A model of an SU-8 neural probe electrode containing both an embedded fluid channel for fluid delivery and nerve stimulation and recording abilities was created using COMSOL software. A mechanical model of the neural probe electrode was simulated using COMSOL while varying several design parameters in order to better optimize the physical design of the electrode. It was found that the thickness of the neural probe should be from 0.35 mm to 0.5 mm, as the effects of increasing thickness beyond 0.5 mm on maximum stress were not very significant. Additionally, the ideal length of the neural probe was found to be between 4.5 and 5.5 mm to minimize stresses in the neural probe. The ability of the neural probe device to record electrical signals was tested in biological tissue, specifically in frog nerves, using LabVIEW software and myDAQ hardware as well as a device designed for electrophysiology experiments called a "SpikerBox." Compound action potential signals from exposed frog nerves were successfully recorded using the neural probes and the SpikerBox device.

Cardiac pacemakers have evolved over the years from the original version with external leads to the miniaturized leadless version that is implanted completely inside the ventricle. The leadless pacemakers offer advantages in simpler surgical procedures, easier device operation, and better patient comfort. However, the reduced size of the pacemaker substantially restricts battery capacity, reducing the battery life from 13-16 years to as few as 5-8 years. The reduced battery longevity often requires the patient to return for a pacemaker replacement surgery. This could result in increased medical cost, inconvenience, and potential risk to the patients. To address this issue, many researchers have examined different methods of harvesting energy for the pacemaker, mainly focusing on piezoelectric energy conversion. The results, however, were not promising due to the low energy conversion efficiency and potential material failure of the brittle piezoelectric materials.This thesis is aimed at exploring an alternative solution based on electromagnetic induction to convert mechanical energy generated at each systolic and diastolic cycle into electricity. The human heart is an inexhaustible mechanical energy source that is constant and consistent in its mechanical motion. Taking this into our advantage, the research aimed at utilizing the heart’s own mechanical motion to generate electrical energy to power the pacemaker. During the course of the research, multiple design iterations, experimenting with solid magnet cores, ferrofluid, and finally, the concentric double ring magnet design were developed. Many proof-of-concept testing and feasibility testing have been conducted to prove the viability of the design and the structural materials. The research will continue with more simulation testing on the materials and electrical circuit design for signal amplification and storage.

ABSTRACT OF THE DISSERTATION In vitro hippocampal network axonal transmission during patterned theta burst stimulation and a platform for recording in 3D

By: Ruiyi Chen Doctor of Philosophy in Chemical and Biochemical Engineering University of California, Irvine, 2022 Professor William Tang, Chair

Neuronal network dynamics by in vitro electrophysiology serves as an objective and convenient method to explore neurophysiological mechanisms and communication. Theta burst stimulation (TBS) recapitulates natural brain rhythms which is efficacious for synaptic potentiation in hippocampal circuits. TBS is typically applied to a bundle of axons to measure the immediate response in a single downstream subregion like the CA1. Yet little is known about axonal transmission between subregions as the response to TBS propagates to other subregions from upstream stimulation in the entorhinal cortex. We reverse engineered the hippocampal network on micro-electrode arrays (MEAs) contained in a four-chambered silicon rubber device with interconnecting microfluidic. Tunnels. The micro tunnels allow monitoring single axon transmission which is hard to realize in vivo or in slices. The patterned TBS was delivered to the entorhinal cortex (EC), the gateway to cortical entry into the hippocampus. Temporal Jaccard distance was used to quantify the spike pattern similarity. We recorded the network responses to stimulation patterns that produced unique response patterns on axons at three timescales. The response to short-term stimulus repeats at 0.2 s has high variability. The 10 s repeats show some retention of similar responses, especially in the axons from CA3 to CA1, suggestive of pattern completion. While in EC to DG, the repeats evoked unique responses with similarity significantly lower than random, implying pattern separation. Between-tunnel similarity in CA3-CA1 was higher for single site stimulation than from multisite stimulation. Using the temporal pattern metric, axons carried similar responses when an incomplete stimulating pattern was presented. Our design and interrogation approach offers understanding of dynamic pattern variations at the subregional level in response to TBS. To extend this 2D network model, a 3D model was designed to bridge the gap between multi-subregion electrophysiology in vitro and in vivo recordings with high complexity from the dense packing of neurons at single regions in vivo. Here, we report fabrication of a transparent 60-electrode array that forms a second layer of recording sites above a commercial MEA. This 3D culture chamber enables recording from a 400 m thick reconstruction of four hippocampal subregions. The electrodes are easily fabricated and assembled. Optical and electrical characterizations of the electrodes have been performed. Good biocompatibility enabled successful electrophysiological recording. Two hydrogel substrates and solid glass beads for the integrated 3D culture scaffold were evaluated. Only the micro glass beads supported the 3D neuronal network formation on the platform over 21 days. Building this 3D signaling system demonstrates feasibility to access the information coded in the 3D hippocampal network in vitro for comparison to the 2D network spike and burst dynamics in response to stimulation.

