VictorJuiz/thesis huggingface dataset:
Precise and automatic verification of container-manipulating programs [electronic resource]

A key challenge for program verification systems is precise reasoning about the contents of unbounded data structures. A particularly important and widely-used family of data structures is containers, which support operations for inserting, retrieving, removing, and iterating over sets of elements. Typical examples of containers include arrays, lists, vectors, maps, sets, deques, queues, etc. In this thesis, we propose a novel static analysis technique that allows precise reasoning for container-manipulating programs. We describe a symbolic heap abstraction which integrates reasoning about containers directly into a heap analysis, allowing the technique to precisely track heap objects as they flow in and out of containers. The proposed analysis is fully automatic and practical, scaling to real programs of up to 100,000 lines of code. Furthermore, the abstraction we propose can reason about key-value correlations and supports arbitrary nestings of container data structures. More specifically, in this thesis, we first describe a static analysis for a language with only the most basic kind of container, namely arrays. We then refine this basic analysis to obtain a more precise heap abstraction, which is always guaranteed to be relational. We then generalize the framework used for reasoning about arrays to general-purpose containers, which may not expose a notion of position. The symbolic heap abstraction we describe reduces a large part of the difficulty of reasoning about containers to linear inequalities over integers. Thus, the efficiency of our static analysis is contingent upon practical techniques for solving systems of linear integer inequalities. Another contribution of this thesis is a new and practical algorithm called Cuts-from-Proofs for solving linear inequalities over integers.

Advisor: Aiken Alexander primary advisor. Thesis advisor
Dill David L. advisor. Thesis advisor
Sagiv Mooly
Precision cosmology with galaxy cluster surveys [electronic resource]

The acceleration of the universe, which is often attributed to "dark energy, " has posed one of the main challenges to fundamental physics. Galaxy clusters provide one of the most sensitive probes of dark energy because their abundance reflects the growth rate of large-scale structure and the expansion rate of the universe. Several large galaxy cluster surveys will soon provide tremendous statistical power to constrain the properties of dark energy; however, the constraining power of these surveys will be determined by how well systematic errors are controlled. Of these systematic errors, the dominant one comes from inferring cluster masses using observable signals of clusters, the so-called "observable--mass distribution." This thesis focuses on extracting dark energy information from forthcoming large galaxy cluster surveys, including how we maximize the cosmological information, how we control important systematics, and how precisely we need to calibrate theoretical models. We study how multi-wavelength follow-up observations can improve cluster mass calibration in optical surveys. We also investigate the impact of theoretical uncertainties in calibrating the spatial distributions of galaxy clusters on dark energy constraints. In addition, we explore how the formation history of galaxy clusters impacts the self-calibration of cluster mass. In addition, we use N-body simulations to develop a new statistical sample of cluster-size halos in order to further understand the observable--mass distribution. We study the completeness of subhalos in our cluster sample by comparing them with the satellite galaxies in the Sloan Digital Sky Survey. We also study how subhalo selections impact the inferred correlation between formation time and optical mass tracers, including cluster richness and velocity dispersion.

Keywords: Physics
Advisor: Allen Steven W. (Steven Ward) primary advisor. Thesis advisor
Wechsler Risa H. (Risa Heyrman) primary advisor. Thesis advisor
Blandford Roger D. advisor. Thesis advisor
Church Sarah Elizabeth advisor. Thesis advisor
Prediction and novelty in the human medial temporal lobe [electronic resource]

