VictorJuiz/thesis huggingface dataset:
Measuring microbes [electronic resource] : leveraging quantitative imaging to characterize heterogeneous systems across length scales

This dissertation addresses the question of spatial organization in living systems, a fundamental problem in understanding the physics of living systems. The structure and layout of the cell plays a key role in biophysical processes such as force transduction, diffusion, transport, and signaling. Using bacteria as a model system, I will present two examples of how cells generate, exploit, and interact with the spatial organization of their intracellular and extracellular environments. First, at the single-cell scale, I will discuss how L-forms (spheroplast-like, cell-wall deficient bacteria) of Escherichia coli can recover their normal rod-like shape without a pre-existing template. I will give a detailed, quantitative characterization of the recovery process at the morphological, biochemical, and molecular level. I will also discuss how our study of L-forms led us to investigate the mechanical properties of the bacterial outer membrane. Finally, I will propose that cell-wall synthesis is regulated by the local shape of the cell, giving rise to a biophysical model for rod morphogenesis. Second, at the community scale, I will discuss the vast, diverse, and poorly understood microbial ecosystem that resides in our digestive systems. I will present a quantitative image analysis platform for measuring host-microbe and microbe-microbe association in fixed sections of the intestinal tract, and show how diet shifts drive changes in the organization of the gut microbiome in gnotobiotic mice. In particular, I will demonstrate that polysaccharide starvation thins the host mucus layer, drives bacteria closer to host tissue, and alters clustering of several bacterial taxa.

Keywords: Physics.
Advisor: Doniach S. primary advisor. Thesis advisor
Huang Kerwyn Casey
Sonnenburg Justin
Measuring the standard model and searching for new physics with jet substructure using the ATLAS detector [electronic resource]

Collisions at the Large Hadron Collider have offered an unprecedented window into some of the highest energy scales ever observed in experiments. Understanding these collisions, especially those that produce particles charged under quantum chromodynamics (QCD), requires a deep understanding of jets: the collimated sprays of particles produced by the parton shower and hadronization processes which emerge from the asymptotic freedom of QCD. Recent theoretical advances and the unprecedented capabilities of the ATLAS detector have enabled a new class of jet physics measurements based on the internal structure of jets, referred to as jet substructure. Three new types of measurements relying on jet substructure are presented. The first is a set of measurements sensitive which can discriminate between jets initiated by quarks and gluons. Separation is possible by studying variables sensitive to the magnitude of the color charge. Several such variables are measured, and a data-driven technique is used to construct a tagger, the first of its kind at a hadron collider, which can improve the sensitivity of searches for new physics in hadronic final states. A second measurement studies the color connections of jets in top-antitop events using an observable called the jet pull angle: sensitivity to the color representation of particles decaying to dijet pairs at a hadron collider is demonstrated for the first time. A final analysis searches for R-parity violating supersymmetry (SUSY) in all hadronic final states. These classes of models remove the characteristic missing energy signature which existing SUSY searches rely on, and require new discrimination techniques. Jet substructure provides a powerful handle to analyze these very high multiplicity states using a variable called the total jet mass. No signal is observed over the Standard Model (SM) prediction, and new limits are set on these previously unexplored models. The techniques of jet substructure lie at the hearts of all of these analyses, enabling both new measurements of SM phenomena and entirely new searches for physics beyond the SM.

Keywords: Physics.
Advisor: Schwartzman Ariel G.
Su Dong
Wacker Jay advisor. Thesis advisor
Mechanisms of deformation and instability in crystalline rocks at the pore scale [electronic resource]

