VictorJuiz/thesis huggingface dataset:
Molecular determinants of T cell receptor specificity and activation [electronic resource]

Molecular diversity is a fundamental property of the adaptive immune system. T cells, via the T cell receptor (TCR), have defined rules of recognition where a TCR must recognize a peptide presented in the context of an MHC molecule (pMHC) -- also known as MHC restriction. This allows for the sensitive discrimination between 'self' and 'foreign' antigens. The essentially infinite potential combinations of TCRs, and pMHC ligands, combined with the necessity to have high sensitivity and specificity, have made understanding molecular mechanisms behind TCR recognition and activation a central question of immunology. The overarching theme and objective of this thesis is to interrogate the key molecular and genetic determinants of T cell receptor specificity and activation. In Chapter 2, the TCR V-gene usage bias is examined at the population level -- the results provide a refined framework for the genetic pre-disposition of MHC specificity by the TCR. In Chapter 3, I examine naturally occurring high-affinity but non-agonist TCR-pMHC interactions in order to isolate key determinants of T cell activation. Finally, in Chapter 4, I use protein engineering techniques to engineer a "surrogate co-receptor" to both potentiate low affinity TCR-pMHC interactions, and to examine the cross-reactivity landscape of TCR-pMHC interactions within a lower affinity regime. Overall, this work brings new mechanistic, and potential therapeutic insight into understanding this sensitive, specific, and diverse receptor-ligand interaction network.

Advisor: Garcia K. Christopher
Butte M. (Manish)
Davis Mark M. advisor. Thesis advisor
Jardetzky Theodore advisor. Thesis advisor
Moments and zeros of L-functions over function fields [electronic resource]

In this thesis we study some questions related to L-functions over function fields. We obtain asymptotic formulas for the first four moments of the family of quadratic Dirichlet L-functions, when the size of the finite field is fixed and the genus goes to infinity. For the first moment we also compute an explicit lower order term of size approximately the cube root of the main term. In joint work with Hung Bui, we study low-lying zeros in the same family of L-functions. For the one-level density of zeros, we detect a lower order term when the support of the Fourier transform of the test function is sufficiently restricted. We also compute the pair correlation of zeros and obtain a non-vanishing result and a lower bound for the proportion of simple zeros in the family.

Keywords: Mathematics.
Advisor: Soundararajan Kannan
Conrad Brian
Entin Alexei advisor. Thesis advisor
Venkatesh Akshay
Monolithic three-dimensional integration of III-V compound semiconductors on silicon [electronic resource]

The planar scaling of silicon-based electronics technology has become much more challenging. Stacking devices in the vertical direction provides possible better performance and higher device density. Integrating different electronic or even optical components on top of silicon integrated circuits (ICs) can realize multi-functional ICs or ultimately, a system-on-chip. III-V semiconductor compounds have been used in optoelectronics and are also promising candidates for alternative channel materials in the next generation complementary-metal-oxide-semiconductor (CMOS) technology. Hetero-integration of high quality III-V single crystals on top of Si ICs will enable a wide variety of applications. However, there are three major challenges in building monolithic 3-dimensional integration circuits (3DICs): obtaining single crystalline device-grade semiconductor films; transfer of these films on to prefabricated silicon wafers; and fabricating devices that are compatible with existing structures in the silicon wafer. A possible experimental solution is to use the rapid-melt-growth (RMG) method to prepare single crystalline materials on silicon, which could solve the first two challenges together. In the first part of this dissertation, a modified RMG process is proposed and examined specifically for GaSb and InAs growth on silicon in order to solve the low III-V single crystalline yield problem using the conventional RMG method. Several possible causes of the low yields in the process design and conditions are identified, and experimental solutions are given. The geometry dependence of the RMG structure and the scaling potential are also discussed. III-V MOSFETs using the RMG-grown GaSb and InAs crystals are then fabricated to demonstrate the viability of 3DIC hetero-integration, under low thermal-budget (< 400oC) constraints. The second issue discussed in this work is using the wafer bonding method to realize monolithic 3D integration. Comparisons between wafer bonding and the RMG approach are made.

