Applying Mathematical Models to Study the Role of the Immune System in Chronic Myelogenous Leukemia

Although tyrosine kinase inhibitors (TKIs) such as imatinib have transformed chronic myelogenous leukemia (CML) into a chronic condition, these therapies are not curative in the majority of cases. Most patients must continue TKI therapy indefinitely, a requirement that is both expensive and that compromises a patient's quality of life. While TKIs are known to reduce leukemic cells' proliferative capacity and to induce apoptosis, their effects on leukemic stem cells, the immune system, and the microenvironment are not fully understood. A more complete understanding of their global therapeutic effects would help us to identify any limitations of TKI monotherapy and to address these issues through novel combination therapies. Mathematical models are a complementary tool to experimental and clinical data that can provide valuable insights into the underlying mechanisms of TKI therapy. Previous modeling efforts have focused on CML patients who show biphasic and triphasic exponential declines in BCR-ABL ratio during therapy. However, our patient data indicates that many patients treated with TKIs show fluctuations in BCR-ABL ratio yet are able to achieve durable remissions. To investigate these fluctuations, we construct a mathematical model that integrates CML with a patient's autologous immune response to the disease. In our model, we define an immune window, which is an intermediate range of leukemic concentrations that lead to an effective immune response against CML. While small leukemic concentrations provide insufficient stimulus, large leukemic concentrations actively suppress a patient's immune system, thus limiting it's ability to respond. Our patient data and modeling results suggest that at diagnosis, a patient's high leukemic concentration is able to suppress their immune system. TKI therapy drives the leukemic population into the immune window, allowing the patient's immune cells to expand and eventually mount an efficient response against the residual CML. This response drives the leukemic population below the immune window, causing the immune population to contract and allowing the leukemia to partially recover. The leukemia eventually reenters the immune window, thus stimulating a sequence of weaker immune responses as the two populations approach equilibrium. We hypothesize that a patient's autologous immune response to CML may explain the fluctuations in BCR-ABL ratio that are regularly seen during TKI therapy. These fluctuations may serve as a signature of a patient's individual immune response to CML. By applying our modeling framework to patient data, we are able to construct an immune profile that can then be used to propose patient-specific combination therapies aimed at further reducing a patient's leukemic burden. Our characterization of a patient's anti-leukemia immune response may be especially valuable in the study of drug resistance, treatment cessation, and combination therapy.

Dynamic Coculture of a Prevascularized Engineered Bone Construct

The generation of functional, vascularized tissues is a key challenge for the field of tissue engineering. Before clinical implantations of tissue engineered bone constructs can succeed, in vitro fabrication needs to address limitations in large-scale tissue development, including controlled osteogenesis and an inadequate vasculature network to prevent necrosis of large constructs. The tubular perfusion system (TPS) bioreactor is an effective culturing method to augment osteogenic differentiation and maintain viability of human mesenchymal stem cell (hMSC)-seeded scaffolds while they are developed in vitro. To further enhance this process, we developed a novel osteogenic growth factors delivery system for dynamically cultured hMSCs using microparticles encapsulated in three-dimensional alginate scaffolds. In light of this increased differentiation, we characterized the endogenous cytokine distribution throughout the TPS bioreactor. An advantageous effect in the ‘outlet’ portion of the uniaxial growth chamber was discovered due to the system’s downstream circulation and the unique modular aspect of the scaffolds. This unique trait allowed us to carefully tune the differentiation behavior of specific cell populations. We applied the knowledge gained from the growth profile of the TPS bioreactor to culture a high-volume bone composite in a 3D-printed femur mold. This resulted in a tissue engineered bone construct with a volume of 200cm3, a 20-fold increase over previously reported sizes. We demonstrated high viability of the cultured cells throughout the culture period as well as early signs of osteogenic differentiation. Taking one step closer toward a viable implant and minimize tissue necrosis after implantation, we designed a composite construct by coculturing endothelial cells (ECs) and differentiating hMSCs, encouraging prevascularization and anastomosis of the graft with the host vasculature. We discovered the necessity of cell to cell proximity between the two cell types as well as preference for the natural cell binding capabilities of hydrogels like collagen. Notably, the results suggested increased osteogenic and angiogenic potential of the encapsulated cells when dynamically cultured in the TPS bioreactor, suggesting a synergistic effect between coculture and applied shear stress. This work highlights the feasibility of fabricating a high-volume, prevascularized tissue engineered bone construct for the regeneration of a critical size defect.

PARTICIPATORY PLANNING PILOT CASE STUDY IN CHINA: REALITY, CHALLENGES & LESSONS LEARNED FROM US

Urban planning in China is in a period of change, where participatory planning may supplement the traditional planning system. Since the beginning of the 21st century, several pilot participatory planning projects have responded to the new challenge. The author collected eight cases from the Chinese planning institution to explore the possible models of and barriers to participatory planning. On the other hand, public participation has been a concrete component of planning and implementation process in the United States. The author will also elaborate on one practical case of the planning process in the United States to compare the two countries on planning methods and barriers.

