VictorJuiz/thesis huggingface dataset:
A pixel-size receiver with integrated subarray beamformer for 3-dimensional photoacoustic imaging [electronic resource]
Keywords: Electrical Engineering.

Photoacoustic imaging is an emerging imaging modality based on light excitation and acoustic sensing, providing valuable diagnostic information through the optical absorption contrast in the object. Due to the same receiving scheme, photoacoustic imaging is often combined with ultrasound imaging to provide both the functional information and the structural information at the same time. Therefore, current photoacoustic imaging setups often reuse the existing ultrasound imaging instruments and therefore suffer from the same limitations as those present in today's ultrasound imaging systems. The current 2-Dimensional (2D) medical ultrasound system is a mature and prevalent technology; however, the development of a 3-Dimensional (3D) system faces substantial challenges due to the large channel count. In a conventional 2D system, each element of a 1-Dimensional (1D) array is directly accessed through a coaxial cable by a main system that processes the signal; however, this approach is not feasible for a 2D array in a 3D system. To address this issue, recent work has proven the viability of flip-chip bonding or direct transducer integration. This shifts the burden to a CMOS substrate, which must be designed within the same pixel pitch and must provide dense signal conditioning and processing to ensure the compatibility of the output channel count with the current cable connections. A common approach for data reduction is to employ subarray beamforming, which applies delay-and-sum (DAS) operations within a group of pixels. Conventional digital beamforming involves high complexity analog-to-digital converter (ADC) design and is difficult to be integrated within the pixel area. Alternatively, prior works apply analog beamforming for its simplicity and, yet, suffer from a combination of issues related to limited delay, coarse delay resolution and low signal-to-noise-ratio (SNR). In this thesis work, we leverage the integration density of fine line CMOS and implement pixel-size receivers with efficient integrated ΔΣ digital subarray beamformer. To simplify the building block, design specification are appropriately tailored to the system requirements derived from imaging simulation results. In addition, we combine functional blocks and utilize inverterbased amplifiers to achieve compact layout in the pixel-size receiver. This thesis work is realized in a receiver chip fabricated in a 28nm CMOS process, demonstrating the first pitch-matched receiver electronics with in-pixel A/D conversion and subarray beamformer.
Plasmonic nanomaterials for biological sensing and biomedical diagnostics [electronic resource]
Keywords: Chemistry.

This thesis describes the development of plasmonic nanomaterials and their spectroscopic applications in biological sensing and clinical diagnostic applications. Gold nanomaterials and their assemblies possess unique localized surface plasmon resonances in the visible and near-infrared (NIR). The enhancement of both the local electric field and NIR fluorescence emission rate via the coupling of scattering nanoparticle plasmon modes can lead to NIR fluorescence enhancement (NIR-FE) under appropriate conditions. Here, those conditions are optimized to yield the NIR-FE effect in the context of immunoassays. A novel solution-phase methodology was developed to prepare plasmonic chip and beads at large scale. Surface chemistry were explored on the so-called "nano-bio interface" for improved biocompatibility, enhanced targeted biomolecule immobilization, and reduced non-specific binding. Multiplexed protein assays are constructed on the nanostructured, plasmonic gold film to enjoy ~ 100-fold fluorescence enhancement, extending the protein/nucleic acid detection dynamic range by ~3 orders of magnitude towards the 1fM regime. Compared to conventional assays on commercial substrates, the plasmonic surface based immunoassays achieve vastly higher signal-to-noise ratios and broader dynamic range, owing to the large fluorescence boost and unique surface chemistry. The methodology developed affords high sensitivity detection of cancer biomarkers, cytokines, antibodies, DNA and microRNA, offering a broad dynamic range applicable to a wide variety of assays. The fast, simple, sensitive, multiplex and low-cost immunoassay based on plasmonic nanomaterials has great potential in both research and clinical settings.
Plotting the Wild West: Action and Description in the Dime Novel Western
Keywords:  Department of English
Stanford University
Department of English
dime novel
western
digital humanities
escape fiction
genre fiction
19th century
nineteenth century literature
Deadwood Dick
Edward L. Wheeler
Beadle and Adams
description
action
plot
Thesis

This thesis investigates the roles of action and description in the dime novel western. Text mining and machine learning tools show that the dime western uses a significant amount of description - much more than standard critical reception would have you believe - and uses it in surprising ways. Closer investigation of a particular kind of descriptive moment shows just how important description can be, for the novel, the happy ending, and the reader's experience of escape.
Pooled sequencing links variation in transcription factor binding and chromatin accessibility to disease risk [electronic resource]
Keywords: Biology.

