VictorJuiz/thesis huggingface dataset:
Microfluidic, gradient-generator devices as in vitro mimics of cellular microenvironments [electronic resource]
Keywords: Mechanical Engineering

The larger goal of this work is to engineer an appropriate in vitro platform to understand the complex interplay of various effectors in vivo. The specific approach taken was to develop and utilize microfluidic devices to study the impact of stable soluble biochemical gradients on cellular behaviors. Microfluidic devices are tools capable of recreating many critical aspects of the natural microenvironments of cells and tissues in a controllable and reductionist manner. Several microfluidic device geometries were evaluated through computational finite element modeling and experimental characterization studies to produce predictable and stable concentration gradients over multiple days of cell culture. We implemented these helpful devices in order to study the mechanism of cellular responses to various biochemical and biomechanical factors in both two and three dimensions for several cellular applications. First, this device was used to perform an in depth study of the complex interplay between soluble biochemical and biomaterial effectors of endothelial cell sprouting. The sprouting of endothelial cells into capillary-like structures is an early critical step in angiogenesis, the formation of new blood vessels from existing conduits. Time-lapse microscopic images of endothelial sprouts within the devices were quantified to determine the role of matrix density in regulating sprout initiation, elongation, and navigation. Matrix density was found to have profound effects on sprout kinetics, morphology, and alignment within gradients of vascular endothelial growth factor. Use of these novel microfluidic devices was expanded to include proof-of-concept experiments demonstrating the high-throughput screening of multiple engineered biomaterials to identify scaffold properties conducive to endothelial network formation. Finally, the microfluidic devices were utilized in preliminary studies of neuronal cell behavior within gradients of various neurotrophins and bone marrow derived mast cell chemotaxis within gradients of Kit ligand. Taken together, the results of this thesis demonstrate the usefulness of microfluidic devices as well-controlled in vitro culture platforms capable of creating stable, soluble biochemical gradients. Furthermore, these devices may lead to future techniques to provide directional cues during cell and tissue growth for regenerative medicine applications. For example, our results may be useful for developing potential pro- and anti-angiogenic therapeutic strategies for clinical treatment of ischemia and cancer, respectively.
Micro-structured adhesives for climbing applications [electronic resource]
Keywords: Mechanical Engineering

Researchers seeking to expand the capabilities of mobile robots have begun looking to biological systems for inspiration. One particularly agile creature, the gecko lizard, is remarkably adept at maneuvering across both flat and vertical surfaces. Some species of gecko are even capable of climbing across inverted surfaces. The study of the gecko's adhesive system has informed the design of several synthetic adhesives in recent years. However, these adhesives generally fail to match the gecko adhesive's performance in one fashion or another. Many previous synthetic gecko adhesives are not reusable or they lack a method of control. Others do not have the ability to conform to surfaces with any roughness, or to distribute forces across the many thousands of fibers evenly. This presentation focuses on the design of a gecko-like adhesive system that achieves the level of performance necessary for implementation on a small-scale climbing robot. A gecko's adhesive structure has a strong directional preference, allowing the animal a method to control the stickiness of its feet. When loaded from the tip of the toe towards the palm, the material exhibits high adhesion in both the shear and normal direction. However, when this load is released, or when the toe is loaded in a different direction, no adhesion is present. First, I will discuss the creation of a synthetic micro-structure that also displays a directional adhesive dependence. This begins with the presentation of a new lithographic process used to create asymmetric wedge-shaped cavities in a photo-sensitive epoxy at the scale of tens of microns. Elastomeric materials were cast into these molds to produce the synthetic micro structures. Analysis and laboratory testing of this material show its strong directional dependence. Its performance for robotic climbing applications was promising at small sample sizes when tested on smooth surfaces like glass. However, the material proved inadequate for climbing because its performance could not be scaled to areas greater than about 1 cm2, nor could it adhere to rough surfaces. The gecko uses a multi-tiered hierarchy to insure that its millions of sub-micron sized spatulae make intimate contact with a surface regardless of its roughness. The gecko's system conforms across multiple length scales, distributing climbing forces and allowing rapid locomotion with seemingly minimal control effort. In the second portion of the talk, hierarchical suspensions for fibrillar adhesives are analyzed, and three iterations of a synthetic hierarchical adhesive design are detailed. The use of these hierarchical suspensions with modified wedge micro-structures similar to those mentioned above turned out to be successful enough to allow a mobile robot platform named Stickybot to climb multiple vertical surfaces ranging in roughness from glass to drywall. Data from large patches, well over 100 cm2, are also included. Discussion of these results and their implications for human climbing applications will conclude the presentation.
Migration-velocity analysis using image-space generalized wavefields [electronic resource]
Keywords: Geophysics

