluorescence Microscopic Imaging, Bingbing Cheng

Bioengineering Dissertations - Archive

Fluorescence microscopic imaging in centimeter-deep tissue has been highly sought-after for many years because much interesting in vivo micro-information—such as microcirculation, tumor angiogenesis, and cancer metastasis—may deeply locate in tissue. However, it is very challenging because of strong tissue light scattering. This includes: how to confine the fluorescence emission into a small volume to achieve high spatial resolution; how to increase fluorescence emission efficiency to compensate the signal attenuation caused by small emission volume and tissue scattering/absorption; and how to reduce background fluorescence noise and exclusively differentiate signal photons from background photons to increase signal-to-noise ratio (SNR) and sensitivity. Ultrasonic …

Nanosturctured Biomaterials For Tissue Regeneration And Repair, Primana Punnakitikashem

Bioengineering Dissertations - Archive

Nanostructured materials have been explored in biomedical field especially in tissue engineering over a past decade. This type of material can be processed into biomaterial scaffolds; revealed many advantages to be used in human living system such as restoring, healing, replacing and improving the function of interested tissues or organs. In this work, nanostructured materials were synthesized as a nanofibrous scaffold or nanoparticles, which were characterized and tested for their biofunctions in the regeneration of blood vessels, lung and skin tissues. Firstly, biodegradable polyurethane nanofibrous scaffolds with dipyramole were electrospun to create a vascular graft, and results demonstrated that this …

Mapping Of Prefrontal Hemodynamic Responses To Noxious Stimulation And Chronic Pain Related Resting-State Functional Networks Assessed By Fnirs, Amarnath Yennu

Bioengineering Dissertations - Archive

Neural representations of chronic pain are complex and are least understood. Numerous magnetic resonance imaging (MRI) studies have revealed structural and functional abnormalities in several cortical and sub-cortical regions in subjects with chronic low-back pain (CLBP). A more recent MRI study has reported that structural and functional brain abnormalities in pain-treated patients with CLBP are reversible, demonstrating that an appropriate treatment of chronic pain can restore normal brain functions for the patients. Due to high cost, non-portability, and other restrictions of MRI, the development of a complementary brain imaging tool is therefore crucial in order to improve the understanding of …

Cellno Trap: Novel Device For Quantitative, Real-Time, Direct Measurement Of Nitric Oxide From Cultured Raw 267.4 Macrophages, Weilue He, Megan C. Frost

Michigan Tech Publications, Part 1

Nitric oxide (NO), is arguably one of the most important small signaling molecules in biological systems. It regulates various biological responses in both physiological and pathological conditions, often time producing seemingly contradictory results. The details of the effects of NO are highly dependent on the level of NO that cells experience and the temporal aspect of when and how long cells are exposed to NO. Herein, we present a novel measurement system (CellNO trap) that allows real-time NO measurement via chemiluminescence detection from general adhesive cultured cells using standard cell culture media and reagents that does not perturb the cells …

Development Of Orthogonally Crosslinked Thiol-Ene Hydrogels For Encapsulation Of Pancreatic Beta-Cells, Han Shih

Open Access Dissertations

Type I diabetes mellitus (T1DM) is an autoimmune disease caused by auto-reactive T-cell-mediated destruction of insulin-producing β-cells. Effective encapsulation strategies can protect the transplanted islets from direct attack by host immune cells while maintaining insulin secretion. To achieve this goal, I have developed a hydrogel conformal coating using a visible light-mediated interfacial thiol-ene photopolymerization. Unlike conventional chain-growth visible light polymerizations, no additional cytotoxic co-initiator or co-monomer was required in thiol-ene gelation scheme for rapid gelation. More importantly, islets coated with thiol-ene gel maintained their viability and function in vitro. In addition to microencapsulate β-cells, the second objective of my …

Development And Initial Validation Of A Surgical Instrument For In Situ Mechanical Characterization Of Surgical Mesh-Tissue Composites, Jorge Ivan Hernandez Sanchez

All Theses

Approximately 5 million Americans have an abdominal wall hernia, and over 700,000 undergo surgical procedures every year to treat them. Surgical procedures have evolved with the goal of preventing recurrences, leading to the current gold standard of treatment: hernia repair with mesh. Hernia repair with mesh consists on augmenting the weakened abdominal wall by implanting a synthetic or biological mesh. Although the adoption of hernia repair with mesh has improved outcomes, recurrence from primary repair procedures with large incisions (>10 cm) remains an alarming 32%.

