VictorJuiz/thesis huggingface dataset:
Mechanisms of resistance switching in various transition metal oxides [electronic resource]

Several materials, especially transition metal oxides, undergo abrupt changes in resistance, known as resistance switching, driven by various external stimuli such as temperature, electric field, etc. through several mechanisms such as Mott transition, Peierls transition, etc. Such a change in resistance and other intrinsic material properties have enabled many applications, specifically, in an upcoming computer memory technology called Resistive Random Access Memory (RRAM), where information is stored in distinct resistance states of the material, owing to the phase-transition. In this work, we understand mechanisms of phase transitions in two oxide systems, namely, VO2 and TaOx+TiOx. We use multiple advanced in-situ spectro-microscopy techniques to understand the switching process driven by different stimuli including uniform material temperature and local Joule-heating.

Keywords: Electrical Engineering.
Advisor: Nishi Yoshio
Brongersma Mark L. advisor. Thesis advisor
Pianetta Piero advisor. Thesis advisor
Mechanisms underlying state-dependent modulation of cortical activity [electronic resource]

The processing of information in cortical circuits is dynamic and varies widely across behavioral and cognitive states. In the cortex, sensory information from the periphery is transformed by a combination of local recurrent connections, interactions with other cortical areas, and inputs from several ascending neuromodulatory systems. However, the precise cellular mechanisms underlying state-dependent modulation of cortical circuits remain poorly understood. Here, I describe two approaches to address this question: an in vitro approach to study the impact of cholinergic signaling on cortical circuits, and an in vivo approach to investigate cellular mechanisms underlying modulation of visual responses in the awake, behaving mouse. Many lines of evidence suggest that the cholinergic system plays an important role in coordinating many large-scale changes in brain activity associated with behavioral state. To investigate how activation of cholinergic axons modulates cortical circuits, we developed methods to transduce cholinergic neurons in the basal forebrain with channelrhodopsin-2. This approach allowed us to selectively activate cholinergic terminals in the cortex in vitro and study (1) the cortical cell-types targeted by cholinergic axons and (2) the kinetics and synaptic properties of cholinergic signaling. To study the cellular mechanisms underlying state-dependent modulation of visual responses, we obtained whole-cell recordings from visual cortical neurons in the awake, behaving mouse. We characterized two cortical network states that were tightly correlated with distinct wakeful behavioral states: quiet wakefulness and locomotion. We demonstrated that subthreshold responses to visual stimulation were larger and more reliable during locomotion due to an increase in excitatory and inhibitory conductances and a shift in the stimulus-evoked reversal potential. Furthermore, by obtaining two simultaneous whole-cell recordings from visual cortical neurons, we were able to measure how correlated subthreshold activity was modulated by behavioral state and the patterns of excitatory and inhibitory synaptic inputs that generate these correlations. Together, these experiments provide insight into the cellular mechanisms that underlie state-dependent changes in cortical activity, sensory processing, and behavior.

Advisor: Hestrin Shaul
Huguenard John advisor. Thesis advisor
Knudsen Eric I. advisor. Thesis advisor
Raymond Jennifer L. advisor. Thesis advisor
Medical image similarity perception for content-based image retrieval [electronic resource]

Content-based image retrieval (CBIR) of perceptually similar images for medical decision support may improve the accuracy and efficiency of radiological diagnosis. A robust reference standard for perceptual similarity in medical images is vital to CBIR applications, but is challenging to create due to the large amount of observer data necessary as well as high inter-observer variability. The aims of this thesis are (1) to develop techniques for creating reference standards based on perceptual similarity that are scalable for large databases, and (2) to model inter-reader variability in observer assessments of image similarity. This thesis first discusses a novel technique for predicting visual similarity for pairs of images in a database from perceptual data obtained by viewing each image individually. In an observer study using 19 CT liver lesions in the portal venous phase, three radiologists provided point-wise ratings for visual attributes of images containing liver lesions displayed individually and also for perceptual similarity in all pair-wise combinations of these images. Using the data generated from viewing images individually, this work develops a scheme to generate ratings of pair-wise similarity using linear fitting, and demonstrates that this is a scalable technique for developing a reference standard. This work also develops a statistical model from these data that may be used to predict inter-reader variability and accuracy of similarity estimates in larger sets of data. Finally, this thesis discusses leveraging compressive sensing techniques, which may be used to complete highly sparse matrices, to impute similarity matrices from a small subset of observer ratings. By being scalable for large databases, this technique may be a reliable and efficient method for creating similarity reference standards. The results of this work thus provide a better understanding of perception of medical image similarity, which may in turn be used to train and validate medical decision support systems.