An accurate depth-velocity model is the key for obtaining good quality and reliable depth images in areas of complex geology. In such areas, velocity-model definition should use methods that describe the complexity of wavefield propagation, such as focusing and defocusing, multiple arrivals, and frequency-dependent velocity sensitivity. Wave-equation tomography in the image space has the ability to handle these issues because it uses wavefields as carriers of information. However, its high cost and low flexibility for parametrizing the model space has prevented its routine industrial use. This thesis aims at overcoming those limitations by using new wavefields as carriers of information: the image-space generalized wavefields. These wavefields are synthesized by using a pre-stack generalization of the exploding-reflector model. Cost of wave-equation tomography in the image space is decreased because only a small number of image-space generalized wavefields are necessary to accurately describe the kinematics of velocity errors and because these wavefields can be easily used in a target-oriented way. Flexibility is naturally incorporated into wave-equation tomography in the image space by using these wavefields because their modeling have as the initial conditions some key selected reflectors, allowing a layer-based parametrization of the model space. To use the image-space generalized wavefields in wave-equation tomography in the image space, the method is extended from the shot-profile domain to the image-space generalized-sources domain. In this new domain, the velocity updates are very fast. Migration with the optimized velocity model provides good quality and reliable depth images, as can be seen in a 3D-field data example.
Miniature and mass-producible fluorescence microscopes for biomedical imaging [electronic resource]
Keywords: Electrical Engineering

Fluorescence microscopy has emerged as a workhorse of modern biology and medicine. Fluorescence microscopes are indispensable as tools for basic research in the biological sciences, enable platforms for drug discovery in the biotechnology and pharmaceutical industries, and are increasingly aiding in several clinical diagnostic applications. However, state-of-the-art fluorescence microscopes remain bulky and expensive benchtop instruments with an architecture that impedes usage in certain applications and a cost that precludes adoption in large numbers. For example existing benchtop fluorescence microscopes are not amenable for in vivo imaging in animals, with the mouse being a common animal subject, especially during awake, active behavior. For the field of neuroscience in particular, such an experimental capability permits correlating causal cellular processes with animal behavior -- a longstanding goal. Inspired by this need, we have designed a miniature fluorescence microscope that can be borne by a mouse during active behavior. We have fabricated several such microscopes, each less than 2 g in mass, perhaps heralding a transformation in fluorescence microscopy from today's bulky and expensive benchtop paradigm towards miniature and mass-producible devices. Our fabricated microscopes achieve 2.5 [mu]m spatial resolution imaging fields-of-view up to 800 [mu]m x 600 [mu]m at 36 Hz, suitable for cellular-level imaging at high temporal resolution. To facilitate design of our microscopes, we have adopted a modeling-based microscope design methodology, akin to that used in the design of integrated circuits, and have developed a set of tools to model the microscope as an integrated device from the specimen to final digital image. We have experimentally validated fabricated microscopes for in vivo brain imaging in freely behaving mice, specifically using them for: 1) Imaging cerebellar vasculature and hemodynamics during activity; and 2) Imaging cerebellar Purkinje cell Calcium dynamics, analyzing spiking activity of populations of neurons with single neuron specificity during different motor behaviors. We also show how several of these microscopes imaging in parallel can enable new high-throughput imaging solutions with the potential to achieve broad impact, specifically demonstrating high-throughput image-based assays for: 1) Mutant phenotype screening in genetic model species such as the zebrafish; and 2) Multiple well plate cell analyses. Finally, we use a Bayesian iterative image restoration algorithm to enhance acquired microscope images, and show how spatial resolution can be further scaled into the sub-micron regime by leveraging advances in digital image sensing technology in conjunction with our post-acquisition image restoration algorithm.
Mobile collection routing protocol [electronic resource]
Keywords: Electrical Engineering

The dissertation presents an in-depth study of mobile routing protocols, particularly mobile collection protocols through a literature study, a theoretical model, and thorough experimental studies both in simulation and testbeds. A mobile collection service provides data delivery from stationary source nodes to a mobile user (or a sink) over multihop networks. One of the main contributions of this dissertation research is the Whirlpool Adhoc Routing Protocol (WARP), which efficiently routes data to a mobile destination within a static network. The key insight in WARP's design is that, when a destination moves, data traffic can use the existing topology to efficiently probe, repair, and communicate changes with the few control packets. Using simulation, controlled testbeds, and real mobility experiments, we find that using the data plane, rather than control plane, is highly effective due to the incremental nature of mobility updates. WARP leverages the fact that converging flows at the destination makes it the region of highest traffic. The dissertation also provides a theoretical basis for WARPs behavior, defining an update area where the topology must adjust when a destination moves. As long as packets arrive at a destination before it moves outside of the update area, WARP can repair the topology with the data plane.
Mobile Medic: Extending the Effective Reach of Mobile Data Infrastructure for Data Collection Applications in Emerging Regions
Keywords: Computer Science.
Cell phones
Community health services
Data collection
ICTD
Community healthcare workers
Thesis