The wide variety of implanted surgical mesh (materials, structure) and surgical variability (attachment method, …

A Transcutaneous Data And Power Transfer System For Osteogenesis Monitoring Sensors, Deepak Dileepkumar

Masters Theses

Implant devices are widely used in health care applications such as life support systems, patient rehabilitation devices and patient monitoring devices. Medical implants have enabled physicians to obtain relevant real time information regarding an organ, or a site of interest with in the body and suggest treatment accordingly. In some cases, the position of the implant within the body or threats of infections prevents wired communication techniques to extract information from the implant. Wireless communication is the alternative in such cases. Distraction osteogenesis is one such application where wireless communication can be established with callus growth monitoring sensors to obtain …

Investigation Of Copling Strength And Directionality Between Eeg And Fnirs At Resting State Using Permutation Conditional Mutual Information, Gowtham Krishnan Murugesan

Bioengineering Theses - Archive

The motivation of study is to combine multimodality approach EEG-fNIRS to study relationship between neural activity and hemodynamic response applying information theory concepts. Investigating human brain function can be improved by employing a multimodal neuroimaging approach. Since each neuroimaging modality has its own characteristic features especially in terms of spatial and temporal resolution integrating fNIRS responses with EEG could accurately characterize the neurovascular coupling in cortical regions selected as part of the brain network involved in motor and cognitive behavior. Simultaneous recording of fNIRS-EEG is therefore an important resource for studying aspects of neurovascular coupling and its relationship with pathological …

Investigating Causal Interactions In The Human Brain Using Eeg And Fnirs, Borzou Alipourfard

Bioengineering Theses - Archive

It is necessary for distributed neural assemblies to work in collaboration to achieve the most elementary brain functions. Activities within segregated neural assemblies are integrated to process an incredibly diverse collection of cognitive tasks. Measures such as correlation, cross-correlation, coherence and phase delay make limited use of the information that is available with the advanced multichannel and multimodal recordings of the brain’s activity. They can also give spurious and false results. Most importantly, these bivariate measures are not capable of describing the interaction among multiple neural assemblies and the effective connectivity among them. Through causality analysis, we can identify these …

Three-Dimensional Adult Cardiac Extracellular Matrix Promotes Maturation Of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes, Ahsley H. Fong, Mónica Romero-López, Christopher M. Heylman, Mark Keating, David Tran, Agua Sobrino, Anh Q. Tran, Hiep H. Pham, Cristhian Fimbres, Paul D. Gershon, Elliot L. Botvinick, Steven C. George, Christopher C.W. Hughes

Biomedical Engineering

Pluripotent stem cell-derived cardiomyocytes (CMs) have great potential in the development of new therapies for cardiovascular disease. In particular, human induced pluripotent stem cells (iPSCs) may prove especially advantageous due to their pluripotency, their self-renewal potential, and their ability to create patient-specific cell lines. Unfortunately, pluripotent stem cell-derived CMs are immature, with characteristics more closely resembling fetal CMs than adult CMs, and this immaturity has limited their use in drug screening and cell-based therapies. Extracellular matrix (ECM) influences cellular behavior and maturation, as does the geometry of the environment—twodimensional (2D) versus three-dimensional (3D). We therefore tested the hypothesis that native …

Gamma-Radiation Exposure Alters The Cardiovascular Extracellular Matrix., Nicholas Allen