The Effect of Architecture and Shear Stress on Endothelialization of 3D Printed Vascular Networks

Despite significant progress in the field of tissue engineering within the last decade, a number of unsolved problems still remain. One of the most relevant issues is the lack of proper vascularization that limits the size of engineered tissues to smaller than clinically relevant dimensions. In particular, the growth of engineered tissue in vitro within bioreactors is plagued with this challenge. Specifically, the tubular perfusion system bioreactor has been used for large scale bone constructs; however these engineered constructs lack inherent vasculature and quickly develop a hypoxic core, where no nutrient exchange can occur, thus leading to cell death. Through the use of 3D printed vascular templates in conjunction with a tubular perfusion system bioreactor, we attempt to create an endothelial cell monolayer on 3D scaffolds that could potentially serve as the foundation of inherent vasculature within these engineered bone grafts.

Architectural-Physical Co-Design of 3D CPUs with Micro-Fluidic Cooling

The performance, energy efficiency and cost improvements due to traditional technology scaling have begun to slow down and present diminishing returns. Underlying reasons for this trend include fundamental physical limits of transistor scaling, the growing significance of quantum effects as transistors shrink, and a growing mismatch between transistors and interconnects regarding size, speed and power. Continued Moore's Law scaling will not come from technology scaling alone, and must involve improvements to design tools and development of new disruptive technologies such as 3D integration. 3D integration presents potential improvements to interconnect power and delay by translating the routing problem into a third dimension, and facilitates transistor density scaling independent of technology node. Furthermore, 3D IC technology opens up a new architectural design space of heterogeneously-integrated high-bandwidth CPUs. Vertical integration promises to provide the CPU architectures of the future by integrating high performance processors with on-chip high-bandwidth memory systems and highly connected network-on-chip structures. Such techniques can overcome the well-known CPU performance bottlenecks referred to as memory and communication wall. However the promising improvements to performance and energy efficiency offered by 3D CPUs does not come without cost, both in the financial investments to develop the technology, and the increased complexity of design. Two main limitations to 3D IC technology have been heat removal and TSV reliability. Transistor stacking creates increases in power density, current density and thermal resistance in air cooled packages. Furthermore the technology introduces vertical through silicon vias (TSVs) that create new points of failure in the chip and require development of new BEOL technologies. Although these issues can be controlled to some extent using thermal-reliability aware physical and architectural 3D design techniques, high performance embedded cooling schemes, such as micro-fluidic (MF) cooling, are fundamentally necessary to unlock the true potential of 3D ICs. A new paradigm is being put forth which integrates the computational, electrical, physical, thermal and reliability views of a system. The unification of these diverse aspects of integrated circuits is called Co-Design. Independent design and optimization of each aspect leads to sub-optimal designs due to a lack of understanding of cross-domain interactions and their impacts on the feasibility region of the architectural design space. Co-Design enables optimization across layers with a multi-domain view and thus unlocks new high-performance and energy efficient configurations. Although the co-design paradigm is becoming increasingly necessary in all fields of IC design, it is even more critical in 3D ICs where, as we show, the inter-layer coupling and higher degree of connectivity between components exacerbates the interdependence between architectural parameters, physical design parameters and the multitude of metrics of interest to the designer (i.e. power, performance, temperature and reliability). In this dissertation we present a framework for multi-domain co-simulation and co-optimization of 3D CPU architectures with both air and MF cooling solutions. Finally we propose an approach for design space exploration and modeling within the new Co-Design paradigm, and discuss the possible avenues for improvement of this work in the future.