Keywords: Electrical Engineering.
Advisor: Napel Sandy primary advisor. Thesis advisor
Van Roy Benjamin primary advisor. Thesis advisor
Rubin Daniel (Daniel L.) advisor. Thesis advisor
Memory and object management in RAMCloud [electronic resource]

Traditional memory allocation mechanisms are not suitable for new DRAM-based storage systems because they use memory inefficiently, particularly under changing access patterns. This dissertation presents an alternative, describing how a log-structured approach to memory management -- called "log-structured memory" -- allows in-memory storage systems to achieve 80-90% memory utilisation while still offering high performance. One of the key observations of this approach is that memory can be managed much more efficiently than traditional garbage collectors by exploiting the restricted use of pointers in storage systems. An additional benefit of this technique is that the same mechanisms can be used to manage backup copies of data on disk for durability, allowing the system to survive crashes and restarts.

Advisor: Mazières David (David Folkman)
Ousterhout John K. primary advisor. Thesis advisor
Rosenblum Mendel advisor. Thesis advisor
Memory-efficient image databases for mobile visual search [electronic resource]

Mobile visual search (MVS) systems compare query images captured by the mobile device's camera against a database of labeled images to recognize objects seen in the device's viewfinder. Practical MVS systems require a fast response to provide an interactive and compelling user experience. We show how a memory-efficient database stored on a mobile device can effectively enhance the capabilities of MVS systems and enable fast and accurate queries in different environments. The image signatures stored in the database on the mobile device must be compact to fit in the device's small memory capacity, capable of fast comparisons across a large database, and robust against large visual distortions. We first develop two methods for efficiently compressing a database constructed from feature histograms. Our methods reduce the database memory usage by 4-5 times without any loss in matching accuracy and possess fast decoding capabilities. Subsequently, we develop a third database representation based on feature residuals that is even more compact. Compressed residuals reduce the database memory usage by 12-14 times, require only a small codebook, and enable image matching directly in the compressed domain. With a compact database stored on a mobile device, we implement an MVS system that can recognize media covers, book spines, outdoor landmarks, artwork, and video frames in less than 1 second per query. Our system uses robust motion analysis on the device to automatically infer user interest, select high-quality query frames, and update the pose of recognized objects for accurate augmentation. We also demonstrate how a continuous stream of compact image signatures enables a low bitrate query expansion onto a remote server. The query expansion improves image matching during the current query and updates the local on-device database to benefit future queries.

Keywords: Electrical Engineering.
Advisor: Girod Bernd primary advisor. Thesis advisor
Gray Robert
Grzeszczuk Radek
Metal insulator multi-layer surface plasmon devices [electronic resource]

Surface plasmon based devices have attracted significant of attention over the last decade with exciting applications like negative refraction, optical cloaking, perfect lenses, and meta-surfaces. They have also enabled highly efficient and compact electro-optical devices bridging the gap between optical (micron) and the electronics (nano) scale devices. At the heart of many of these devices and applications are multi-layer metal insulator structures, where the interaction of surface plasmons at various interfaces unlock these surprising properties. This thesis focuses on the scattering and transmission properties of plasmon modes in metal insulator multilayer structures. In the first part of the thesis, we will describe a theoretical model for standing wave resonances in Metal-Insulator-Metal surface plasmon cavities. These calculations, which are in excellent agreement with full field finite difference simulations, aid in furthering our understanding of plasmon phase pickup on reflection from the cavity terminations. This phase pickup is associated with the near-field energy storage at those terminations, and the imaginary part of the reflection coefficient is shown to be approximately proportional to the stored energy. We then focus on a different, yet related geometry for a surface plasmon antenna, a metal stripe wave guide above a metallic ground plane. Staggered confocal microscopy is used to study the scattering properties of the stripe antenna. CdSe/ZnS quantum dots are sandwiched between the stripe and ground plane. Dual purposing of the stripes as electrical lead and an optical element is illustrated through low temperature quantum confined stark effect measurements. Finite difference calculations of the surface plasmon transmission spectra through the truncated stripe waveguide cavity is shown to be well modeled by a two-path-two-mode coupled cavity model.

Keywords: Materials Science and Engineering.
Advisor: Brongersma Mark L. primary advisor. Thesis advisor
Dionne Jennifer Anne advisor. Thesis advisor
Fan Shanhui
Metal silicide nanoelectromechanical relays for low power applications [electronic resource]