Context: Globally, more than 15 million preterm infants are born annually. Oral feeding is a major requirement for discharge from the neonatal intensive care unit. 80% of all preterm infants will struggle to achieve safe and efficient oral feeding, consequently delaying discharge or causing readmission. Inappropriate discharge timing increases risk for neonatal morbidity, infections, chronic complications as well as psychological distress on parents and immense financial burden. Current methods of determining oral feeding readiness are subjective, inconsistent, and ultimately lacks an objective assessment.

Method: This dissertation describes the design, fabrication and characterization of the frontend hardware and software of a portable medical device that will measure transthoracic impedance (TI), pre-process data, ascertain the respiratory waveform variation (RWV) by computing the sample entropy (SE), and output the result as the key contributor to the health score correlating oral feeding readiness and eventually to days till discharge. Two generations of the device, Pedi-Sync, was designed with off-the-shelf components and built to be a plug-in module compatible with existing cardiopulmonary monitors and/or to serve as a standalone device. Additionally, it will also measure blood oxygen saturation (SpO2) as a supplemental data to strengthen the health score correlation with oral feeding readiness and days till discharge. Verification and validation testing of the system was conducted in simulated neonatal data, healthy adults, and preterm infants.

Summary: The device demonstrates technical feasibility to collect and analyze preterm infant TI as a robust oral feeding adaptability score. Moreso, preliminary use of the analysis showed that preterm infants will exhibit a decrease in SE (or less variability) during oral feeding compared to baseline. Further, SpO2 histogram recorded throughout total length of stay may be a supplemental contributor to the health score.

In the path to finding a cure for cancer and saving a life it is essential to detect the disease

in its early stages and to be able to eradicate it. In most cases of cancer, the disease is not

detected until it is in later stages and has metastasized to vital organs. However, with current

advances in medicine the doctors are able to extend the life expectancy of the patient through the

use of chemotherapy drugs, radiation therapy and radical surgeries. Currently the focus of the

researchers has been put on developing immunotherapy drugs, which are targeted therapies.

Chemotherapy has been a somewhat effective therapy, but the side effects of chemotherapy are

often too much to bear, loss of hair, loss of appetite, severe nausea, and lack of energy all

contribute to a lower quality of life.

In order for the scientist to be able to design targeted therapies with much less side effect

and higher rate of success in curing or managing the disease they need be able to have access to

the cancer cells in the early stages of the disease. They need to be able to study the cell and its

genomic makeup.

The objective of this research is to find a more effective and accurate way of screening for

cancer cells, isolating and collecting them. Through the design of microfluidic devices, one can

hope to be able to detect the circulating tumor cells in the blood, trap them and separate them

from the other contents of blood for study.