Prediction is at the core of memory. A memory system stores information about the past in service of preparation for the future, and thus the act of memory retrieval may be viewed as an act of prediction about upcoming events. Converging evidence from animal and compuational models suggests that within the hippocampus, stored memories are compared to current sensory input in order to compute novelty -- when expectation deviates from actual outcome. Specifically, hippocampal subfield CA1 is thought to support this computation of mismatch between past and present. Detection of novelty in turn is hypothesized to modulate encoding processes, providing a mechanism for gating the entry of information into long-term memory. Using high-resolution functional MRI, I examined hippocampal subfield (CA1, CA23/DG[dentate gyrus], subiculum) and medial temporal lobe (MTL: entorhinal, perirhinal, parahippocampal) cortical activation during associative retrieval and associative mismatches in humans. In Experiment 1, subjects performed cued image retrieval and made explicit comparisons of memory to matching or mismatching decision probes. Activity in multiple hippocampal and MTL cortical subregions tracked associative retrieval success, whereas activity in CA1 and perirhinal cortex tracked the presence of associative mismatches. In Experiment 2, subjects viewed sequences of images while performing an incidental task (1-back target detection). In CA1, CA23/DG, and perirhinal cortex, activation was greater when image sequences were presented in rearranged order (mismatch with memory) compared to repeated order (match with memory). In CA1 only, this mismatch enhancement was significantly modulated by prediction strength: the mismatch enhancement was greater when predictions were stronger. In a separate behavioral experiment, recognition memory was found to be better for images that had appeared in rearranged-order (mismatch) than repeated-order (match) sequences, supporting the notion that mismatch detection leads to encoding upregulation. In Experiment 3, subjects viewed sequences of images containing either temporal predicitive information only or combined temporal and spatial predictive information. When novel images were embedded within previously viewed sequences, activation in CA1 was significantly related to subsequent memory for items which had violated predictions (remembered > forgotten), with this enhancement modulated by the amount of predictive information. Together, these data are consistent with the hypothesis that CA1 acts as a comparator, detecting when memory for the past and sensory input in the present diverge. More broadly, the current studies reveal the dynamics of the human hippocampus and MTL cortices during the acts of prediction, novelty detection, and memory encoding -- a continuous cycle of events that enable preparation for the future based on past experience.

Keywords: Psychology
Advisor: Wagner Anthony David primary advisor. Thesis advisor
McClelland James L. advisor. Thesis advisor
McClure Samuel M. advisor. Thesis advisor
Pre-leukemic hematopoietic stem cells are clonal antecedents of human acute myeloid leukemia [electronic resource]

Cancer is a clonal disease in which multiple mutations are sequentially acquired. Little is known about the genetics of founding and early mutations in most forms of cancer, including acute myeloid leukemia (AML), because pre-cancerous cells are generally clinically silent and are outcompeted by their malignant descendants. We report the identification of a panel of cell surface markers that enable the prospective separation of rare, residual hematopoietic stem cells (HSC) from human AML patient samples. Subsequently, we used targeted exome sequencing to identify cancer-associated mutations in five leukemia genomes and, in two of these cases, identified a subset of mutations in patient-matched HSC. Through the genetic investigation of pre-leukemic HSC, we identify a clonal progression of multiple mutations in AML with relevance to design of targeted therapies. The existence of such pre-leukemic HSC reveals the clonal evolution of AML with HSC as the AML cell of origin, and identifies a potential mechanism behind relapse.

Advisor: Majeti Ravindra
Weissman Irving L. primary advisor. Thesis advisor
Clarke Michael F.
Levy Ronald
Mitchell Beverly S. advisor. Thesis advisor
Proteomic single-synapse analysis with array tomography [electronic resource]

Array tomography (AT) is a high-resolution proteomic imaging method that exploits a combination of light and EM techniques to resolve fine details at the synapse level across large fields of view spanning entire circuits. Much of my graduate work has centered on helping to shape AT into an imaging method fit for rigorous use, by developing computational algorithms which take advantage of AT's particular qualities to automate its operation. Among them are: a mapping tool for microscopy software to automate the imaging of AT's unique section layout; Multistackreg, an alignment plugin which is capable of registering multiple imaging sessions on the same piece of tissue; a cross-correlation algorithm for fluorescent channel validation; the synaptogram, a tool for visualizing synapse-scale high-dimensional proteomic molecular complexes; and an active learning paradigm for large-scale synapse quantification.