The recent explosion of mobile phone penetration in developing regions enables a variety of empowering new applications for mobile devices. A significant example of such an application is communication between hospitals in developing regions and their rural healthcare workforces.
The challenges of designing a data collection tool for healthcare workers in these environments are substantial: financial constraints prevent reliance on SMS as a go-to data transport mechanism, but infrastructural limitations prevent reliance on GPRS or other more sophisticated mobile web protocols. The complexity of these data transport requirements can necessitate limitations on data input, which must not interfere with the functionality needs of the target user group, which has little technical knowledge. This paper examines a number of methods that can be employed to design a better data collection tool targeted at community healthcare workers in developing regions, and presents a prototype tool that incorporates these advances.
Model citizens, mural painting, pageantry, and the art of civic life in progressive America [electronic resource]
Keywords: Art and Art History

This dissertation focuses on the related arts of mural painting and pageantry in Progressive America and considers how civic artists participated on a grand scale in the era's campaigns for reform. Examining the ways in which period creatives made reform into something visible, dramatic, and vital, this study asks: What did Progressivism look like? What civic lessons did murals and pageants activate, and for which publics? How did civic art's classical forms and consensual narratives resonate with its viewing communities, and how did those communities respond? Artistic Progressives positioned their art forms at the center of the era's broader campaign to expand participatory democracy, improve social conditions, and impose a sense of order. Through paint and playacting, they entered into cultural and political debates on Americanization, immigration, citizenship, suffrage, and the new pedagogy of learning by doing. Mural painting and pageantry served as collaborative meeting points for art-minded citizens as well as contested zones of cultural agency. The study's five chapters examine the mural programs at the Library of Congress (1895-1897) and the Massachusetts State House (1900-1904), the Pageant of Illinois (1909), the Suffrage Pageant-Procession (1913), and mural painting and pageantry in Madison, Wisconsin (1908-1917).
Modeling and compensation of modal dispersion in graded-index multimode fiber [electronic resource]
Keywords: Electrical Engineering

Multimode fiber (MMF) has been used traditionally in local-area and campus-area networks. The large core size facilitates laser-to-fiber and fiber-to-fiber coupling, reducing component costs and the cost of setting up and maintaining a network. The propagation of multiple modes leads to modal dispersion, which traditionally has limited the bit rate-distance product to less than about 2 Gbit/s-km. Models for modal dispersion must take account of mode coupling by fiber imperfections and bents. Traditionally, mode coupling has been studied using a power-coupling model, which can accurately predict the population in different modes when using incoherent sources, such as light-emitting diodes. But the power coupling model is inherently unable to describe some effects in high-speed links using coherent laser sources, such as polarization dependence of impulse response. In the first part of this dissertation, we describe a field-coupling model for propagation in MMF, which is analogous to the model used to study polarizationmode dispersion in single-mode fiber. Our model allows computation of the fiber impulse response, given a launched electric-field profile and polarization. In order to model both spatial- and polarization-mode coupling, we divide the fiber into numerous short sections, each having random curvature and random angular orientation. This model can be described using only a few parameters. With the help of this model we investigate first-order and higher-order modal dispersion effects. We describe principal modes (PMs), which are free of modal dispersion. We describe how the PM group delays depend on the strength of mode coupling in the low-coupling regime (e.g., glass fibers) and the high-coupling regime (e.g., plastic fibers). We also explain the observed polarization dependence of the impulse response. Considering terms of higher order (in frequency), our model accounts for an observed filling-in between peaks in the impulse response and predicts a nonlinear relationship between input and output intensity waveforms. In the second part of this dissertation, we describe the use of an adaptive spatial light modulator (SLM) to launch light into PMs, preventing modal dispersion. Previously this technique has enabled transmission at bit rate-distance products over 200 Gbit/skm. We have extended the adaptive optics technique to include control of signal polarization. We have studied several alternative adaptive optical systems and have derived the optimal solution for each system. We show that the best performance is obtained by controlling each polarization independently using two SLMs.
Modeling and mitigation of information technology risks [electronic resource]
Keywords: Management Science and Engineering