ABSTRACT Scaling down the metal-oxide-semiconductor field effect transistor (MOSFET) has continuously brought lower cost, higher density and increased performance since the 1960s. However, as MOS transistors scaled down, the standby power dissipation increased due to thermodynamically limited finite subthreshold slope, which possibly limits transistors scaling. Thus, novel devices are required to solve the power dissipation issue. Nanoelectromechanical (NEM) relays have attracted attention due to their steep on-off characteristics with zero off-state leakage current, unlike MOSFET relays which show severe deterioration of the subthreshold characteristics with scaling down. However, the dynamic power dissipation of NEM relays is still larger than MOSFET relays due to high actuation voltage. Therefore, scaling down of NEM relays are critical for low power applications. In my dissertation, I will focus on scaling down actuation voltage and improving contact properties of NEM relays. First, laterally actuating NEM relays design and materials selection by COMSOL simulation based structural optimization will be proposed for sub 1V actuation. The electrical test results of fabricated Si NEM relays will be presented compared with COMSOL simulation results, as well. Secondly, in addition to the scaling down, improving contact properties will be discussed since NEM relays physically contact the drain electrode for current flowing. However, Si suffers from oxidation. If NEM relays are oxidized, the relay performance will be degraded due to the deteriorated contact property. There have been many efforts to improve switching contact such as using metal beams or metal sidewall coatings. Metal silicide processes have been widely used in MOS technology due to their low junction leakage and low sheet resistance. To improve the relay contact, metal silicide processes were selected. Moreover, the materials characterization and fabrication process of metal silicide NEM relays will be presented followed by electrical test results including promising sub 1V actuated Nickel silicide NEM relay test results. This dissertation will end by discussing the implications of experimental achievements for low power NEM relays.

Keywords: Electrical Engineering.
Advisor: Nishi Yoshio
Howe Roger Thomas advisor. Thesis advisor
Wong Hon-Sum Philip
The metastasis-associated immune response in pancreatic cancer [electronic resource] : pathogenic role for a discrete dendritic cell population

Presentation with advanced disease and distant recurrence following surgery typify pancreatic ductal adenocarcinoma (PDAC), underscoring the need for new treatments targeting metastasis in this cancer. Because elements of the immune system can both prevent and promote tumor progression, we studied the metastasis-associated immune response in PDAC models. We find that developing metastases are bordered by dense networks of CD11b+ dendritic cells (DC), which derive from monocytes exposed to tumor-released GM-CSF and drive Foxp3+ T regulatory cell (Treg) responses. Leveraging their selective expression of the C-type lectin MGL2, we show that depleting this DC population from metastatic tissues activates cytotoxic lymphocytes, reduces Tregs, and inhibits metastasis development. These DC also uniquely express PD-L2 in the metastatic microenvironment and thereby inhibit CD8 T cell-mediated antitumor immunity. Similar DC accumulate in PDAC tissues from other models and cancer patients, supporting the broad applicability of our findings. These results reveal that a specific DC subset both suppresses CD8 T cells and supports Tregs to create a microenvironment conducive to metastasis in pancreatic cancer. Targeting such immunosuppressive stromal cells represents a novel strategy for preventing the progression of this deadly disease.

Advisor: Engleman Edgar G. primary advisor. Thesis advisor
Contag Christopher H. advisor. Thesis advisor
Giaccia Amato J. advisor. Thesis advisor
Strober Samuel
Methodology for the application of bim-based decision support methods to evaluate sustainability metrics for master plans of a large-scale development [electronic resource]

To achieve successful implementation of a large-scale development, a master plan for a large-scale development must create sufficient alternatives in a structured way and analyze multiple performance metrics, taking into account economic, social, and environmental sustainability in a timely manner. In addition, the master plan must analyze both construction and operation-related metrics over time. However, unstructured decision management and the inability to integrate multiple attributes of the traditional master plan prevent project participants from creating sufficient alternatives in a structured way. In addition, manual mapping and an unintegrated reasoning process prevent the participants from quickly analyzing multiple performance metrics over time. For this study, the CIFE team investigated the existing Virtual Design and Construction (VDC) methods to determine how to overcome the problems. Since the existing VDC methods had several limitations, the CIFE team was required to develop a methodology specific to the master plan of a large-scale development as well as an integrated decision-support system capable of 4D visualization, multiple metrics analysis, and display of the metrics over time. Specifically, the CIFE team, based on the VDC, has developed the Development Strategy Formulation and Evaluation Methodology (DSFEM); it moreover has developed the Development Strategy Simulator (DSS). The DSFEM supports the quick creation of alternative scenarios in a structured way, as well as a quick information search. The DSFEM also supports 4D visualization and analysis over time for multiple metrics. The DSS provides an automatic linking and mapping process that enhances the speed and consistency of the analysis. In addition, an integrated reasoning process enables the DSS to simulate development scenarios, analyze multiple metrics over time, and display the metrics simultaneously and in a timely manner. However, since there still are limitations in both the DSFEM and the DSS, the CIFE team recommends further development of the DSFEM and the DSS.