The ultimate objective of this project is to design and fabricate a device capable of using

Dielectophoresis to separate cancer cells from blood cells accurately. The design of the

Microfluidic devices is done using the software SolidWorks, the simulation is ran using the

software COMSOL, and the fabrication is done in the lab using photolithography. However due

to the time constraints and not having the required trainings or certificates for handling live cells

and blood specimens this project was not tested with cancer cells.

Global surveillance by the World Health Organization (WHO) has indicated a large stagnancy over the past few years in global efforts to eliminate malaria. Limited access to health care and proper diagnosis for endemic populations were emphasized as factors that attribute to such high morbidity and mortality rates. Rapid diagnostics tests (RDTs) have been reported to mitigate these factors, as well as other contributors to disease prevalence. The purpose of this thesis is to further demonstrate the feasibility of developing a quantitative, label-free RDT for disease biomarkers. The scope of this study is limited to the detection of plasmodium lactate dehydrogenase (pLDH) by electrochemical impedance spectroscopy (EIS) analysis of aptamer-protein complex formation as self-assembling monolayers (SAMs) on gold interdigitated electrodes (IDE). Notably, a Wheatstone bridge is integrated into the sensor design, improving system stability for accurate detection of pLDH in low concentrations. This demonstrates the feasibility of salivary detection of Plasmodium falciparum as a noninvasive method of malaria detection, which is especially important for addressing the needs of children in developing countries, who encompass a large portion of the global endemic population. To demonstrate [portability and cost-effectiveness, simple hardware was implemented in the design of this device. Together, the biosensor and hardware are designed to innovatively detect the charge transfer resistance (RCT) of an electrified interface as a simple impedance difference without the high costs and complexities of modern EIS instrumentation. The frequency domain of three different sensor designs will be analyzed for sensor optimization.

Rapid Diagnostic tests (RDTs) products for malaria available on market today are all blood-based. Massive research have been done to find a cheap and convenient method to diagnose malaria using saliva samples. In this project, an innovative approach by converting electrochemical impedance change to voltage difference variation was demonstrated. Through the functionalization of Au electrode surface with pLDH aptamers and construction of Wheatstone bridge using interdigitated electrodes, a significant voltage difference was measured which showed potential for not only qualitative but also for quantitative detection of malaria utilizing saliva specimen. An electrical circuit prototype was also assembled demonstrating the feasibility of making a portable device for measurement.

Retinal degeneration (RD) is a leading cause of vision impairment and blindness worldwide and treatment for advanced RD does not exist. Stem cell-derived retinal organoids (RtOgs) became an emerging tool for tissue replacement therapy. However, existing RtOg production methods are highly heterogeneous. Besides, subjective tissue selection reduces the repeatability of organoid-based scientific experiments and clinical studies. Controlled and predictable methodology and tools are needed to standardize RtOg production, characterization and long-term maintenance.To optimize and standardize RtOg long-term maintenance, we designed a shear stress-free micro-millifluidic bioreactor platform for nearly labor-free retinal organoid maintenance. We compared different 3D printers for fabricating the mold from which Polydimethylsiloxane (PDMS) was cast to create the bioreactor. We optimized the bioreactor design using in silico simulations and in vitro evaluation to optimize mass transfer efficiency and concentration uniformity. Once assembled, we successfully cultured RtOgs using different designs of the bioreactors for up to 4 months. We used different quantitative and qualitative techniques to characterize the RtOgs produced with our bioreactors and compared with those produced with conventional culture to demonstrate the superiority of our approach. At the same time, to improve the quality control of organoids, we introduced a live imaging technique based on two-photon microscopy (2PM) to non-invasively monitor RtOgs’ long-term development. Fluorescence Lifetime Imaging Microscopy (FLIM) was used to monitor the metabolic trajectory, and hyperspectral imaging (HSpec) was applied to characterize structural and molecular changes. These live imaging experimental results were confirmed with endpoint biological tests, including quantitative polymerase chain reaction (qPCR), single-cell RNA sequencing, and immunohistochemistry. In addition, we applied an advanced electrophysiology testing system to further verify the functionality of matured RtOgs cultured in the bioreactor platform. Spontaneous and light-stimulated spiking activities were observed. In summary, we designed and optimized a bioreactor for long term RtOg culture in a low shear stress environment that was also compatible with multimodal imaging. We have demonstrated a 2PM-based non-invasive imaging technique to monitor RtOg metabolic and structural changes at the cellular level throughout the entire differentiation and development process. The health of mature RtOgs were further verified with electrophysiological measurements. The methodology and the findings of this study are of great value in live RtOgs long-term maintenance, characterization and monitoring, offering potentially powerful tools in screening and quality control for RtOg production.