Physical Design Methodologies for Low Power and Reliable 3D ICs

As the semiconductor industry struggles to maintain its momentum down the path following the Moore's Law, three dimensional integrated circuit (3D IC) technology has emerged as a promising solution to achieve higher integration density, better performance, and lower power consumption. However, despite its significant improvement in electrical performance, 3D IC presents several serious physical design challenges. In this dissertation, we investigate physical design methodologies for 3D ICs with primary focus on two areas: low power 3D clock tree design, and reliability degradation modeling and management. Clock trees are essential parts for digital system which dissipate a large amount of power due to high capacitive loads. The majority of existing 3D clock tree designs focus on minimizing the total wire length, which produces sub-optimal results for power optimization. In this dissertation, we formulate a 3D clock tree design flow which directly optimizes for clock power. Besides, we also investigate the design methodology for clock gating a 3D clock tree, which uses shutdown gates to selectively turn off unnecessary clock activities. Different from the common assumption in 2D ICs that shutdown gates are cheap thus can be applied at every clock node, shutdown gates in 3D ICs introduce additional control TSVs, which compete with clock TSVs for placement resources. We explore the design methodologies to produce the optimal allocation and placement for clock and control TSVs so that the clock power is minimized. We show that the proposed synthesis flow saves significant clock power while accounting for available TSV placement area. Vertical integration also brings new reliability challenges including TSV's electromigration (EM) and several other reliability loss mechanisms caused by TSV-induced stress. These reliability loss models involve complex inter-dependencies between electrical and thermal conditions, which have not been investigated in the past. In this dissertation we set up an electrical/thermal/reliability co-simulation framework to capture the transient of reliability loss in 3D ICs. We further derive and validate an analytical reliability objective function that can be integrated into the 3D placement design flow. The reliability aware placement scheme enables co-design and co-optimization of both the electrical and reliability property, thus improves both the circuit's performance and its lifetime. Our electrical/reliability co-design scheme avoids unnecessary design cycles or application of ad-hoc fixes that lead to sub-optimal performance. Vertical integration also enables stacking DRAM on top of CPU, providing high bandwidth and short latency. However, non-uniform voltage fluctuation and local thermal hotspot in CPU layers are coupled into DRAM layers, causing a non-uniform bit-cell leakage (thereby bit flip) distribution. We propose a performance-power-resilience simulation framework to capture DRAM soft error in 3D multi-core CPU systems. In addition, a dynamic resilience management (DRM) scheme is investigated, which adaptively tunes CPU's operating points to adjust DRAM's voltage noise and thermal condition during runtime. The DRM uses dynamic frequency scaling to achieve a resilience borrow-in strategy, which effectively enhances DRAM's resilience without sacrificing performance. The proposed physical design methodologies should act as important building blocks for 3D ICs and push 3D ICs toward mainstream acceptance in the near future.

Bodies on the Line: Violence, Disposable Subjects, and the US-Mexico Border Industrial Complex

Bodies On the Line: Violence, Disposable Subjects, and the Border Industrial Complex explores the construction of identity and notions of belonging within an increasingly privatized and militarized Border Industrial Complex. Specifically, the project interrogates how discourses of Mexican migrants as racialized, gendered, and hypersexualized “deviants” normalize violence against border crossers. Starting at Juárez/El Paso border, I follow the expanding border, interrogating the ways that Mexican migrants, regardless of sexual orientation, have been constructed and disciplined according to racialized notions of “sexual deviance." I engage a queer of color critique to argue that sexual deviance becomes a justification for targeting and containing migrant subjects. By focusing on the economic and racially motivated violence that the Border Industrial Complex does to Mexican migrant communities, I expand the critiques that feminists of color have long leveraged against systemic violence done to communities of color through the prison industrial system. Importantly, this project contributes to transnational feminist scholarship by contextualizing border violence within the global circuits of labor, capital, and ideology that shape perceptions of border insecurity. The project contributes an interdisciplinary perspective that uses a multi-method approach to understand how border violence is exercised against Mexicans at the Mexico-US border. I use archival methods to ask how historical records housed at the National Border Patrol Museum and Memorial Library serve as political instruments that reinforce the contemporary use of violence against Mexican migrants. I also use semi-structured interviews with nine frequent border crossers to consider the various ways crossers defined and aligned themselves at the border. Finally, I analyze the master narratives that come to surround specific cases of border violence. To that end, I consider the mainstream media’s coverage, legal proceedings, and policy to better understand the racialized, gendered, and sexualized logics of the violence.

the plenoptic sensor

In this thesis, we will introduce the innovative concept of a plenoptic sensor that can determine the phase and amplitude distortion in a coherent beam, for example a laser beam that has propagated through the turbulent atmosphere.. The plenoptic sensor can be applied to situations involving strong or deep atmospheric turbulence. This can improve free space optical communications by maintaining optical links more intelligently and efficiently. Also, in directed energy applications, the plenoptic sensor and its fast reconstruction algorithm can give instantaneous instructions to an adaptive optics (AO) system to create intelligent corrections in directing a beam through atmospheric turbulence. The hardware structure of the plenoptic sensor uses an objective lens and a microlens array (MLA) to form a mini “Keplerian” telescope array that shares the common objective lens. In principle, the objective lens helps to detect the phase gradient of the distorted laser beam and the microlens array (MLA) helps to retrieve the geometry of the distorted beam in various gradient segments. The software layer of the plenoptic sensor is developed based on different applications. Intuitively, since the device maximizes the observation of the light field in front of the sensor, different algorithms can be developed, such as detecting the atmospheric turbulence effects as well as retrieving undistorted images of distant objects. Efficient 3D simulations on atmospheric turbulence based on geometric optics have been established to help us perform optimization on system design and verify the correctness of our algorithms. A number of experimental platforms have been built to implement the plenoptic sensor in various application concepts and show its improvements when compared with traditional wavefront sensors. As a result, the plenoptic sensor brings a revolution to the study of atmospheric turbulence and generates new approaches to handle turbulence effect better.