VictorJuiz/thesis huggingface dataset:
Characterization of hydrogen-terminated diamond devices for extreme environment applications

This thesis presents diamond as a promising platform for devices and electronics for harsh environment operation. However, the theme of this work is not to present wildly innovative device architectures, but rather, to gain an understanding of the properties that substantiate the promise of new materials for devices. Namely, for the case of diamond, the experimental electrical performance is thus far limited. To realize diamond's full potential, it is therefore essential to illuminate the fundamental barriers that inhibit its performance. This thesis is dedicated to this understanding. In the ﬁrst part of this thesis, a fabrication process for hydrogen-terminated diamond (H:diamond) devices is presented. Moreover, a theoretical model is developed to understand the hole mobility of the p-type conductive channel on the diamond surface (2DHG). The model is used to ﬁt to experimental measurements to demonstrate that multiple mobility-limiting mechanisms exist for the diamond surface conductive channel, and one of these mechanisms are widely unaccounted for in literature. Next, H:diamond-based ﬁeld eﬀect transistor operation is demonstrated. The transfer characteristics exhibit high ON/OFF ratios and good sub-threshold slopes. Further, the oxide quality is robust, as shown by the capacitance measurements, as well as the high-temperature Hall-eﬀect measurements up to 700 K. The resistance to radiation was demonstrated by irradiating the diamond substrates to 2 MeV proton irradiation at multiple ﬂuences. It was shown that negative charge build-up is generated in the oxide, which degrades the mobility and enhances the 2DHG accumulation (thus increasing the sheet density). In order to illuminate all of the mobility-limiting mechanisms as induced via irradiation, unpassivated H:diamond samples were also irradiated. It was shown that the conductivity also decreased. It is reasoned that lattice damage is unlikely the cause of this degradation. Rather, the degradation is likely caused by the proton-induced ionization, which can dissociate the C-H surface dipoles. These results further support the conclusion that surface disorder related to the C-H dipoles contributes signiﬁcantly to the degraded 2DHG mobility. Finally, this thesis contributes to a well-known phenomenon related to the irradiation-induced annealing. This is in the context of 3C-silicon carbide (SiC), which, also has a diamond crystal structure. When defective 3C-SiC is irradiated with high-energy ions, annealing is observed. Similar eﬀects are observed in other polytypes, such as 4H-SiC. It is demonstrated that when such ionization events occur in the vicinity of high electric ﬁelds, the annealing eﬀect can be en-hanced. This provides avenues for applications requiring low-temperature and localized annealing solutions

Keywords: Electrical Engineering.
Advisor: Senesky Debbie
Chowdhury Srabanti 
Saraswat Krishna
Characterization of LSST camera sensor effects during integration and testing

Integration and testing of the Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) Camera is currently being performed at the SLAC National Accelerator Laboratory. Once completed, the LSST Camera will be used to perform one of the largest wide-field astronomical surveys in the optical, generate an unprecedented amount of data, and allow for cosmological analyses with great statistical power. In order to realize the full benefit of the increase in statistical precision that the LSST aims to accomplish, it is necessary to have a deep understanding of systematic effects that may negatively impact the accuracy of the survey science results. One particular type of systematic effects are those resulting from aspects or behavior of the charge-coupled devices (CCDs) used for digital imaging. The LSST Camera focal plane is heavily segmented, consisting of 189 CCDs arranged into 21 stand-alone Raft Tower Modules (RTMs), each of which must be carefully verified and tested to ensure that they adhere to the requirements of the project. In this thesis I present the results of electro-optical testing of the focal plane electronic crosstalk, astrometric and shape distortions due to static pixel area variations, and deferred charge effects

Keywords: Physics.
Advisor: Roodman Aaron J. (Aaron Jay)
Burchat P. (Patricia)
Macintosh Bruce
Characterization of the human uterus using single cell RNAseq for mechanistic elucidation and clinical tool development