Keywords: Electrical Engineering.
Advisor: Griffin Peter
Plummer James D. primary advisor. Thesis advisor
Saraswat Krishna advisor. Thesis advisor
Wong S.
Monotone interactions of random walks and graphs [electronic resource]

This thesis deals with the behavior of random walks on monotonically time-varying graphs, where due to this monotonicity we can establish certain universality properties. In Chapter 1, we consider normally reflected Brownian motion (RBM) and simple random walk (SRW) on independently growing-in-time d-dimensional domains, d> =3. We establish a sharp criterion for recurrence versus transience in terms of the growth rate. For more general growing subgraphs of an infinite graph, we use evolving sets to establish heat kernel bounds that yield sufficient transience/recurrence criteria. In contrast, we demonstrate rich and non-universal behavior of certain non-Markovian models of random walks, in which monotone interaction enforces domain growth as a result of visits by the walk (or probes it sent), to the neighborhood of domain boundary. This is complemented by Chapter 2, where we address stability issues for random walks among time-dependent conductances. For both the discrete-time uniformly-lazy and continuous-time constant-speed random walks (DTRW/CSRW), we show that Gaussian heat kernel estimates are not stable under perturbations. As a by-product, we refute an open question about inhomogeneous merging of finite Markov chains. We establish matching Gaussian upper and lower transition density bounds for the CSRW among time-increasing conductances on any graph satisfying a uniform-in-time Poincare inequality and volume growth regularity. In contrast, stability is known for the variable-speed random walk (VSRW), for which the counting measure is the reversing measure.

Keywords: Statistics.
Advisor: Dembo Amir primary advisor. Thesis advisor
Chatterjee Sourav advisor. Thesis advisor
Diaconis Persi advisor. Thesis advisor
Mountains and messiahs [electronic resource] : the Roshaniyya, revelation, and Afghan becoming

This dissertation analyzes a sixteenth-century Sufi messianic movement known as the Roshaniyya ("the illuminated ones") popular among the Afghan communities of the northwestern regions of the Mughal Empire. While the Roshaniyya under the leadership of Bayazid Ansari and his family clashed with Mughal armies, there was a more profound contest over the nature of language and divine revelation. How does a "vernacular" language become the language of God? By telling a history of the "practice of revelation" amid the Afghan highlands, this project rejects the over-reliance upon tribe and ethnicity as explanatory categories that isolate the Roshaniyya movement. Rather, through an immanent reading of Roshani texts and the text of their critics, this project traces rival ideologies of language and temporality, demonstrating the significance of these contests in the emergence of new imaginings of Afghan identity and the role of Pashto. The Roshaniyya experimentation with language reveals a community that engaged the Qur'an and the concept of revelation as an open, continuous phenomenon that could be grasped through dhikr practice, narratives of dreams and saints, and literary techniques such as repetition, imitation, and rhyme. The Roshaniyya thus offer both a demonstration of the participation of Afghans in larger, Persianate religio-cultural trends as well as a striking example of the diverse ways premodern Muslims engaged the Qur'an and prophetic history. This dissertation also analyzes sources from a wide range of contexts that engage, critique, and remember the Roshaniyya in diverse ways for multiple ideological purposes. Among the sources considered are Mughal courtly chronicles, Persian biographical dictionaries, the reports of nineteenth-century British scholars and soldiers, and various works by a popular seventeeth-century heresiographer and Sunni scholar by the name of Akhund Darweza.

Keywords: Religious Studies.
Advisor: Bashir Shahzad
Crews Robert D.
Fonrobert Charlotte Elisheva advisor. Thesis advisor
Gin Lum Kathryn advisor. Thesis advisor
Multifunctional separators for improving battery safety [electronic resource]

Rechargeable lithium-ion batteries have without a doubt transformed the world of portable electronics and consumer devices. However, recent high-profile failures of lithium-ion batteries caused by internal short-circuits have led to numerous fires and explosions. As the industry moves to higher energy-density electrode materials to satisfy consumer demand, the consequences and severity of failures will only increase. There is a clear need for improved safety mechanisms to enable the safe use of lithium-based batteries. Particularly for lithium metal electrodes where the continuous formation of dendrites during cycling increases the likelihood of failure by short-circuits. In this dissertation, I will discuss my work on developing in-situ detection and protection schemes using the battery separator as a platform. In the first part I will present an in-situ method for detecting the penetration of dendrites into the battery separator via a bifunctional separator with a conductive metal interlayer. Both metallic and carbon-based bifunctional separators are demonstrated with aluminum and carbon showing excellent stability in the battery environment. In the worst case scenario of a pinhole which extends through the entire separator, the advance warning preceding failure can be extended to several hours. In the second part, I will present a lithium cobalt oxide (LCO) coated separator which is demonstrated as a temperature sensor to reversibly and accurately measure the internal temperature of a battery. A heating fault is detected internally via the LCO separator as a 25C differential over the temperature measured at the cell surface. In the final section, the reaction of lithium with a silica nanoparticle-coated separator is demonstrated as a mechanism for suppressing the further growth of lithium dendrites which penetrate into the separator. This reaction-protective separator can greatly slow the growth of dendrites and extend the battery lifetime up to five times over traditional separators. Together these detection and protection schemes can be simultaneously used to improve the safety of lithium-based batteries.