Electronic Theses and Dissertations

Ionizing radiation has been associated with various cardiovascular complications; however, the associated molecular changes from radiation exposure still remain largely uncharacterized. Alterations to the cardiovascular tissue microenvironment, i.e. the extracellular matrix (ECM), directly affect the function of integrated vascular cells, including cell adhesion, potential to form vessels, and endothelial permeability, which can promote cardiovascular pathologies. The ECM is constantly remodeled in response to stimuli, such as TGF-β1, which leads to excessive ECM accumulation. We hypothesize that radiation exposure will alter the cardiovascular ECM. Human Cardiac Fibroblasts (HCFs) were utilized to produce ECM as an in vitro model to study changes …

Autologous Protein Solution Exhibits Potential To Mitigate Osteoarthritis (Oa) Progression In A Human Explant Co-Culture Model, Kathleen Emily Steckbeck

All Theses

Osteoarthritis (OA) is a debilitating and painful disease that affects upwards of one in every eight adults1,2. OA influences the entire joint, but is traditionally characterized by cartilage degradation3. OA is a multifactorial disease with genetic, biological, and biochemical consideration, but there has been a recent shift in scientific opinion that the pathological progression of OA stems from an inflammatory milieu produced by the feed-forward progressive pathway as evidenced by simultaneous cartilage and synovium co-culture4–7. Autologous protein solution (APS) poses as an intriguing potential OA therapy by possessing a high anti-inflammatory and anabolic mediator concentration profile that could potentially mitigate …

Fluid Flow Characterization And In Silico Validation In A Rapid Prototyped Aortic Arch Model, Alexandra Mariel Knauer

Master's Theses

Transcatheter aortic heart valve replacement (TAVR) is a procedure to replace a failing aortic valve and is becoming the new standard of care for patients that are not candidates for open-heart surgery [2]. However, this minimally invasive technique has shown to cause ischemic brain lesions, or “silent infarcts”, in 90% of TAVR patients, which can increase the patient’s risk for stroke by two to four times in future years [3]. Claret Medical Inc., a medical device company, has developed a cerebral protection system that filters and captures embolic debris released during endovascular procedures, such as TAVR. This thesis utilized CT …

Augmenting Sensorimotor Control Using “Goal-Aware” Vibrotactile Stimulation During Reaching And Manipulation Behaviors, Emmanouil Tzorakoleftherakis, Todd D. Murphey, Robert A. Scheidt

Biomedical Engineering Faculty Research and Publications

We describe two sets of experiments that examine the ability of vibrotactile encoding of simple position error and combined object states (calculated from an optimal controller) to enhance performance of reaching and manipulation tasks in healthy human adults. The goal of the first experiment (tracking) was to follow a moving target with a cursor on a computer screen. Visual and/or vibrotactile cues were provided in this experiment, and vibrotactile feedback was redundant with visual feedback in that it did not encode any information above and beyond what was already available via vision. After only 10 minutes of practice using vibrotactile …

Functional Vasodilation And Vascular Reactivity In Arteriolar Collaterals In The Spinotrapezius Of Males And Females, Britta C. Nelson

Biomedical Engineering

Peripheral arterial occlusive disease (PAOD) occurs when there is narrowing or blockage of the peripheral arteries that carry blood to the extremities, most commonly the legs. The most common symptom of PAOD is intermittent claudication, or ischemic pain during exercise. Women with PAOD experience a greater extremity functional impairment than men. Since impaired vasodilation might cause the ischemic pain from PAOD, we should evaluate vasodilation post ligation in males and females in collateral vessels, which connect two arterial segments to maintain blood flow to an otherwise hypoxic area. First, we need to examine collateral vasodilation in unoperated male and female …

Chlorine Demand Shows Thresholds And Hierarchy With Source Water Quality At Beaver Lake, Arkansas, Jaime M. Gile

Graduate Theses and Dissertations

This study investigated the effects of source water quality in Beaver Lake on the amount of chlorine (Cl) needed to develop decision support system to help guide chlorination practices in pre-treatment of source water. Chlorine demand assays were performed on water samples from Beaver Lake collected from the intake structure at Beaver Water District from March 2014 through August 2015, and using data from these assays, the two points of interest in this study were the Cl dose at which Cl residuals began to accumulate and the mean Cl demand occurring after that dose. Three methods of analysis were used …