Single cell RNAseq (scRNAseq) has been available to general laboratories for only a few years. The technology, however, has revolutionized our understanding of cellular hierarchies of primary tissues and advanced the completeness and accuracy of human transcriptomics. As one of the first generation researchers who were equipped with this technology, I spent my PhD evaluating methods to be incorporated into the scRNAseq pipeline as well as leveraging the resolution of scRNAseq to better understand biology and to create diagnostic and therapeutic tools for clinics. In the enclosing dissertation, you will first find my evaluation of a novel strategy for preserving primary tissue specimen, as we came to realize the importance of this seemingly trivial step in the entire scRNAseq pipeline for high fidelity and high quality data procurement. You will then see that I settled in the niche of female reproductive health to explore and utilize the analytical potential of scRNAseq, as I started to become aware of the unique complexity of the human uterus - which is unlike any other human organs and unparalleled by most animal models. I was able to delve deep into two processes in the human uterus, one physiologically normal (menstrual cycle) and the other pathological (uterine fibroids). In one project, I profiled the transcriptomic dynamics of the human endometrium across an entire menstrual cycle at single cell resolution, and captured the unique transcriptomic characteristics of the window of implantation (WOI), which points towards a simpler and more accurate diagnostics of WOI for embryo transfer in in vitro fertilization. In another project, I dissected the cellular hierarchy of uterine fibroids, a benign yet prevalent uterine tumor that inflicts women worldwide in their reproductive age with surgeries being the current gold standard for treatments. By comparing the cellular hierarchies of tumor and tumor-free tissues, I identified candidate cell states and markers that are unique to the tumor, which can be used to eliminate the tumor in a more direct and targeted manner. Through my PhD, I came to realize and was often challenged by the striking contrast between the importance of female reproductive health and our lack of understanding of the human uterus with molecular details, due to reasons including but not limited to cultural taboos, lack of scientific attentions, technological limitations, and a lack of systematic theoretical unification as well as stratification. The studies herein are therefore an enthusiastic, sincere and early attempt to facilitate the advance of this research domain in these various directions

Keywords: Bioengineering.
Advisor: Quake Stephen Ronald 
Camarillo David 
Wang Bo (Researcher in bioengineering)
Characterization of the long noncoding RNA DINO in the DNA damage response and JUN in cutaneous scarring

Long noncoding RNAs (lncRNAs) are emerging as important regulatory elements involved at different levels of regulation. Several lncRNAs have been identified as part of the p53 network. The p53-dependent response is critical for normal cell proliferation and suppression of cancer. It is known that sustained DNA damage stabilizes p53, and p53-responsive genes are activated, leading to cell cycle arrest, apoptosis, or senescence. However, the specificity of this response needs further study. It is thought this response elicits a signal amplification mechanism that needs a p53 co-activator because fine-tuning the choice and amplitude of p53 target genes is a critical aspect. In this dissertation, I described the characterization of the novel, long noncoding RNA DINO as a key component of p53-dependent DNA damage response. Chapter 2 focuses on identifying the role of DINO in guiding organismal response to DNA damage as part of the p53-dependent response. Chapter 3 focuses on investigating Dino's contribution to p53-dependent transcriptional heterogeneity in response to DNA damage at the single-cell level. Chapter 4 describes the work done to study the transcription factor JUN as a critical regulator of skin scarring through the regulation of CD36

Keywords: Genetics.
Advisor: Chang Howard Y. (Howard Yuan-Hoa)
Attardi Laura 
Fire Andrew Zachary 
Greenleaf William James
Characterizing the Development of Relational Reasoning in India

English speakers in the U.S. show a puzzling decline in relational reasoning between 18 months and 3 years old, whereas Mandarin speakers in China show steady improvement over this period. What causes this variation in early relational reasoning, and how general are these two patterns? This project seeks to inform these questions by characterizing the development of relational reasoning in a novel cultural context. In order to understand the mechanisms through which variation in the learning environment influences the development of relational reasoning, we examine early relational reasoning in Punjabi speakers in India, who share some cultural and linguistic elements of their experience with children in China and the U.S. In Experiment 1, we find that 3-year-olds in India exhibit numerically intermediate performance that does not differ significantly from either their high performing peers in China or the poor performance observed in the U.S. at this age. Experiments 2a and 2b test for baseline differences in bias toward relational or object-based solutions, and cultural factors that may influence the development of relational reasoning, and again find mixed results. Preliminary data from 3-4-year-olds in India suggest that they exhibit a preference for object-based solutions over relational solutions in an ambiguous match-to-sample task, resembling the performance of 3-year-olds in the U.S. but not those in China. However, children in India tend to show more relation-focused responding than their U.S. peers in a collection of visual and social tasks. Together, these results highlight complexity and variability in the development of relational reasoning and lay a foundation for future research designed to tease apart the factors associated with early diversity in relational reasoning.

Keywords:  Department of Symbolic Systems
Program on Symbolic Systems
Relational Reasoning
Thesis
Advisor: Frank Michael C.
Kachergis George
"Charlotte Salomon’s Message in a Bottle: A philosophical meditation on Charlotte Salomon’s Leben? oder Theater? and the meaning of artistic creation in the face of mortality, told in three parts"

This thesis project explores the art of Charlotte Salomon, who created a gesamtkunstwerk entitled “Life? or Theatre?” — chronicling her life story — in the midst of WWII, while hiding in exile from the Nazis. Applying the philosophies of Nietzsche and Kierkegaard, this thesis argues that Salomon’s project was an artistic leap of faith, evidencing her belief in life despite the darkness that surrounded her. It explores the redemptive aspects of art amidst great loss, and how this artistic redemption differs from notions of Judeo-Christian redemption. Finally, the thesis talks about what it means to be a receiver of a work of art, analogizing the experience to that of the serendipity of receiving a message in a bottle from the sea.