Advisor: Smith Stephen J.
Hestrin Shaul
Lewis Richard (Richard Sheridan)
Luo Liqun
Public matters in communication policymaking [electronic resource] : the media ownership debate, 2002-2007

This dissertation critiques the prevailing logics that shape public participation in rulemaking at the Federal Communications Commission (FCC). Influenced by deliberative democratic theory, it argues that an FCC which values public acceptance of its actions shares a responsibility alongside civil society actors and media institutions to welcome, speak with, and answer to publics in communication policy debates. It develops a system of participation that relies on support structures both inside and outside the agency which prioritize inclusive public discussions and which facilitate translation between publics, policymakers, and other stakeholders in rulemaking debate. Using the above framework, which I refer to as a "deliberative model of participation, " this inquiry turns to the case of the media ownership debate. Between the years 2002 and 2007, the FCC conducted two landmark proceedings concerning regulations that limit concentration of ownership in broadcast media. Using interview materials with commissioners and permanent staff as well as FCC, press, and civil society documents, this analysis shows that the complementary efforts of minority leadership at the agency and media reform groups gave new visibility to publics in a rulemaking environment that typically constrains citizen involvement. They engaged in translational activities that educated publics and policymakers, summarized public opposition to media concentration, and amplified public concern to policymakers at the FCC. Though ownership rules were relaxed, the FCC was compelled to explain its decisions and its manner of interactions with publics and to shift its participatory strategies. The analysis suggests that translation is both a process and an outcome and that a fairer, more just framework for participation requires a deeper commitment to citizen-centered debate. The agency needs to commit to new practices that privilege citizens' collective consideration of policy problems and solutions. In line with its discretionary power to enhance notice-and-comment procedures, the agency can—and must—offer a more inclusive environment that supports the communicative actions of publics.

Keywords: Communication
Advisor: Glasser Theodore Lewis
Bailenson Jeremy advisor. Thesis advisor
Ho Daniel E. advisor. Thesis advisor
Turner Fred advisor. Thesis advisor
Punishers become more deviant [electronic resource]

Five studies demonstrate that people who punish are more likely to indicate that they will behave in a deviant manner, relative to non-punishers. Study 1 showed that being the agent of norm enforcement in an economic game resulted in increased deviance intentions. Study 2 provided evidence that the effects on deviant behavior are unique to punishing by ruling out possibilities that merely condemning the transgression, or witnessing another person punish, would lead to deviance. Additionally, an increased sense of power did not mediate the relationship between punishment and deviance. Studies 3 and 4 showed that punishers reported increased moral self-regard, relative to non-punishers and those who condemned. In Study 5, participants who were randomly assigned to sanction a thief by assigning a fair amount of punishment reported increased deviance relative to participants who over-punished or did not punish.

Keywords: Business.
Advisor: Miller Dale T. primary advisor. Thesis advisor
Monin Benoît
Mullen Elizabeth primary advisor. Thesis advisor
Punishers become more deviant [electronic resource]

Five studies demonstrate that people who punish are more likely to indicate that they will behave in a deviant manner, relative to non-punishers. Study 1 showed that being the agent of norm enforcement in an economic game resulted in increased deviance intentions. Study 2 provided evidence that the effects on deviant behavior are unique to punishing by ruling out possibilities that merely condemning the transgression, or witnessing another person punish, would lead to deviance. Additionally, an increased sense of power did not mediate the relationship between punishment and deviance. Studies 3 and 4 showed that punishers reported increased moral self-regard, relative to non-punishers and those who condemned. In Study 5, participants who were randomly assigned to sanction a thief by assigning a fair amount of punishment reported increased deviance relative to participants who over-punished or did not punish.