Numerical Modeling Of Virus Transport Through Unsaturated Porous Media, Kandala Rajsekhar, Pramod Kumar Sharma, Sanjay K. Shukla

Research outputs 2014 to 2021

This paper describes the movement of virus in one-dimensional unsaturated porous media. The governing virus transport equations consider the inactivation in liquid phase, liquid–solid interface, air–liquid interface, and sorption in both liquid–solid and air–liquid interfaces. Finite-volume method has been used for solving the advection and dispersion processes of the virus transport equation. The effects of transport parameters on virus concentration profiles have been investigated for virus present in liquid phase, adsorbed liquid–solid and liquid–air phases. The results show that the movement of viruses in three phases is affected by soil moisture, inactivation rate, pore velocity, and mass transfer coefficients. It …

Alginate Hydrogels As Three-Dimensional Scaffolds For In Vitro Culture Models Of Growth Plate Cartilage Development And Porcine Embryo Elongation, Taylor D. Laughlin

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

The establishment of in vitro culture models utilizes tissue engineering principles to design functional mimics of in vivo environments in vitro. Advantages for the use of in vitro culture models include ethical alleviation of animal models for therapeutic testing, cost efficiency, and a greater ability to study specific mechanisms via a systematic, ground-up approach to development. In this thesis, alginate hydrogels are utilized in the development of in vitro culture models of porcine embryo elongation and growth plate cartilage development. First, the effect of scaffold and modifications to the scaffold were explored in both projects. In order to modulate …

Prefrontal Responses To Stroop Tasks In Subjects With Post-Traumatic Stress Disorder Assessed By Functional Near Infrared Spectroscopy, Amarnath Yennu, Fenghua Tian, Alexa Smith-Osborne, Robert J. Gatchel, Fu Lye Woon, Hanli Liu

Bioengineering Faculty Publications - Archive

No abstract provided.

Blinking Phase-Change Nanocapsules Enable Background-Free Ultrasound Imaging, Alexander S. Hannah, Geoffrey P. Luke, Stanislav Y. Emelianov

Dartmouth Scholarship

Microbubbles are widely used as contrast agents to improve the diagnostic capability of conventional, highly speckled, low-contrast ultrasound imaging. However, while microbubbles can be used for molecular imaging, these agents are limited to the vascular space due to their large size (> 1 μm). Smaller microbubbles are desired but their ultrasound visualization is limited due to lower echogenicity or higher resonant frequencies. Here we present nanometer scale, phase changing, blinking nanocapsules (BLInCs), which can be repeatedly optically triggered to provide transient contrast and enable background-free ultrasound imaging. In response to irradiation by near-infrared laser pulses, the BLInCs undergo cycles of …

Student Spotlight | Biological Engineering, Usu College Of Engineering

College of Engineering News

July 2016 - Q&A with Biological Engineering student Harsh Singh

Methods For Culturing Retinal Pigment Epithelial Cells: A Review Of Current Protocols And Future Recommendations, Aaron H. Fronk, Elizabeth Vargis

Biological Engineering Faculty Publications

The retinal pigment epithelium is an important part of the vertebrate eye, particularly in studying the causes and possible treatment of age-related macular degeneration. The retinal pigment epithelium is difficult to access in vivo due to its location at the back of the eye, making experimentation with age-related macular degeneration treatments problematic. An alternative to in vivo experimentation is cultivating the retinal pigment epithelium in vitro, a practice that has been going on since the 1970s, providing a wide range of retinal pigment epithelial culture protocols, each producing cells and tissue of varying degrees of similarity to natural retinal pigment …

Cuny Summer Stem Institute: Experimental Research In Engineering For High School Students, Maribel Vazquez

Open Educational Resources

Summer HS students were engaged in hands-on experimental research in engineering laboratories in mentorship with CCNY Engineering Undergraduate Researchers. This course was part of the Summer STEM Institute directed by Dr. Joe Barba and Mr. Otto Marte.