Keywords: Symbolic Systems Department
Art History
psychiatry
philosophy
Nietzsche
Kierkegaard
Michelangelo
Charlotte Salomon
Raphael
Vincent Van Gogh
Thesis
Chimeric dinucleotides : expanding the DNA polymerase toolkit

DNA polymerases constitute a class of enzymes that catalyze the synthesis of DNA molecules from their building blocks, the deoxynucleoside triphosphates (dNTPs). These enzymes are responsible for accurately replicating the entire genome of organisms across the domains of life. They have also found widespread utility in nucleic acid amplification techniques such as polymerase chain reaction (PCR). Using chemical strategies, we have sought to expand the functionality of DNA polymerase enzymes with the development of two novel classes of chimeric dinucleotides that can substitute for canonical dNTPs as substrates of DNA polymerase: ATP-releasing nucleotides (ARNs) and dicaptides. ARNs are comprised of four dinucleotide compounds each with a riboadenosine moiety linked via a tetraphosphate bridge to one of the four canonical deoxynucleoside bases found in DNA. We demonstrated that ATP released upon incorporation of ARNs by DNA polymerase could be quantified using a luciferase-based assay, effectively linking DNA synthesis to luminescence signaling. We employed ARNs in this strategy to report on DNA polymerase activity. This led to the development of a new method, polymerase-amplified release of ATP (POLARA) to detect point mutations associated with specific cancers and diseases. In addition to being rapid and sensitive, this method is luminescence-based and isothermal, indicating its potential for diagnostic testing in point-of-care and low-resource environments. A second class of chimeric dinucleotides known as dicaptides consists of two deoxynucleoside heads bridged by a pentaphosphate linker. Existing as either of two pseudocomplentary pairs, dicaptides replace dNTPs in DNA synthesis and contain the reactivity of two nucleotides at once. Dicaptides offer several benefits including increased thermal stability and decreased production of the inhibitory pyrophosphate byproduct, two issues that hinder the effectiveness of dNTPs. Dicaptides were shown to outperform dNTPs during PCR under extended thermal cycling conditions. Overall, these examples represent a general strategy wherein polymerase substrates can be synthetically modified such that their capacity to be accepted is not significantly affected, in order to generate certain desirable effects. In this case, modifications to the γ-phosphate of dNTPs to introduce a second nucleoside enabled replacing the traditional pyrophosphate leaving group, a molecule with low utility, with another nucleotide capable of powering a secondary enzymatic reaction. This strategy could be expanded to other classes of enzymes with the ultimate goal of expanding functionality beyond what would typically be expected in a biological context

Keywords: Chemistry.
Advisor: Kool Eric T.
Trost Barry M. 
Xia Yan
Chinese verb phrases : continuum of patterns with different lexical statuses

This dissertation explores how Chinese verbs and verb phrases can be best understood given that the boundary between the two categories are non-binary (Lu 1957, Chao 1968, and many others). In terms of morphological typology, compared with other languages like English, Chinese is more analytic and isolating, and more frequently uses compounding as a word-formation strategy. This study proposes a continuum between the lexical word and syntactic phrase to account for the blurry boundary between verbs and verb phrases. This dissertation approaches the V N sequences and V1 V2 sequences that are verbal compounds from the perspective of a continuum. Although the boundary between a word and a phrase is not clear-cut, the present study proposes a set of criteria to visualize systematically the lexicalization (Brinton & Traugott 2005) degrees of various V N sequences and V1 V2 sequences. Three major criteria with diagnostics are used to determine the lexical properties of the compounds in terms of form and meaning. The present study finds that a given V N sequence can be treated in four distinct manners: as a verb, if inseparable by the perfective aspect marker le; a word-like verb, if separable by aspectual marker le; a phrase-like verb, if separable by aspectual marker le with a non-referential N; or a verb phrase with a referential N. Like V N sequences, V1 V2 sequences in a continuum are compounds of different degrees of lexicalization (Brinton & Traugott 2005). Similarly, a V1 V2 sequence can take on four distinct patterns: as a change-of-state result verb (Tham 2012, 2013), if inseparable by infixal potential marker de or the negative bu; a word-like verb (also known as resultative compound), if separable by the infixal de or bu; a phrase-like verb (resultative compounds with a directional compound in the V2 position); or a verb phrase, when the phrase-like verb can take the perfective le or a nominal element between V1 and V2. Corpus search results with different collocational patterns and restrictions were found to support the V1 V2 resultative continuum hypothesis. The dissertation provides a new understanding of the non-binary distinctions between various verbal constructions. This constructional approach has significant implications to Teaching Chinese as a Second Language