Advisor: Miller Dale T. primary advisor. Thesis advisor
Monin Benoît
Mullen Elizabeth primary advisor. Thesis advisor
Purifiation and characterization of the in vivo behvoirs of natural killer cell progenitors and hematopoietic stem cells [electronic resource]

Hematopoietic stem cells (HSC) are at the top of hematopoietic hierarchy and give rise to functional effector cells through a succession of increasingly committed downstream progenitor cells. Based upon data obtained from transplantation and in vitro culture experiments we have constructed a model of hematopoietic development by which small numbers of HSCs generate large numbers of mature effector cells through the successive amplification of transiently proliferating progenitor cells downstream of HSCs. HSCs have been extensively characterized based on their cell surface phenotype and functional activities during transplantation assays. Here we describe a marker, CD11a, which allows for the enhanced purification of murine HSCs. We have shown that upregulation of CD11a on HSCs denotes the loss of self-renewal potential, and that CD11a-Slam+CD34-c-kit+Sca1+Lin- are the true HSC. Natural killer (NK) cells develop in the bone marrow and are known to gradually acquire the ability to eliminate infected and malignant cells, yet the cellular stages of NK lineage commitment and maturation are incompletely understood. Using 12-color flow cytometry, we identified a novel NK-committed progenitor (pre-NKP) that is a developmental intermediate between the upstream common lymphoid progenitor (CLP) and the downstream NKP, previously assumed to represent the first stage of NK lineage commitment. Taken together, our data provide a high-resolution in vivo analysis of the earliest steps of NK cell commitment and maturation.

Advisor: Weissman Irving L. primary advisor. Thesis advisor
Negrin Robert S. advisor. Thesis advisor
Shizuru Judith Anne advisor. Thesis advisor
Sunwoo John B. advisor. Thesis advisor
A quantitative analysis of the structure and dynamics of the bacterial chromosome [electronic resource]

Replication and segregation of the chromosome in the bacterium Caulobacter crescentus takes place simultaneously. Although it is known that each arm of the circular chromosome is on average linearly positioned along the cell length, the detailed configuration of the DNA in the cell is not well understood. Furthermore, in replicating bacterial cells, the centromere is segregated by a ParA-dependent mechanism and anchored at the pole, but the segregation mechanism for the rest of the chromosome is not known. To address these questions, I tracked the position and motion of multiple chromosomal loci both in non-replicating and replicating cells. By characterizing compaction of the DNA in non-replicating cells, I show that the DNA in the Caulobacter cells has the mean end-to-end distance that scale as (contour length)0.22, which suggests that compaction of the bacterial DNA is primarily driven by supercoiling. Analysis of the replication/segregation dynamics revealed that Caulobacter chromosome segregation is bimodal: Centromere-proximal DNA is segregated with the centromere at a slow pace whereas the rest of the DNA is segregated much faster. The dynamics of the centromere-distal DNA are consistent with a model where continuous compaction pulls the DNA toward the pole. The results provide a new perspective on the physical configuration of the non-replicating DNA and on the movement and compaction of newly replicated DNA immediately after replication and during its transport from the replisome to the cell poles.

Keywords: Physics
Advisor: Doniach S. primary advisor. Thesis advisor
McAdams Harley primary advisor. Thesis advisor
Shapiro Lucy advisor. Thesis advisor
Quantum coherence and interactions in quantum dots [electronic resource]