Keywords: Materials Science and Engineering.
Advisor: Cui Yi
Brongersma Mark L. advisor. Thesis advisor
Chueh William
Multilingual Students as Ethnographers: Toward a Culturally Sustaining Education Model for Elementary School Indigenous-Language Speakers

Starting in the 1980s and 90s, indigenous Mayan communities began to form in the US. Many members of these communities speak a language besides English or Spanish natively and are subject to a number of social barriers and discrimination, including access to a quality education. Situated in a bilingual Spanish-English elementary school in the Pacific Northwest, the study explored the multilinguistic practices of nine 4th grade Mayan Mam speakers using PhotoVoice. After being asked to show “the languages of [their] lives,” students took photos using a disposable camera for a period of three weeks. Afterward, students were asked to select one photo each and participated in PhotoVoice interviews conducted in a group setting. Students were asked about the photo they selected, as well as more about their linguistic practices inside and outside of school. Using a combination of both a-priori and emergent codes, 102 photos in total were coded. The photos as well as recordings and transcripts of the PhotoVoice interviews and participant demographic information informed analysis. Analysis results showed student conceptions of Fishman’s sociolinguistic domains. Actual participant descriptions of place-based linguistic practices complicate this finding somewhat, suggesting that languages described by participants as separate may see considerable overlap in practice. The study also found that although Mam was not described as a language used in school by the students, Mam was incredibly present in the home and with family; furthermore, half of prompted participants expressed some interest in the possibility of using Mam in school in the future. Finally, although some students described the utility of Mam as a common language in order to help those who don’t speak another language, others described a preference for Mam as a motivating factor for use. Building on Martínez’ work on language ideologies, these findings suggest that although students did express attitudes that reflected dominant language ideologies whereby Mam is deemed a non-academic language, student interest in the use of Mam in school simultaneously challenges this notion. Therefore, some students articulated what Martínez refers to as counter-hegemonic language ideologies, in which a language is valorized in spite of its current subordination in society. These findings demonstrate the potential benefits of facilitating autoethnographic exploration of linguistic practices in the classroom, particularly in a culturally responsive context.

Keywords: Stanford School of Education
bilingual education
photovoice
ethnography
autoethnography
language ideology
culturally sustaining pedadogy
culturally responsive education
indigenous languages of Guatemala
Mayan languages
Mam
Kanjobal
Spanish
dual-immersion school
Thesis
Multiphase Equilibrium Calculations with Gas Solubility in Water for Enhanced Oil Recovery

In this thesis, we have developed a robust algorithm for three phase compositional simulation of gas injection (especially CO2) in the presence of water. In this work, Henry’s law is applied to calculate component fugacities in the aqueous phase, while an equation of state (EOS) is used for the hydrocarbon vapor and liquid phases.
The basis of the algorithm is stability analysis in combination with phase split calculations. The stability analysis and phase split kernels can be framed as optimization problems. Specifically, stability analysis involves locating the minimum of the tangent plane distance function. The phase split calculation seeks to find the minimum Gibbs free energy of the system.
Successive substitution iteration method, Newton’s method and Trust Region method are applied to ensure robust and efficient computations. We tested two-phase cases and three-phase cases, and compared results with WinProp in CMG. Complex three-phase cases were also tested and phase diagrams were generated to verify our algorithm.

Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Petroleum Engineering Program
Thesis
Advisor: Tchelepi Hamdi
Multivariate methods for the analysis of structured data [electronic resource]

We describe methods for incorporating information about variable structure in multivariate analysis. We are motivated by the example of microbiome data, where we have species abundances in addition to information about the evolutionary history of those species. However, the methods we develop are applicable to more general types of structure on the variables, and we expect to find many other applications both in biology and in other fields. We develop a method for structured dimensionality reduction, adaptive gPCA. This method allows for tunable incorporation of the variable structure, so that the fine-scale structure of the variables, the global structure, or anything in between can be brought out. We then move to the problem of incorporating sparsity in addition to the structure to obtain a sparse and structured PCA as well as sparse and structured discriminant analysis for classification problems. The primary motivation behind incorporating sparsity and structure together is to obtain more interpretable results, but we also show that incorporating these two elements can substantially improve classification accuracy in the supervised setting.