Information technology security has become a critical component of managing the risks associated with communication networks that support the global economy. Unlike the financial markets where a rich set of tools exist to measure and control the risks associated with financial decisions, no such tools exist for risk associated with information technology. Quantitative methods that have been studied to date are quantitative only in that they involve the measurements of some metrics. A model, however, should enable management to explain current phenomena or potentially provide qualitative arguments for policies. The tools today do not permit such discussion. In this dissertation, the models I develop address some of the fundamental nuances of information technology security. First, the topology of the network influences the nature of the risks associated with each node and should be accounted for. Second, such a model must incorporate the non-symmetric relationship found in the network. The relationships are typically bi-directional with unequal weights. Within this context, the models here attempt to answer the fundamental question: "How should I allocate my resources in order to manage the information technology risks I face?" This allocation can occur at an industry level amongst multiple corporations, within a company amongst a multitude of nodes or even at the vulnerability level. Within this context, I present three models. First, I develop a prioritization model that balances the impact of the topology of the network and the level of potential impact of an individual vulnerability. Second, I create a class of interdependent security investment models to incorporate asymmetries of utility functions and a mixture of positive and negative externalities. Lastly, I generate a novel formulation of a dynamic risk networks model with interdependent states. Overall, the models provide anchor points in the largely uncharted field of IT risk management.
Modeling of III-V nanoscale field-effect transistors for logic circuits [electronic resource]
Keywords: Electrical Engineering

As silicon CMOS technology continues to scale down its minimum critical dimension, it becomes increasingly difficult to enhance device switching speed due to fundamental limitations. Innovations in device structure and materials are pursued to accommodate improvement in performance as well as reduction in transistor size. For beyond-22-nm CMOS technology, III-V channel FETs are considered as a compelling candidate for extending the device scaling limit of low-power and high-speed operation, owing to their superb carrier transport properties and recent experimental advancements. In this thesis, device simulation, compact modeling, circuit design, circuit performance assessment and estimation of III-V logic transistors are carried out to study key considerations such as device pitch, parasitics, and the importance of PMOS for circuit-level performance. To effectively connect device characteristics with circuit design, a physics-based compact model for digital logic is constructed. The model encompasses effects such as field-confined and spatially-confined trapezoidal quantum well sub-band energies, gate leakage tunneling current and parasitic capacitance. The developed compact model contains only three fitting parameters and is verified by experiment and circuit simulations. The compact model enables other bodies of work for the purpose of circuit-level design and performance estimation. To demonstrate the capability of the model in a circuit environment we apply the compact model to composite circuits such as FO4 inverter chains and SRAM cache to evaluate and project performance and power trends for beyond-22-nm technology.
Modified nucleotides and nucleic acids as molecular probes [electronic resource]
Keywords: Chemistry

This thesis discusses a number of projects involving the use of modified nucleotides and oligonucleotides in addressing some basic science questions and some clinical and technological applications.The first chapter details our efforts at using telomere-encoding circular DNA in elongating zebrafish telomeres. We microinjected our synthetic circular DNA into zebrafish embryos and studied their telomere length 24 hrs later. Using Quantitative Fluorescence in situ Hybridization (Q-FISH) as the analytical tool to determine telomere length, we observed no significant difference in telomere length between the group injected with the synthetic DNA and the control group. In the second chapter we studied the potential of a non-polar shape mimic of iodo-uracil as an imager of tumors. We continued discussing our work with non-polar nucleotide isosteres in the third chapter where we used them in investigating a novel active site in polymerase from Pyrococcus furiosus (Pfu). From our studies we concluded that although shape was an important factor in distinguishing bases, this binding site also employed hydrogen bonding to identify nucleoabases. The lack of any recognition of the syn-oxidized bases suggested that the enzyme preferred to recognize bases in the anti conformation rather than syn. In the fourth chapter we were interested in understanding the factors determining the fidelity and selectivity observed in RNA Polymerase II mediated transcription. Once again we used non-polar shape mimics of thymidine (dF) and adenine (dQ) to study the importance of shape and hydrogen bonding. We observed that the thymidine mimic was recognized better by the RNA Polymerase II active site than the mis-match bases. The adenine isostere on the other hand, was poorly recognized. This preliminary study demonstrates the importance of both shape and hydrogen bonding. The last chapter discusses our studies using polyfluorophores on a DNA backbone to detect gases. Following a combinatorial method, a library of oligodeoxyfluorosides (ODFs) were synthesized from which sensors of gases were selected. Using this method we were able to select optical sensors for a diverse set of small molecules in vapor state.