Keywords: Civil and Environmental Engineering.
Advisor: Fischer Martin
Methods for binary symbolic execution [electronic resource]

Binary symbolic execution systems are built from complicated stacks of unreliable software components, process large program sets, and have few shallow decisions. Failure to accurately symbolically model execution produces infeasible paths which are difficult to debug and ultimately inhibits the development of new system features. This dissertation describes the design and implementation of klee-mc, a novel binary symbolic executor that emphasizes self-checking and bit-equivalence properties. This thesis first presents cross-checking for detecting causes of infeasible paths. Cross-checking compares outputs from similar components for equivalence and reports mismatches at the point of divergence. This approach systematically finds errors throughout the executor stack from binary translation to expression optimization. The second part of this thesis considers the symbolic execution of floating-point code. To support floating-point program instructions, klee-mc emulates floating- point operations with integer-only off-the-shelf soft floating-point libraries. Symbolically executing these libraries generates test cases where soft floating-point implementations and floating-point constraint solvers diverge from hardware results. The third part of this thesis discusses a term rewriting system based on program path derived expression reduction rules. These reduction rules improve symbolic execution performance and are machine verifiable. Additionally, these rules generalize through further processing to optimize larger classes of expressions. Finally, this thesis describes a flexible mechanism for symbolically dispatching memory accesses. klee-mc forwards target program memory accesses to symbolically executed libraries which retrieve and store memory data. These libraries simplify access policy implementation and ease the management of rich analysis metadata.

Advisor: Engler Dawson R. primary advisor. Thesis advisor
Aiken Alexander advisor. Thesis advisor
Mazières David (David Folkman)
Microfabricated Thermionic Electron Emitters

Thermionic energy converters (TECs) convert very high temperature to electricity without any moving parts. Specifically, the heat gives rise to electron emission from one electrode (‘emitter’) to a nearby electrode (‘collector’) and the resulting current can drive a load. To produce a useful current, both the temperature and the work functions of the emitter and collector must be sustainably controlled. Previous work established that the gap between the two electrodes should be in the range of 1 - 10 μm to minimize space charge at larger gaps and excessive heat transfer at smaller gaps. The microfabricated thin-film emitter is thermally isolated from the substrate by a poly-SiC suspension. This thesis describes the redesign of the suspended emitter and its fabrication process. The suspended plate is optimized for vertical emission by eliminating the recessed emitter surface in the previous design. Furthermore, the process includes the etching of apertures in the silicon substrate, so that underside of the suspended plate can be heated by laser illumination. The thermal resistance of the emitter suspension beams is increased by 50% in the new designs. The five-mask fabrication process is in progress in the Stanford Nanofabrication Facility.

Keywords: Stanford Nanofabrication Facility
thermionics
emitter
MEMS
thermionic emission
µTEC
energy converter
Thesis
Advisor: Howe Roger
Microtubule stability mediated by new mammalian STOP family members [electronic resource]

Stable Tubule Only Polypeptides or STOP proteins are a class of microtubule-associated proteins that are unique in that they have been shown to protect microtubules from depolymerization under destabilizing conditions. To date, MAP6 and the related protein MAP6 domain containing 1 (MAP6D1) are the only known mammalian STOP related proteins. However, through a recent screen identifying genes upregulated during ciliogenesis in multiciliated tracheal cells, we have identified two new uncharacterized mammalian MAP6 related proteins, FAM154A and FAM154B. Though MAP6 has not been previously shown to localize to the primary cilium and centrosome, we sought to assess the ability of these new proteins to stabilize microtubules and their potential function at the cilium and centrosome. Proteins related to FAM154A and FAM154B are found in all vertebrates and most organisms containing cilia and centrosomes including drosophila and chlamydomonas. A C. elegans homolog of the protein has been localized to neuronal cilia and mammalian FAM154B, much like MAP6 is expressed in mammalian cortical neurons. Overexpressed FAM154A and FAM154B localize to the centrosome and the primary cilium and overexpressed FAM154A protein and deletion variants stabilize microtubules against cold treatment in RPE1 cells. Endogenous FAM154A and FAM154B localize to centrosomal structures and cilia respectively in multi-ciliated cells. Similar to MAP6, FAM154A and Fam154B also contain repeated motifs in their amino acid sequences, however their protein level similarity to MAP6 is very limited. We have shown that FAM154A is a bona-fide microtubule associated protein via biochemical assays and can interact directly with microtubules and with calcium calmodulin which may modulate its microtubule binding affinity, similar to MAP6. Ongoing work to resolve the molecular structure of these MAP6 related proteins will illuminate their exact mechanism of microtubule stabilization.

Keywords: Molecular and Cellular Physiology.
Advisor: Stearns Tim primary advisor. Thesis advisor
Downing Kenneth (Kenneth H.) advisor. Thesis advisor
Yang Yanmin