The second chapter of this thesis focuses on identifying cis-regulatory variants that affect transcription factor (TF) binding. Broadly, we discovered thousands of cis-acting binding quantitative trait loci (bQTLs) that affect TF binding, that CTCF can recruit multiple TFs, and that bQTLs can link genetic variation to 3D-genome architecture and complex disease traits. This chapter uses a pooling-based experimental approach and a custom analysis pipeline to map QTLs that affect TF binding. Chromatin immuno-precipitation followed by high-throughput sequencing (ChIP-seq) in a population of 60-71 genotyped individuals, allows for the genetic mapping of variants affecting TF binding in a systematic way. Those variants that affect binding are likely causal for modifying the binding of the TF to the protein and are therefore, a priori more likely to affect disease phenotypes. Therefore, this framework provides a candidate molecular mechanism by which the variant is acting. The custom pipeline I developed can be used for any pooled data such as ChIP-seq, without any modifications to the pipeline. All scripts and documentation are freely available and can be found here: https://github.com/tehranchi/public . This chapter is from work published in Cell in April 2016. The third chapter uses the same pooling approach and analysis pipeline to investigate a more broad class of QTLs that affect chromatin accessibility (caQTLs). Because these caQTLs mark regions of open chromatin and subsequently actively transcribed regions, they may also contain bQTLs that modify transcription factor binding. Therefore, this approach can be used together with software that can predict TF binding in open regions to obtain a more comprehensive understanding of the binding landscape. Similar to chapter 2, this method focuses on finding cis-regulatory variants that affect chromatin accessibility. Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) was performed in 10 global populations of genotyped individuals to allow for the mapping of variants affecting chromatin accessibility. Briefly, in this chapter we found tens of thousands of caQTLs per population, we fine-map shared caQTLs and used them to identify CTCF as the major motif relevant to open chromatin, and we find that caQTLs can link transcription factor binding to chromatin architecture and complex disease traits. This large-scale project with 1000 individuals in total, would not be tractable in the lab without pooling. Using the pooling approach drastically saves time and cost associated with sequencing and reagents. This chapter corresponds to work from a manuscript currently in prep.
Poor defenses [electronic resource] : the American legal profession and the problem of the "indigent accused" in the twentieth century
Keywords: History.

This dissertation reconstructs the history of public defender offices in the United States and, more generally, the American legal profession's efforts to conceptualize and institutionalize a right to state-provided counsel in criminal cases, from the first public defender experiments beginning in the 1910s through the troubled implementation of the Supreme Court case Gideon v. Wainwright in the 1960s and 1970s. Although journalists and legal scholars have told parts of this story, this dissertation is the first historical study to piece together the story as a whole, using not just published judicial opinions and legal writings, but also a variety of archival materials, including lawyers' personal papers, correspondence, and organizational records. The dissertation argues that the problem of the "indigent accused" was both produced by and rendered ultimately insoluble by two enduring features of American law and governance, each of which has cultural, social, and political dimensions: adversarialism and federalism.
Post-selection inference for models characterized by quadratic constraints [electronic resource]
Keywords: Statistics.

To address the fundamental statistical problem of conducting inference after model selection a recently developed approach conditions on the selected model and uses the corresponding truncated probability laws for inference. Though relatively simple to state, the application of this principle varies in difficulty depending on which model selection procedure is under consideration. This work identifies a general mathematical framework encompassing many model selection procedures. The simple algebra of quadratic constraints allows computation of one-dimensional truncated supports for conditional versions of standard test statistics like the chi-squared and F tests used in regression. Several important examples illustrate the utility of this framework, including forward selection with groups of variables and linear model selection with cross-validation.
Power of graph-based two-sample tests [electronic resource]
Keywords: Statistics.

Testing equality of two multivariate distributions is a classical problem for which many non-parametric tests have been proposed over the years. Most of the popular tests are based either on geometric graphs constructed using inter-point distances between the observations (multivariate generalizations of the Wald-Wolfowitz's runs test) or on multivariate data-depth (generalizations of the Mann-Whitney rank test). These tests are known to be asymptotically normal under the null and consistent against fixed alternatives. In this thesis, a general framework for graph-based tests will be introduced that includes all these tests. The asymptotic efficiency of a general graph-based test can be derived using Le Cam's theory of local asymptotic normality, which provides a theoretical basis for comparing the performances of these tests. As a consequence, it will be shown that tests based on geometric graphs such as the Friedman-Rafsky test (1979), the test based on the $K$-nearest neighbor graph (1984), the minimum matching test of Rosenbaum (2005), among others, have zero asymptotic (Pitman) efficiency against $O(N^{-\frac{1}{2}})$ alternatives. On the other hand, the tests based on multivariate depth functions (the Liu-Singh rank sum statistic (1993)), which includes the Tukey depth (1975) and the projection depth (2003), have non-zero asymptotic efficiency. Finally, the limiting normal distribution of tests based on stabilizing random geometric graphs will be derived in the Poissonized setting. This can be used to compute the power of such tests against local alternatives, which validates the various applications of these tests and provides a way to compare between tests with zero Pitman efficiency.
A practical implementation of the modulated wideband converter compressive sensing receiver architecture [electronic resource]
Keywords: Electrical Engineering.

