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In this thesis we construct a new model of the immune response to the growth of breast cancer cells and investigate the impact of certain drug therapies on the cancer. We use delay differential equations to model the interaction of breast cancer cells with the immune system. The new model is constructed by combining two previous models. The first model accounts for different cell cycles and includes terms to evaluate drug treatments, but ignores quiescent tumor cells. The second model includes quiescent cells, but ignores the immune response and drug treatments. The new model is obtained by combining and modifying these two models to account for quiescent cells, immune cells and includes drug intervention terms. This new model is used to evaluate the effects of pulsed applications of the drug Paclitaxel for models with and without quiescent cells. We use sensitivity equation methods to analyze the sensitivity of the model with respect to the initial number of immune cytotoxic T-cells. Numerical experiments are conducted to compare the model predictions to observed behavior. / Master of Science

Adult hippocampal neurogenesis entails a continued recruitment of neural precursor cells (NPCs) into active cell cycle and their progressive transition into post-mitotic granule cells. These adult born neurons integrate into the existing circuitry and confer structural plasticity, which aids in key hippocampal functions. For sustained neurogenesis, the cell cycle entry of the NPCs has to be tightly controlled. Environmental cues strongly, and differentially, regulate this checkpoint. Voluntary physical activity represents such an established strong stimulus that results in enhanced proliferation within the neurogenic niche. However, mechanistic insights into the maintenance and regulation of quiescence and the responsiveness of the NPCs to acute physical activity, as a form of adaptive neurogenesis, are yet to be elucidated. In my doctoral studies, we identified redox regulation as a key pathway regulating the cellular state equilibrium. I further explored the role of cellular oxidative stress in the neurogenic course and in adaptive neurogenic responses. Our results show that non-proliferative precursors within the hippocampal dentate gyrus, unlike in other stem cell systems, are marked by high levels of cellular reactive oxygen species (ROS). Using cytometric methodologies, ex vivo bioassays and transcriptional profiling, we revealed that classifying cells based on intracellular ROS content identified functionally defined sub-populations of adult NPCs. We propose that a drop in intracellular ROS content precedes the transition of cellular states, specifically from quiescence to active proliferation. Acute physical activity involves the activation of non- proliferating cells through a transient Nox2-dependent ROS surge in high-ROS, quiescent NPCs. In the absence of Nox2, baseline neurogenesis was unaffected, but the activity- dependent response was abolished. These findings shed new light on the discrete cellular events, which maintain the homeostasis between distinct cellular states of NPCs within the adult murine hippocampus.:Zusammenfassung 3 Summary 4 Acknowledgements 5 Index 8 List of figures 10 List of tables 11 Abbreviations 12 Publications 14 Introduction 15 Adult hippocampal neurogenesis 16 Adult subventricular neurogenesis 21 Methods to study adult neurogenesis 23 Environmental regulation of neurogenesis 26 Redox regulation in a stem cell 29 Working hypothesis 31 Specific aims 31 Materials and methods 32 Mice 34 Physical activity paradigm 35 Thymidine labelling and tissue preparation 35 Fluorescence immunohistochemistry 35 DG and SVZ dissection and dissociation 36 Flow cytometry 36 Gating for ROS classes 36 Neurosphere culture 37 Generation of monolayer culture 37 Inducing quiescence through BMP4 treatment 38 Next Generation sequencing (NGS) 38 RNA extraction 38 Quality control and differential expression 39 Functional enrichment and expression profiles 41 RNA isolation and quantitative RTPCR (qRT-PCR) 43 Ki67 immunochemistry and quantification of in vivo proliferation 45 Quantification and statistical analysis 46 Data and software availability 48 Results 49 Intracellular ROS content functionally delineates subpopulations of neural precursor cells 49 Resolution of ROS profiles of DG and SVZ and neurosphere bioassay 49 Distribution of Nes-GFP cells into different ROS classes 54 Neural precursors of the different ROS classes have distinct molecular profiles 55 Changes in intracellular ROS content precede cell fate changes 65 ROS profiling of other cell types within the DG 70 ROS profiling of Astrocytes and type-1 cells 70 ROS profiling of Doublecortin (Dcx)positive cells of the neurogenic lineage 74 ROS profiling of microglial cells within the DG 77 Resolving the response of Nes-GFP subpopulations to environmental stimulus 78 Nes-GFP+ cells of the hiROS class specifically respond to physical activity 81 Changes in ROS content are not driven by mitochondrial activity 83 In vitro monolayer culture of NPCs as an independent corroboration 86 Discussion 89 The organization of an active stem cell niche with respect to redox content 89 Cytometric classification of cells within the DG 91 Establishing the cellular states of redox defined subsets of Nes-GFP+ adult precursors within the DG 95 Timeline of baseline proliferation within precursors and identifying the subset of precursors responsive to de novo physical activity 97 Monolayer culture to study cellular states and redox regulation 100 Nox2 dependency as a discriminatory feature of adaptive neurogenesis 101 Conclusion 103 References 104 Declarations 122 Anlage 1 122 Anlage 2 124