Deformation mechanisms at the pore scale are responsible for producing large strains in porous rocks. They include cataclastic flow, dislocation creep, dynamic recrystallization, diffusive mass transfer, and grain boundary sliding, among others. In this work, we focus on two dominant pore-scale mechanisms resulting from purely mechanical, isothermal loading: crystal plasticity and micro-fracturing. We examine the contributions of each mechanism to the overall behavior at a scale larger than the grains but smaller than the specimen, which is commonly referred to as the mesoscale. Crystal plasticity is assumed to occur as dislocations along the many crystallographic slip planes, whereas micro-fracturing entails slip and frictional sliding on microcracks. It is observed that under combined shear and tensile loading, micro-fracturing generates a softer response compared to crystal plasticity alone, which is attributed to slip weakening where the shear stress drops to a residual level determined by the frictional strength. For compressive loading, however, micro-fracturing produces a stiffer response than crystal plasticity due to the presence of frictional resistance on the slip surface. Behaviors under tensile, compressive, and shear loading invariably show that porosity plays a critical role in the initiation of the deformation mechanisms. Both crystal plasticity and micro-fracturing are observed to initiate at the peripheries of the pores, consistent with results of experimental studies. We next develop a computational framework that captures the microfracture processes triggering shear band bifurcation in porous crystalline rocks. The framework consists of computational homogenization on a representative elementary volume (REV) that upscales the pore-scale microfracture processes to the continuum scale. The assumed enhanced strain (AES) finite element approach is used to capture the discontinuous displacement field generated by the microfractures. Homogenization at the continuum scale results in incrementally nonlinear material response, in which the overall constitutive tangent tensor varies with the stress state as well as with the loading direction. Continuum bifurcation detects the formation of a shear band on the REV level; 3D strain probes, necessitated by the incremental nonlinearity of the overall constitutive response, determine the most critical orientation for shear band bifurcation. Numerical simulations focus on microfracturing at the pore scale with either predominant interface separation or predominant interface contact modes. Results suggest a non-associative overall plastic flow and shear band bifurcation that depends on the microfracture length and the characteristic sliding distance related to slip weakening.

Keywords: Civil and Environmental Engineering.
Advisor: Borja Ronaldo I. (Ronaldo Israel)
Deierlein Gregory G. (Gregory Gerard)
Linder Christian (Engineering professor) advisor. Thesis advisor
Mechanistic understanding of cell fate decisions towards neuronal lineage [electronic resource]

Direct lineage reprogramming is a promising approach for human disease modeling and regenerative medicine with poorly understood mechanisms. Here we reveal a hierarchical mechanism in the direct conversion of fibroblasts into induced neuronal (iN) cells mediated by the transcription factors Ascl1, Brn2, and Myt1l. Ascl1 acts as an "on target" pioneer factor by immediately occupying most cognate genomic sites in fibroblasts. In contrast, Brn2 and Myt1l do not access fibroblast chromatin productively on their own; instead Ascl1 recruits Brn2 to Ascl1 sites genome-wide. A unique trivalent chromatin signature in the host cells predicts the permissiveness for Ascl1 pioneering activity among different cell types. Finally, we identified Zfp238 as a key Ascl1 target gene that can partially substitute for Ascl1 during iN cell reprogramming. Thus, precise match between pioneer factor and the chromatin context at key target genes is determinative for trans-differentiation to neurons and likely other cell types. Long noncoding RNAs (lncRNAs) are potential regulators of cell fate but often ignored in human genetics. We describe an integrative strategy to identify lncRNAs mutated in neurodevelopmental disorders. Direct reprogramming of fibroblasts to induced neuronal (iN) cells identified a family of lncRNAs that are largely brain-specific, and suffice to promote neurogenesis or neuronal maturation in vitro. Copy number variation morbidity map of a large cohort of children with autism spectrum disorder or intellectual disability vs. healthy controls revealed recurrent focal genomic mutations affecting five iN lncRNA loci, and thus potentially contributing to pathogenesis. Lnc-NR2F1 is an evolutionarily conserved lncRNA that promotes iN cell maturation, and is disrupted by a t(5:12) chromosomal translocation in a family manifesting neurodevelopmental symptoms. Lnc-NR2F1 transcriptionally regulates an autism gene network controlling neuronal and axonogenesis pathways. Thus, integration of direct lineage reprogramming and human genetics is a promising approach for discovering lncRNAs involved in human diseases. Overall, this thesis unveils molecular mechanisms of direct lineage reprogramming into neurons by elucidating the role of transcription factors and lncRNAs. Insights from these studies enable better understanding of direct cell conversion processes and sheds light into disrupted pathways in neurological disease.