Keywords: East Asian Languages and Cultures.
Advisor: Sun Chao
Egan Ronald
Matsumoto Yoshiko
Chromatin accessibility dynamics underlie a decline in neural stem cell migratory ability with age

Chromatin accessibility is emerging as a critical component of genetic regulation through its role in physically permitting or restricting access to genomic loci. Here I present two studies from my thesis work on chromatin regulation: one that leverages chromatin accessibility dynamics to identify novel age-related changes to adhesion and migratory pathways in murine neural stem cells, and another that uses dynamic chromatin accessibility changes throughout C. elegans development to identify and spatiotemporally characterize novel functional enhancers. In the murine brain, the adult sub-ventricular zone (SVZ) is a neurogenic niche comprised of a number of rare cell types including quiescent and activated neural stem cells (qNSCs and aNSCs). Epigenomic regulation is tightly linked to cell fate decisions and has been demonstrated to become dysregulated with age in a variety of systems. Yet, how the epigenomic landscape of NSCs changes upon activation and with age remains unknown. Here I profile the chromatin landscape of rare populations of SVZ niche cells, including qNSCs and aNSCs, isolated from young and old adult murine brains. Aging causes a differential response in the global chromatin landscape of qNSCs and aNSCs involving accessibility changes in adhesion and migration pathways. Functionally, old aNSCs migrate slower than young aNSCs while the opposite is true for the quiescent population. This age-related decline in aNSC migratory speed is accompanied by increased staining of the focal adhesion protein vinculin. Inhibiting the cytoskeletal regulator ROCK in old aNSCs improves migration speeds, promotes neurite outgrowth, and reduces actin stress fibers associated with biophysical adhesion. In another model system, the nematode C. elegans, I use chromatin accessibility dynamics throughout development from embryogenesis to adulthood to generate a list of putative enhancers that play a role in development. I then generate multiple transgenic fluorescent reporter strains in order to validate the cis-regulatory activity of these genomic regions and spatiotemporally characterize the activity of multiple novel functional enhancers during C. elegans development. Validated functional enhancers display unique spatiotemporal regulatory activity that corresponds to accessibility dynamics at those chromatin peaks in vivo during C. elegans development. Together, these results demonstrate that chromatin accessibility dynamics can be a powerful tool to uncover previously unknown biology and identify novel cis-regulatory elements during aging and development in multiple systems

Keywords: Genetics.
Advisor: Brunet Anne
Bassik Michael
Kundaje Anshul
Sage Julien
Wyss-Coray Anton
Cinematic virtual reality with head-motion parallax

Even as virtual reality has rapidly gained popularity over the past decade, visual fatigue, imperfect sense of immersion, and nausea remain significant barriers to its wide adoption. A key cause of this discomfort is the failure of the current technology to render accurate perspective changes or parallax resulting from the viewer's head motion. This mismatch induces a visual-vestibular conflict. Moreover, rendering accurate head-motion parallax is essential for making the computer-generated experience immersive and more like reality. The lack of this perceptual cue degrades the feeling of presence and makes the overall experience less compelling. This work addresses the issue by proposing an end-to-end framework that can capture, store, and render natural scenery with accurate head-motion parallax. At the core of the problem is the trade-off between storing enough scene information to facilitate fast, high-fidelity rendering of head-motion parallax and keeping the representation compact enough to be practically viable. In this regard, we explore several novel scene representations, compare them with qualitative and quantitative evaluations, and discuss their advantages and disadvantages. We demonstrate the practical applicability of the proposed representations by developing an end-to-end virtual reality system that can render real-time head-motion parallax for natural environments. To that end, we build a two-level camera rig and present an algorithm to construct the proposed representations using the images captured by our camera system. Furthermore, we develop a custom OpenGL renderer that uses the constructed intermediate representations to synthesize full-resolution, stereo frames in a head-mounted display, updating the rendered perspective in real-time based on the viewer's head position and orientation. Finally, we propose a theoretical model for understanding the disocclusion behavior in depth-based novel-view synthesis and analyze the impact of the choice of intermediate representation and camera geometry on the synthesized views in terms of quantitative image quality metrics and the occurrence of disocclusion holes

Keywords: Electrical Engineering.
Advisor: Girod Bernd
Wandell Brian A.
Wetzstein Gordon