Keywords: Statistics.
Advisor: Holmes Susan
Relman David A. advisor. Thesis advisor
Wong Wing Hung advisor. Thesis advisor
MyHood: Mapping Opportunities Around Every Corner

Many high school mission statements involve transforming the youth into leaders of their community. Yet there appears to be a disconnect between school content and its application to the challenges in the youth’s community that results in a low-level sense of empowerment. MyHood addresses this gap by having the youth see themselves as critical thinkers and citizens fully engaged in the transformation of their communities.
Students are aware of conditions in their communities and opinionated about the changes they would like to see happen. Adolescents need to be able to uncover, explore, and discuss topics related to their territories as a means to engage with their communities and grow up involved in the solution of problems that matter to them. Instead of believing that changes are not possible – or only the government’s responsibility – these learners need to develop a positive, personal and in-depth relationship with the places they live in. By developing youth protagonism and civic engagement, MyHood seeks to give voice to young learners of underprivileged neighborhoods using the Design Thinking framework and digital mapping technologies.
The combination of such elements makes MyHood a distinctive and powerful platform for young underrepresented learners. First, maps help students develop a sense of place toward their own neighborhoods and a sense of belonging to larger urban areas. Using map layers, learners and users will be able to visualize their communities in a powerful, augmented way and, thus, learn to ask different questions and tell different, more critical stories about their lives. Second, learning the human-centered approach of Design Thinking will allow students to dive deep into other realities and different possibilities, developing a critical and mature stance towards reality.

Keywords: civic engagement
design thinking
community
high school
map
mapping
empowerment
awareness
Thesis
Nanoparticle-based emulsions for droplet microfluidics and applications [electronic resource]

Emulsions are a biphasic system with one liquid dispersed as droplets in a second immiscible liquid. They are an important class of materials found in many commercial products. They also play a critical role in emerging microfluidics applications for high throughput screening assays and material design. The objective of my thesis dissertation is to develop nanoparticle-based emulsion systems. My thesis covers two major application areas. The first addresses a key challenge in using emulsion drops as micro-reactors in droplet microfluidics, and the second uses emulsion without stabilizer towards the fabrication of nanocomposites. In the first part of my dissertation, I show that the use of amphiphilic nanoparticles (NPs) as a droplet stabilizer enhances the fidelity of droplet-based biochemical assays with the following advantages. 1) The use of NPs mitigates undesired cross-contamination of molecules between droplets. 2) NP-laden interfaces provide a rigid, solid-like surface to promote the growth of adherent cells, which cannot be achieved in surfactant systems. 3) NP-stabilized drops are more stable against break-up than surfactant-stabilized drops. Such stability increases the throughput of droplet interrogation process by at least three-fold. 4) The covalent conjugation of various molecules on droplet-stabilizing NP surfaces is simple, which opens up opportunities for creating customized fluid-fluid interfaces. In the second part of my dissertation, I present a stabilizer-free emulsion system to prevent the agglomeration of NPs during nanocomposite synthesis. I show that the single encapsulation of NP in the emulsion drop is critical for the fine dispersability of NPs in the nanocomposite. I also demonstrate an application of our method in improving the efficiency of photocatalytic nanocomposite for solar water splitting reactions.

Keywords: Materials Science and Engineering.
Advisor: Heilshorn Sarah primary advisor. Thesis advisor
Tang Sindy (Sindy K.Y.) primary advisor. Thesis advisor
Senesky Debbie advisor. Thesis advisor
Nanostraw platform for nondestructive intracellular sampling and precise delivery [electronic resource]

Nanotechnology has shown great potential in biological, medical and clinical applications. In this thesis, I will describe two novel bio-applications based on a recently-developed nanostraw platform. In the first part of the thesis, I will describe a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 days through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with > 95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual content within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activities such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to have a sight into the dynamic cell behavior, including processes such as induced pluripotency and differentiation. In the second part, I will elaborate a controlled quantitative intracellular delivery by electroporation-assisted alumina NS system (NES). The cell populations that form intimate contact with NS experience localized electric field during delivery and are porated on the tip of the NS. We achieved a quantitative and high uniform delivery of mRNAs and proteins by controlling three variables: (1) delivery duration, (2) electric pulse intensity, and (3) delivery reagent concentration. Fast protein transcription was observed soon after delivery. We also demonstrated ratiometric co-transfection of mRNAs, and showed this system allows high rate transfection to multiple cell lines and difficult-to-transfect primary cells. The NES transfection efficiency is independent of cell density. In addition, we monitored protein delivery and subsequent biological activity, including STIM1 and antibodies. We observed STIM1 peptide binding to cell expressed ORAI protein, immune antibody staining on histone and actin filaments.

Keywords: Materials Science and Engineering.
Advisor: Melosh Nicholas A. primary advisor. Thesis advisor
Santiago Juan G. primary advisor. Thesis advisor
Cui Yi