Advisor: Chang Howard
Brunet Anne
Khavari Paul A. advisor. Thesis advisor
Wernig Marius advisor. Thesis advisor
Mediating digital participation [electronic resource]

Research on the ways that digital tools mediate broader social inequality has traditionally focused on the "digital divide". As social and technological realities shifted over the last two decades, scholars interested in digitally mediated inequality have also shifted to focus on "participation divides". This concept offers a way of understanding how people from different groups are or are not benefitting equally from new information and communication technologies. Participation divides is currently a broad and multiform concept that seeks to understand how people use technology to their benefit, and how technology can be better used for social equity. In this dissertation, I employed study participant accounts to generate a concept of digital participation in communities that connect online. I then used that concept to study participation divides and identify factors related to these divides. I conducted a two-part, mixed-methods study involving responses from 272 college students of varying ages, races, majors, and income levels. Using study participant interviews, I identified 11 forms of community participation that interviewees engaged in online. These forms of participation generally focused on consuming and creating content. Content consumption was viewed as a less engaged approach to participation, and content creation was viewed as a more engaged form of participation. Based on their online activities, study participants occupied positions along a spectrum of depth of engagement in relation to online sites for community participation. Using survey responses, I found that most study participants engaged in moderate levels participation in community practices online. Those whose behavior reflected a deeper level of engagement were seen as more full community participants, even though their behavior was not reflective of the norm. Deeply engaged participants created content more often, and tended to use the Internet in a more robust manner for life goals. There were gender and income differences among the population of deeply engaged participants: women were more likely to be deeply engaged than men, and low-income students were more likely to be deeply engaged than middle-income and high-income students. This represented a divide of sorts, but was a reversal of the classical approach to digital divides. "Feelings of similarity in terms of web use" was a psychological variable that significantly predicted deep engagement. This study contributes to existing research by suggesting that participation be measured through multifaceted profiles with meaning derived from study participant experiences. It further adds nuance to existing accounts of digitally mediated participation by tying together specific forms of participation, goals of participation, and relevant psychological, social, and contextual factors.

Keywords: Education.
Advisor: Barron Brigid primary advisor. Thesis advisor
Brown Bryan Anthony advisor. Thesis advisor
Goldman Shelley V. advisor. Thesis advisor
Meetings of the minds [electronic resource] : knowledge integration processes in transdisciplinary science

Academic institutions invest in interdisciplinary research centers to promote innovative knowledge creation. As prior work on these research efforts has examined either established interdisciplinary collaborations or completed intellectual products, we have a limited understanding of how interdisciplinary research centers emerge and develop over time. This longitudinal ethnographic study on a new Transdisciplinary Premature Birth Research Center sheds light on the early stages of knowledge integration and their impact on the outcomes of interdisciplinary science. The Center's research efforts consisted of four heterogeneous teams: Placental Function, Pattern Recognition, Bioinformatics, and Microbiome. In order to promote knowledge integration among the scientists, the Center organized research group meetings for the different projects. These meetings occurred at various knowledge boundaries that created conditions for the emergence of boundary struggles. Across the four projects, boundaries were established around different objects of contention. I define them as either abstract or concrete scientific objects that demonstrate the points where the scholars' perspectives begin to differ and create boundary struggles in meeting discussions. Whereas in the Placental Function, Pattern Recognition, and Bioinformatics meetings the objects of contention hindered knowledge integration efforts over time, in the Microbiome meetings the actors successfully integrated their varied expertise around a shared goal. I suggest this outcome related to the concrete goal and the fact that the meeting participants navigated differences in their cross-functional roles, rather than disciplinary backgrounds. The different objects of contention and their long-term impact on scientific work shine light on how difficult interdisciplinary collaboration actually is.

Keywords: Education.
Advisor: McFarland Daniel (Daniel A.) primary advisor. Thesis advisor
Powell Walter W. primary advisor. Thesis advisor
Cook Karen S. advisor. Thesis advisor
Willinsky John
Mentoring and the College Experience: Narratives of Filipino American Undergraduate Students at Stanford

This study of the impact of mentoring relationships on the undergraduate experience of Filipino Americans at Stanford University involved extensive interviews with four male and four female self-identified Filipino/ Filipino American fourth-year undergraduate students. The literature review discussed relevant scholarship on Asian Americans, student development theory, and mentorship. Museus and IfItikar’s (2013) AsianCrit Theory and Nora and Crisp’s (2007) multi-dimensional conceptual framework of mentoring laid the foundation for this project. An in-depth phenomenological, semi-structured interview methodology was used to deepen our understanding of student development throughout college. The results of the study contextualized the ways in which students receive advice, counseling, and support from various mentors. The conclusion discusses implications and suggestions for research, policy, and practice in higher education on how to better support college students through mentorship.