The behavior of electrons in solid state systems is determined by the interaction of their charge and spin degrees of freedom with each other and with the degrees of freedom of their environment. Whether the interactions manifest themselves by modifying some of the system's properties such as the effective mass in the Fermi liquid picture, or more directly by suppressing transport in the Coulomb blockade model, depends on the details and complexity of the system. This thesis investigates two cases: the Fermi liquid behavior in a system with exchange interactions (the spin 1/2 Kondo model) and effect of Coulomb interactions on the phase coherence of electrons in a quantum dot with single mode leads. The first experiment tests the Fermi liquid theory prediction of a quadratic power law dependence of the electron scattering rate on energy in the non-equilibrium regime. We measure transport though a lateral GaAs/AlGaAs quantum dot that acts as an artificial magnetic impurity coupled to a single reservoir and find that the low energy conductance obeys universal scaling with temperature and bias with a quadratic exponent as expected for the single channel Kondo state. This single particle picture fails when a second independent channel is added and the quantum correlations lead to non-Fermi liquid behavior. To understand how the short range Coulomb repulsion affects phase coherence we measure the quantum correction due to the weak localization of electrons in a quantum dot coupled to a reservoir via perfectly transmitting quantum point contacts. We extract the dephasing time and observe that it continues to increase down to the lowest temperatures, in accordance with the predictions from Fermi liquid theory and in contradiction with previous experiments in zero-dimensional structures. When the phase coherence time of the electrons becomes large enough, we observe the effects of the long range Coulomb repulsion as Coulomb blockade emerges. This was previously assumed to be characteristic of transport through quantum dots with tunneling quantum point contacts (QPCs). We show that despite the fully open QPCs of our device, the coherent backscattering of electrons at zero magnetic field is responsible for Coulomb charging effects and estimate that the residual charge quantization at the lowest temperature is 1/3 electron charge via charge sensing measurements.

Keywords: Applied Physics
Advisor: Fisher Ian R. (Ian Randal) primary advisor. Thesis advisor
Goldhaber-Gordon David
Kivelson Steven advisor. Thesis advisor
Quantum confinement structures for efficient energy conversion [electronic resource]

Quantum confinement (QC) structures present several opportunities for developing next-generation energy conversion devices, due to the ability to tune the electronic and optical properties of a material as a function of size and shape. In the case of solar cells, the ability to tune the bandgap and modify the kinetics of charge relaxation in QC structures suggests the ability to improve broadband solar absorption, and potentially develop devices in excess of the traditional ~32% efficiency limitation of single bandgap devices. However, the ability to fabricate QC solar cells presents several challenges due to the necessity to precisely control feature size and separation, as well as the inherent challenge to extract excited charge carriers from these features before significant recombination losses occur. In this thesis, atomic layer deposition (ALD) was studied as an enabling technology for fabricating 3-D nanostructured QC solar cell architectures. In the first part, the ability to fabricate PbS quantum wells by ALD was developed, and QC effects on the bandgap were demonstrated as a function of film thickness using scanning tunneling spectroscopy (STS). In order to pattern the ALD PbS films in the lateral direction, area-selective ALD of PbS was developed at the micro- and nanoscale using patterned self-assembled monolayers (SAMs). Additionally, a new technique to directly deposit quantum dots (QDs) was developed by utilizing nucleation-limited growth during the initial ALD cycles. The evolution of the size and shape of these dots was studied using plane view transmission electron microscopy (TEM). In the second part, 3-D QC solar cell architectures were developed by ALD. ALD of Al-doped ZnO (AZO) was studied as a transparent electrode material, and the deposition conditions of these films were optimized with respect to conductivity. A standardized MEMS fabrication process was developed to fabricate p-Si/n-ZnO diodes by ALD to aid in charge extraction from QC layers. A fully integrated QD solar cell with PbS QDs integrated into a p-Si/n-ZnO diode with an AZO top electrode was demonstrated. Additionally, the fabrication of 3-D nanostructured templates, including conducting nanowires and etched quartz substrates was studied in order to aid in light scattering and minimize the required thickness of the QD layer, thereby minimizing the diffusion length required for charge extraction. To demonstrate the power of the ALD technique, a single layer of PbS QDs was uniformly deposited on the surface of Si nanowires, and photoluminescence measurements were performed to demonstrate the ability to modify their optical properties through QC effects.

Keywords: Mechanical Engineering
Advisor: Prinz F. B. primary advisor. Thesis advisor
Brongersma Mark L. advisor. Thesis advisor
Kenny Thomas William advisor. Thesis advisor