According to the World Health Organization (WHO) in year 2015 alone, 18 million people died from cardiovascular-related diseases, which makes for a staggering 31% of all global deaths. Recent studies of human cardiomyocytes in-vitro have been generating scientific insights beyond traditional approaches. However, in general, human cardiomyocytes are difficult to study due to limited sample availability and due to its fragile in-vitro nature. In this work, we studied HL-1 cells, a tumor-cell derived cardiomyocyte, to ultimately quantify the relationship between cell contractility and to investigate the influence of external stimuli. The motivation behind this study was to look into cardiomyocyte contractility as a quantifiable indicator for cardiotoxicity.

We first tried to understand the implications of biomechanical cues on cardiomyocyte orientation. HL-1 cells have the ability to grow in-vitro indefinitely while maintaining the ability to rhythmically contract autonomously upon reaching confluence. We found that HL-1 cells can mimic the characteristics of human cardiomyocyte, making them an excellent candidate for proof-of-concept demonstrations. They differ from human cardiomyocyte in that they lack a natural orientation and striation in-vitro. With the success of integrating substrates to incorporate nanoscale precision surface textures and which allow tissue engineering, the physiological environment of cells and tissues can be re-capitulated in-vitro. The purpose of this research was to align HL-1 cells on a polymer substrate to quantify their uniform contractility. We created an effective platform to observe cardiac contractility where the HL-1 cells are mechanically supported on a polymer substrate micro-machined with patterned grooves and ridges of nanoscale precision. Herein, we report on the quantitative efficiency of HL-1 cardiomyocyte alignment on various micro-patterned surfaces. The experimental results suggest that our micro-platform can promote cardiomyocyte alignment in-vitro, which is a crucial intermediate step towards rapid drug screening for cardiotoxicity.

Two fields of cardiovascular energy harvesting are investigated, (1) stents and (2)

leadless pacemaker. The demand for rechargeable technologies in cardiovascular stents

arose from the unmet clinical need for real-time tracking of re-occlusions in implantable

stents. This thesis entertains the idea of piezoelectric cantilevers positioned at the

inlet/outlets of the stent to harness the pulsatile blood flow within arterial cavities to

power wireless communication circuits to notify physicians of plaque growth. A MATLAB

study utilizing literature-based blood flow velocities in both healthy and diseased patients

yielded 3.5mV energy harvesting potentiality. Then, a large-scale benchtop study

successfully produced a simplistic model to see if the pressure differences expected across

the stent (.4 Pa). Both tests prove the feasibility of such a design. With a 95% reduction in

volume from its predecessors, the leadless pacemaker traded compatibility with battery

longevity going from a 10-year device lifetime to 6 years [3,34]. Enclosed is an energy

harvesting accessory intended to slip around leadless in-ventricular pacemakers such as

the Medtronic Micra. Two designs featured mechanisms to harvest the blood pressure and

the ventricular wall force from within the heart cavity via electromagnetic induction by ferrofluid and solid ring magnets. The team promptly abandoned the ferrofluid mechanism due to its limited induction capabilities after its 20x deficiencies compared to solid core magnets demonstrated by multiple benchtop tests. However, the solid ring magnet design

proved successful after meeting eight out of nine acceptance criteria through simulation

studies [Modal/Fatigue/Induced Voltage/Heat Generation/Mesh compliance] and

benchtop studies [Induced Voltage/Magnet Shielding/Heat Generation].