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The concept of plasma flow control is a relatively new idea based on using atmospheric plasma placed near the edge of an air foil to reduce boundary layer losses. As with any new concept, it is important to be able to quantify theoretical assumptions with known experimental results for validation. Currently there are a variety of experiments being done to better understand plasma flow control, but one particular experiment is through the use of multi-physics modeling of dielectric barrier discharge actuators. The research in this thesis uses optical measurement techniques to validate computational models of flow control actuators being done concurrently at Virginia Tech. The primary focus of this work is to design, build and test plasma actuators in order to determine the plasma characteristics relating to electron temperatures and densities. Using optical measurement techniques such as plasma spectroscopy, measured electron temperatures and densities to compare with theoretical calculations of plasma flow control under a variety of flow conditions. This thesis covers a background of plasma physics, optical measurement techniques, and the designing of the plasma actuator setups used in measuring atmospheric plasmas. / Master of Science

Cultured meat offers a sustainable alternative to traditional meat production, addressing critical environmental and ethical issues. A key aspect of this process is the large-scale proliferation of muscle satellite cells, which can further proliferate and form the primary component of cultured meat. However, ensuring efficient cell proliferation within bioreactors is a significant challenge. Without effective and robust cell proliferation, it would be impossible to meet the production demands of cultured meat. Moreover, 3D cell spheroids tend to form tightly packed structures. As these spheroids grow larger, the limited penetration of oxygen and nutrients can lead to the formation of necrotic cores or cause cells in the central layers to experience cell cycle arrest, resulting in either irreversible senescence or reversible quiescence. This adds complexity to maintaining stable cell growth. To address these challenges, different ECM components, specifically Matrigel and Collagen I, were introduced to alter matrix stiffness and growth factor concentrations. The goal was to address issues of reduced cell proliferation and cell cycle arrest. Results demonstrated that in the absence of ECM, 3D-cultured bovine muscle satellite cells spontaneously formed myospheres but exhibited cell cycle arrest and inhibited proliferation. These issues were reversed with the addition of ECM. Increasing ECM stiffness, particularly through higher concentrations of Matrigel and Collagen I, significantly enhanced cell spreading but had a complex effect on cell proliferation. While Matrigel promoted both cell spreading and proliferation, higher stiffness and growth factor levels were associated with reduced proliferation rates, indicating a trade-off between these processes. Notably, a stiffness of 1.5 Pa with 1.56 mg/ml Matrigel yielded the highest proliferation rate, suggesting this condition might be optimal for use in bioreactor systems. Additionally, increasing matrix stiffness using Collagen I also enhanced cell spreading, indicating that cell spreading is strongly influenced by ECM stiffness. Furthermore, Matrigel reduced the expression of quiescence and senescence markers, helping to maintain cells in a proliferative state. These findings underscore the importance of optimizing ECM properties to balance cell proliferation and structural organization in 3D cultures, providing a foundation for scaling up 3D culture systems in bioreactor settings—a critical step toward large-scale cultured meat production. / Thesis / Master of Applied Science (MASc)

