http://hdl.handle.net/1721.1/7599 Tue, 18 Jun 2013 14:34:06 GMT 2013-06-18T14:34:06Z http://hdl.handle.net/1721.1/79327 Distributed mobile platforms and applications for intelligent transportation systems Gao, Jason Hao Smartphones are pervasive, and possess powerful processors, multi-faceted sensing, and multiple radios. However, networked mobile apps still typically use a client-server programming model, sending all shared data queries and uploads through the cellular network, incurring bandwidth consumption and unpredictable latencies. Leveraging the local compute power and device-to-device communications of modern smartphones can mitigate demand on cellular networks and improve response times. This thesis presents two systems towards this vision. First, we present DIPLOMA, which aids developers in achieving this vision by providing a programming layer to easily program a collection of smartphones connected over adhoc wireless. It presents a familiar shared data model to developers, while underneath, it implements a distributed shared memory system that provides coherent relaxed-consistency access to data across different smartphones and addresses the issues that device mobility and unreliable networking pose against consistency and coherence. We evaluated our prototype on 10 Android phones on both 3G (HSPA) and 4G (LTE) networks with a representative location-based photo-sharing service and a synthetic benchmark. We also simulated large scale scenarios up to 160 nodes on the ns-2 network simulator. Compared to a client-server baseline, our system shows response time improvements of 10x over 3G and 2x over 4G. We also observe cellular bandwidth reductions of 96%, comparable energy consumption, and a 95.3% request completion rate with coherent caching. With RoadRunner, we apply our vision to Intelligent Transportation Systems (ITS). RoadRunner implements vehicular congestion control as an in-vehicle smartphone app that judiciously harnesses onboard sensing, local computation, and short-range communications, enabling large-scale traffic congestion control without the need for physical infrastructure, at higher penetration across road networks, and at finer granularity. RoadRunner enforces a quota on the number of cars on a road by requiring vehicles to possess a token for entry. Tokens are circulated and reused among multiple vehicles as they move between regions. We implemented RoadRunner as an Android application, deployed it on 10 vehicles using 4G (LTE), 802.11p DSRC and 802.11n adhoc WiFi, and measured cellular access reductions up to 84%, response time improvements up to 80%, and effectiveness of the system in enforcing congestion control policies. We also simulated large-scale scenarios using actual traffic loop-detector counts from Singapore. Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 70-75). Tue, 01 Jan 2013 00:00:00 GMT http://hdl.handle.net/1721.1/79327 2013-01-01T00:00:00Z http://hdl.handle.net/1721.1/79326 Swept source optical coherence microscopy for pathological assessment of cancerous tissues Ahsen, Osman Oguz Optical coherence microscopy (OCM) combines optical coherence tomography (OCT) with confocal microscopy and enables depth resolved visualization of biological specimens with cellular resolution. OCM offers a suitable alternative to confocal imaging by providing enhanced contrast due to the additional coherence gate to the inherent confocal gate, increasing the field of view and imaging depth, and eliminating the need of external contrast agents. In the past, development of OCT systems have been focused on time domain and spectral/Fourier domain methods which offer high axial resolution and imaging speeds. However, recent advances in the OCT technology have pushed the development into the direction of swept source OCT technologies, and development of the OCM technology is likely to follow this path. This thesis describes construction, characterization and preliminary imaging results of a swept source OCM (SS-OCM) system utilizing a novel light source, Vertical Cavity Surface-Emission Laser (VCSEL). This swept source laser can reach sweep rates exceeding 1 MHz and provide wide tuning ranges, which will enable both imaging speeds approaching to time domain OCM (TD-OCM) systems, and axial resolution approaching to spectral/Fourier domain OCM (SD-OCM) systems. Several other advantages of SS-OCM compared to TD-OCM and SD-OCM that make this technology a promising alternative to the latter imaging methods are presented. Furthermore, practical concepts in the system development and signal processing, such as compensation for the scan curvatures, methods for calibration of the spectrums, selection of suitable color maps for display, and other related topics are also discussed in the text. In addition to technical description of the OCM system development, an in depth analysis of several clinical applications that will be likely to benefit from this imaging modality is also presented. Real time intraoperative feedback is required in order to reduce the morbidity and the rate of additional operations for the surgical management of several forms of cancer, where a benchtop OCM system residing in the pathology laboratory can be immensely beneficial. Furthermore, with the novel scanning mechanisms that have been developed in the recent years it is possible to translate this imaging modality to an in vivo setting where an OCM probe can be inserted through the working channel of an endoscope and generate cellular resolution images in real time without the need of external contrast agents. Endoscopic management and clinical challenges for a spectrum of lower gastrointestinal (GI) diseases is discussed where an in vivo OCM imaging probe can play an important role in the diagnosis and evaluation of the extend of the particular disease. A review of alternative imaging modalities, such as chromoendoscopy, narrow band imaging (NBI) and confocal laser endomicroscopy (CLE) is also included which outlines the relative strengths and limitations of these imaging modalities for the clinical management of lower GI diseases. Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013.; Cataloged from PDF version of thesis.; Includes bibliographical references. Tue, 01 Jan 2013 00:00:00 GMT http://hdl.handle.net/1721.1/79326 2013-01-01T00:00:00Z http://hdl.handle.net/1721.1/79325 Microfluidic concentration-enhanced single cell enzyme activity assay Sarkar, Aniruddh Cells sense stimuli, process information and respond using signaling networks regulated by enzymatic activity of various proteins. Aberrations in signaling are associated with diseases such as cancer. Most current methods lack the sensitivity to measure enzymatic activity in single cells and instead measure the average of large cell populations. Cellular heterogeneity, overlooked in these methods, is widespread and relevant. Microfabricated tools are uniquely suited to single cell analysis due to the match in size scale which enables high sensitivity, high throughput measurements. In this thesis we develop a microfluidic platform for the direct measurement of enzyme activities from selected single cells without disrupting their extracellular context. We develop modules to: enhance enzyme assay sensitivity by microfluidic confinement, interface microfluidic devices with selected single cells, enable multiplexing and then integrate these modules to perform single cell assays. We first investigate electrokinetic trapping of charged biomolecules in a nanofluidic concentrator for enhancing enzyme assay sensitivity by simultaneously accumulating enzyme and substrate into a reaction plug. Non-linear enhancement of reaction kinetics in this device is predicted by a mathematical model and experimentally verified. A linear enhancement mode is developed where only the enzyme is accumulated and is reacted with substrate later in an enclosed volume defined by integrated pneumatic valves or by micro-droplets formed using an integrated droplet generator. This device is then used to perform high-throughput measurement of secreted cellular proteases. We then develop a nicrofluidic probe for lysis and capture of the contents of selected single adherent cells from standard tissue culture platforms by creating a small lysis zone at its tip using hydrodynamic confinement. The single cell lysate is then divided and mixed with different substrates and confined in small chambers for fluorimetric assays. An integrated nanofluidic concentrator enables further concentration-enhancement. We demonstrate the ability to measure, from selected single cells, the activity of kinases: Akt, MAPKAPK2, PKA and a metabolic enzyme, GAPDH - separately or simultaneously. This assay platform can correlate single cell phenotype or extracellular context to intracellular biochemical state. We present preliminary explorations of the correlation of cell morphology or local cell population density to kinase activity. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013.; Cataloged from PDF version of thesis.; Includes bibliographical references. Tue, 01 Jan 2013 00:00:00 GMT http://hdl.handle.net/1721.1/79325 2013-01-01T00:00:00Z http://hdl.handle.net/1721.1/79324 On the robustness of network infrastructures to disasters and physical attacks Neumayer, Sebastian James Networks are vulnerable to natural disasters, such as earthquakes or floods, as well as to physical attacks, such as an Electromagnetic Pulse (EMP) attack. Such realworld events happen in specific geographical locations and disrupt specific parts of the network. Therefore, the geographical layout of the network determines the impact of such events on the network's connectivity. We focus on network analysis and design under a geographic failure model of (geographical) networks to such disasters. Initially, we aim to identify the most vulnerable parts of data networks to attack. That is, the locations of a disaster that would have the maximum disruptive effect on a network in terms of capacity and connectivity. We consider graph models in which nodes and links are geographically located on a plane, and model the disaster event as a line segment or circular disk. We develop polynomial time algorithms for finding the worst possible cut in this setting. Then, we obtain numerical results for a specific backbone network, thereby demonstrating the applicability of our algorithms to real-world networks. We also develop tools to calculate network metrics after a 'random' geographic disaster. The random location of the disaster allows us to model situations where the physical failures are not targeted attacks. In particular, we consider disasters that take the form of a 'random' circular disk or line in a plane. Using results from geometric probability, we are able to calculate some network performance metrics to such a disaster in polynomial time. In particular, we can evaluate average two-terminal reliability in polynomial time under these 'random' cuts. This is in contrast to the case of independent link failures for which there exists no known polynomial time algorithm to calculate this reliability metric. We present some numerical results to show the significance of geometry on the survivability of the network. This motivates the formulation of several network design problems in the context of randomly located disasters. We also study some min-cut and max-flow problems in a geographical setting. Specifically, we consider the problem of finding the minimum number of failures, modeled as circular disks, to disconnect a pair of nodes and the maximum number of failure disjoint paths between a pair of nodes. This model applies to the scenario where an adversary is attacking the network multiple times with intention to reduce its connectivity. We present a polynomial time algorithm to solve the geographic mincut problem and develop an ILP formulation, an exact algorithm, and a heuristic algorithm for the geographic max-flow problem. Finally, we study the reliability of power transmission networks under regional disasters. Initially, we quantify the effect of large-scale non-targeted disasters and their resulting cascade effects on power networks. We then model the dependence of data networks on the power systems and consider network reliability in this dependent network setting. Our novel approach provides a promising new direction for modeling and designing networks to lessen the effects of geographical disasters or attacks. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 153-158). Tue, 01 Jan 2013 00:00:00 GMT http://hdl.handle.net/1721.1/79324 2013-01-01T00:00:00Z