Cognitive radio systems promise to alleviate the shortage of wireless bandwidth by sensing the entire spectrum and operating in the underutilized whitespace. Prototypes based on the Modulated Wideband Converter (MWC) compressive sensing architecture have demonstrated both fast spectrum sensing and receiver flexibility. In this thesis, we demonstrate a MWC receiver capable of sensing four 1.4 MHz channels between 0 and 900 MHz that is robust to interference and meets the LTE specifications for both sensitivity and maximum allowable input power. The MWC quickly determines the spectral content of the entire input band by multiplying it with a spectrally diverse mixing signal which guarantees that every input channel is represented in measurements taken at baseband. While these spectrally diverse mixing signals are necessary for detection, they provide no blocker rejection, provide a very large effective noise bandwidth, and thus represent the worst-case mixing signal once the input spectrum is characterized. Therefore, in this thesis we introduce a separation between the detection and reception modes of the MWC. Once the detection mode establishes the signal and blocker band locations, we reconfigure the receiver to directly target the desired signals while actively nulling a single strong blocker. In order to null a blocker band, we introduce two independent techniques. In the first sequence-based technique, we develop an algorithm to modify targeted digital mixing sequences so that they additionally null an undesired harmonic. In the second delay-based technique we generalize a technique for harmonic cancellation commonly applied in power inverters. By finely controlling the relative delay between two parallel mixing paths, we are able cancel any single mixer harmonic in their sum, thus preventing a strong blocker in the corresponding band from interfering with the baseband measurements. We design, build, and test an integrated mixer prototype that demonstrates these two rejection techniques and allows us to compare the MWC receiver architecture against recently published alternatives. Our prototype achieves 50.2 dB of sequence-based rejection, 59.3 dB of delay-based rejection, and 62.8 dB of rejection when both techniques are applied to the same blocker. Likewise, the mixer demonstrates a 64.8 dBm IIP2, a 14.3 dBm IIP3, and a 31.5 dB noise figure while consuming 26.6 mW of signal-path power per branch. These performance parameters are in line with recently published harmonic rejection mixers. Additionally, when coupled to a hypothetical LNA that provides 25 dB of gain, 2.5 dB of noise figure, and a -10 dBm IIP3, we calculate a receiver sensitivity of -96.1 dBm and 10 dB of SNDR for up to -25 dBm of input power for the MWC receiver. We thus demonstrate that the MWC is competitive with traditional wideband receivers, while its additional flexibility makes it particularly attractive for cognitive radio systems.
Predicting course completion in massive open online courses [electronic resource]
Keywords: Electrical Engineering.

Between 2012 and 2016, millions of learners have enrolled in massive open online courses (MOOCs). Survey data show that most learners intended to complete their courses, but analysis of the course data shows that only a small fraction of them complete the courses. Educators are trying to support learners before they drop out, but this requires early prediction of who will complete the course and who will not. This thesis presents three techniques for predicting course completion in MOOCs based on data from three different sources: learner demographics, learner engagement with course materials, and learner interactions in course videos. The thesis shows that engagement data provide the highest prediction performance among the three data types, and that prediction performance improves the later in the course the prediction is performed. The results show that the prediction models in this thesis are a step towards in-course support of learners at risk of non-completion.
Predictive ecosystem service valuation model for stakeholders in the private-sector [electronic resource]
Keywords: Civil and Environmental Engineering.

As land development changes our built environment, natural resources are being degraded and depleted, with little knowledge of the lasting impacts. A technique to quantify the economic value of ecosystem services in a predictive method would be useful. For corporations to be more responsible, a clear business case in valuing natural systems is needed. Ecologists define the concepts of ecosystem services as the benefits that humans derive from the environment. Currently, there are no U.S. governing accounting standards for valuing ecosystem services. To determine a market price for natural capital and increasing land value of capital assets for preservation, I propose a Predictive Ecosystem Service Valuation Model. The model will integrate work from biogeochemistry with economic valuation theory. Validation of this innovative model will quantify and measure the coupling of nutrients with a valuation to assist in the operational decision-making process for corporate stakeholders.
Previous selves [electronic resource] : body and narrative in Aelius Aristides' hieroi logoi and Apuleius' metamorphoses
Keywords: Classics.