Keywords: Filipino Americans
Asian Americans
mentorship
college students
support
Stanford University
Thesis
Metafluids and parity-time symmetric metamaterials [electronic resource] : new optical material phases and phenomena

Textbook conceptions of light-matter interactions have been challenged by two recent material advances - the development of metamaterials and the introduction of parity-time (PT)-symmetric media. Metamaterials allow considerable control over the electric and magnetic fields of light, so that the permittivity, permeability, and refractive index can be tuned throughout positive, negative, and near-zero values. They have enabled negative refraction, optical lensing below the diffraction limit of light, and invisibility cloaking. Complementarily, PT-symmetric media allow control over electromagnetic field distributions in systems with balanced amounts of gain and loss, so that light propagation can be asymmetric and directional. They have enabled lossless Talbot revivals, unidirectional invisibility, and, combined with non-linear media, optical isolators. In this thesis, I will elaborate on our efforts to make new types of optical and asymmetric metamaterials, including metamaterials with negative optical permeability, metamaterials in liquid phase, and parity-time symmetric metamaterials. In the first part, I will describe our theoretical and experimental works on plasmonic metamaterials both in the solid state and liquid phase. Here we have designed and demonstrated the first fluidic metamaterial, utilizing protein directed assembly to synthesize the constituent metamolecules. Both individual metamolecules and the bulk metamaterial solution show a strong isotropic magnetic polarizability at optical frequencies. Our calculations also indicate that these meta-molecules could enable negative refractive index liquids. In the second part, I will introduce the concept of PT-symmetric nanophotonic materials. We show how planar metallo-dielectric structures with balanced inclusion of gain and loss can be used for a variety of applications, including i) directional nanophotonic waveguides and modulators; ii) directional metamaterials that have different refractive indices when viewed from different sides; and iii) flat Veselago lenses which can overcome the Rayleigh diffraction limit of conventional optical microscopy. Further, I will show how these metamaterials can be used to control the emission of the electric, magnetic, and chiral emitters and suggest a non-chiral platform for enantio-specific identification and selection.

Keywords: Electrical Engineering.
Advisor: Dionne Jennifer Anne primary advisor. Thesis advisor
Brongersma Mark L. advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
Vuckovic Jelena advisor. Thesis advisor
Methods for quantiative dissection of gene regulation [electronic resource]

Defined regulatory programs effecting diverse cellular processes such as chromatin accessibility, RNA localization or protein modifications largely determine the establishment and maintenance of a cell's identity. Here, we describe the development of quantitative and high-throughput methods for understanding principles of gene regulation. In this work, we repurpose a high-throughput sequencing instrument to develop a platform for high-throughput biochemical assays of RNA. We then develop a method for profiling chromatin accessibility within rare cellular populations or single-cells, called Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq). Furthermore, we apply ATAC-seq to measure chromatin accessibility within defined cellular populations across the human hematopoietic hierarchy and primary Acute Myeloid Leukemia (AML) in effort to determine regulatory principles governing normal hematopoiesis and leukemogenesis. Together, we demonstrate that these methods provide unique insights into the molecular effectors governing normal human development and disease.

Keywords: Genetics.
Advisor: Chang Howard
Greenleaf William James primary advisor. Thesis advisor
Crabtree Gerald R. advisor. Thesis advisor
Li Jin (Billy) advisor. Thesis advisor
Snyder Michael
Methods for quantum field theories at finite density [electronic resource]

This dissertation discusses several approaches to study quantum systems at finite density, in the general framework of quantum field theory. The thesis consists of four parts. The first two parts discuss the application of dualities to study strongly-coupled quantum field theories at finite density. Part one consists of applications of the holographic dualities at finite density; part two extends the three-dimensional mirror symmetry dualities among certain supersymmetric gauge theories to finite density. The later two parts of the thesis study a specific class of finite density system, namely a fermi-surface coupled to critical scalar. In part three, a systematic RG framework tailored to such systems is developed; the framework is then applied in part four to study various possibilities for the low energy phases of a fermi-surface coupled to critical scalar.

Keywords: Physics.
Advisor: Kachru Shamit
Hartnoll Sean
Silverstein Eva