Accurate transistor models are important in wireless and microwave circuit design. Large-signal field-effect transistor (FET) models are generally extracted from current-voltage (IV) characteristics, small-signal S-parameters, and large-signal measurements. This dissertation describes improved characterization and measurement validation techniques for FET models that correctly account for thermal and trapping effects. Demonstration of a customized pulsed-bias, pulsed-RF S-parameter system constructed by the author using a traditional vector network analyzer is presented, along with the design of special bias tees to allow pulsing of the bias voltages. Pulsed IV and pulsed-bias S-parameter measurements can provide results that are electrodynamically accurate; that is, thermal and trapping effects in the measurements are similar to those of radio-frequency or microwave operation at a desired quiescent bias point. The custom pulsed S-parameter system is benchmarked using passive devices and advantages and tradeoffs of pulsed S-parameter measurements are explored. Pulsed- and continuous-bias measurement results for a high-power transistor are used to validate thermal S-parameter correction procedures. A new implementation of the steepest-ascent search algorithm for load-pull is presented. This algorithm provides for high-resolution determination of the maximum power and associated load impedance using a small number of measured or simulated reflection-coefficient states. To perform a more thorough nonlinear model validation, it is often desired to find the impedance providing maximum output power or efficiency over variations of a parameter such as drain voltage, input power, or process variation. The new algorithm enables this type of validation that is otherwise extremely tedious or impractical with traditional load-pull. A modified nonlinear FET model is presented in this work that allows characterization of both thermal and trapping effects. New parameters and equation terms providing a trapping-related quiescent-bias dependence have been added to a popular nonlinear ("Angelov") model. A systematic method for fitting the quiescent-dependence parameters, temperature coefficients, and thermal resistance is presented, using a GaN high electron-mobility transistor as an example. The thermal resistance providing a good fit in the modeling procedure is shown to correspond well with infrared measurement results.

In nature, many of the flapping wings and fins in swimming and flying animals have various degrees of flexibility with strong and coupled solid-fluid interactions between the structure and the fluid. In most cases, the wing structure, the flow and their interactions are complex. This thesis experimentally investigates a ‘simple’ fluid-flexible foil interaction problem: flow generated by a pitching foil with chordwise flexibility. To explore the effect of flexibility on the flow, we study the flow generated in quiescent water (the limiting case of infinite Strouhal number) by a sinusoidally pitching rigid symmetrical NACA0015 foil to which is attached a 0.05 mm thick chordwise flexible polythene flap at the trailing edge. The chordwise length of flap is 0.79 c, where c = 38 mm is the chord length of the rigid foil; span of the foil and flap is 100 mm. Detailed particle image velocimetry (PIV) and flow visualization measurements have been made for twelve cases, corresponding to three pitching amplitudes, ±10◦,± 15◦, ±20◦, and four frequencies, 1, 2, 3 and 4 Hz for each amplitude. For most of these cases, a narrow coherent jet aligned along the center-line, containing a reverse B’enard–K´arm´an vortex street, and a corresponding unidirectional thrust are generated. This thrust is similar to the upward force generated during hovering, but motion of our foil is much simpler than the complex wing kinematics found in birds and insects; also the thrust generation mechanism seems to be different. In our case, the thrust is from a coordinated pushing action of the rigid foil and the flexible flap. Control volume analysis reveals the unsteady nature of thrust generation. In this intricately coupled flow generation problem, chordwise flexibility is found to be crucial in producing the coherent jet. In this thesis, we explore in detail the physics of jet flow produced by the foil with a flexible flap, and identify the importance of flexibility in flow generation. Flap motion ensures appropriate spatial and temporal release of vortices, and also imparts them convective motion, to obtain the staggered pattern that produces the jet. To describe the fluid-flap interaction, we conveniently characterize the flap through a non-dimensional stiffness, ‘effective stiffness’ (EI)∗ of the flap, that captures the effects of both the flap properties as well as the external forcing. With the same flap by changing the pitching parameters, we cover a fairly large (EI)∗ range varying over nearly two orders of magnitude. However, we observed that only moderate (EI)∗ (~0.1 - 1) generates sustained narrow, orderly jet. We provide thrust estimates useful for the design of flapping foil thrusters/propulsors. Although this study has only indirect connections with the hovering in nature, it may be useful in understanding the role of flexibility of bird and insect wings during hovering. In contrast, a foil with a rigid trailing edge produces a weak jet whose inclination changes continually with time. This meandering is observed to be random and independent of the initial conditions over a wide range of pitching parameters.

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No description available.