Aelius Aristides' Hieroi Logoi and Apuleius' Metamorphoses stage prolonged encounters with the failure or refusal of one's own body to function in its capacity as a vehicle for self-presentation -- an especially important function for orators of the second century CE. Both texts explore the degree to which language can remake the narrator's fragmented world. Whereas Aristides' Hieroi Logoi contribute to the orator's healing process, Apuleius' Metamorphoses uses the imagined animal body to demonstrate the elusive nature of constituting a whole self. Throughout his Hieroi Logoi, Aristides employs metaphors to solicit his audience's participation in reconfiguring his relationship to his body and his god. Apuleius' Metamorphoses, on the other hand, dramatizes a paradox: the protagonist, Lucius, achieves his goal of literary memorialization in the form of the book we hold, and yet the self that is on display is ultimately lost to the reader.
Principles of intra- and inter-species cis-regulatory variation in the primate neural crest [electronic resource]
Keywords: Developmental Biology.

Cis-regulatory changes play a central role in normal phenotypic variation within a species as well as in morphological divergence, yet the regulatory principles underlying emergence and modulation of human traits remain poorly understood. As part of my PhD work, I have used epigenomic profiling to annotate and explore the molecular effects of enhancer mutations using in vitro-derived neural crest cells. First, by exploiting high-frequency polymorphisms in human cell lines, we explored how mutations can cooperatively affect binding of key neural crest transcription factors at specific human enhancers. We then extended this analysis across species, using human and chimpanzee cranial neural crest cells to systematically and quantitatively annotate divergence of craniofacial cis-regulatory landscapes genome-wide. We found that epigenomic divergence is often attributable to genetic variation within TF motifs at orthologous enhancers, with a novel motif being most predictive of activity biases. We further explored the properties of this cis-regulatory change, revealing the role of particular retroelements, uncovering broad clusters of species-biased enhancers near genes associated with human facial variation, and demonstrating that cis-regulatory divergence is linked to quantitative expression differences of crucial neural crest regulators. This work provides a wealth of candidates for future studies on human craniofacial development and evolution, and demonstrates the value of "cellular anthropology, " a strategy of using in-vitro-derived embryonic cell types to elucidate both fundamental and evolving mechanisms underlying morphological variation in higher primates.
Priority effects in recruitment to resources between the invasive Argentine ant (Linepithema humile) and the native winter ant (Prenolepis imparis)
Keywords:  Department of Biology
Biology
Behavioral Ecology
Invasive Species
Thesis

The Argentine ant (Linepithema humile), native to South America, has invaded areas with Mediterranean climates worldwide, displacing many native ant species. In northern California, the Argentine ant competes for the use of scale insects as a food resource with the native winter ant (Prenolepis imparis). While previous research shows that the Argentine ant recruits nestmate foragers to a food source faster than does the winter ant, the winter ant has not been completely displaced. Earlier studies show that the winter ant's chemical defenses and differences in seasonal activity may contribute to their continued coexistence. However, the behavioral mechanisms of competition for a food source have not been determined. To investigate this, we tested the effects of priority on the outcome of recruitment to a bait to determine the winner of varying trials of food source competition. In bait trials, we varied the sequence at which ants of each species arrived at the bait and the number of ants first at the bait. The results show that the effects of the order of discovery of a food source on the outcome of competition significantly determined the victor for both species. Priority by winter ants had a stronger effect on Argentine ants than the reverse. This may help to explain the continued coexistence of the two ant species, despite the recruiting success of the invasive Argentine ant. These observations, along with other studies of changing distributions of the two species in the sympatric range, suggest that the Argentine ant will not completely displace the winter ant within northern California.
A probabilistic model of memory acceses for efficient CPU caching [electronic resource]
Keywords: Electrical Engineering.

The memory hierarchy in a modern processor -- the main memory and different cache levels, consumes about half of the full system energy. We reduce the memory hierarchy energy by three methods: a) reducing main memory accesses by building better last level cache replacement policies, b) reducing wire energy in LLCs by doing intelligent placement and movement of data, and, c) reducing L1 access energy by performing accurate assignment of cache ways to memory access instructions. To design these policies, we propose a new model for program access patterns: the IID Sequence Model (ISM), which uses the reuse distance distributions of different cache lines. We show that a) our proposed Probabilistic Replacement Policy (PRP) reduces LLC misses by 6.6% over state-of-the-art replacement policies such as SHiP [91], b) Sub-Level Insertion Policy (SLIP), which places and moves cache lines according to their reuse distance distribution, reduces L2 energy by 35% and L3 energy by 22%, and, c) Cache Way Assignment (CWA) reduces L1D cache energy consumption by 14% by reducing way mispredictions.