VictorJuiz/thesis huggingface dataset:
Toward a coinsurance theory of group formation under risk [electronic resource]
Keywords: Business.

Five experiments show that people's tendency to join resource-sharing groups under environmental risk, or coinsure, depends on the availability of resources. People seek to form groups as a means to diminish the impact of risk in situations characterized by abundance; in situations where resources are scarce, people tend to avoid groups as risk increases to have a chance at a better outcome. This effect generalizes across different levels of wealth (i.e., variance in endowed resources) within groups. Independently of the level of external risk, group formation decisions under conditions of abundance are driven by self-transcendent values and concern for others, while group formation decisions under conditions of scarcity are driven by conservation values. Taken together, these studies introduce a novel perspective on cooperation that provides a useful lens for group formation.
Toward understanding the function of the G2 phase in the mammalian somatic cell cycle [electronic resource]
Keywords: Chemical and Systems Biology.

This thesis contains studies on the G2 phase of the cell cycle, which is arguably the most mysterious aspect of how cells prepare for cell division. Chapter 1 gives a historical overview of research on G2 and introduces key concepts and molecular players. G2 phase differs across model systems. It is absent in budding yeast as well as the early embryos of Xenopus and Drosophila. It is particularly well-understood in later embryonic development of Drosophila and in fission yeast, where an important regulator is mitotic phosphatase Cdc25. In mammalian tissue culture cells, the model system that is closest to cells of the human body, both Cdc25 and RCC1, a protein that emerged out of the analysis of mammalian cell-cycle mutants, present tantalizing possibilities for how the G2 phase may be regulated, but many unanswered questions remain. Chapter 2 presents results on how the duration of G2 phase affects mitotic progression, in particular the timeliness of anaphase. This work uses MCF10A cells that express fluorescently tagged PCNA, a marker of DNA replication, and fluorescently tagged histone H2B, a marker of DNA morphology, in live-cell microscopy to directly measure durations of all cell-cycle phases. G2 phase is then shortened by PD0166285, a drug known to induce premature mitosis. Shortening G2 phase results in a prolonged interval from nuclear envelope breakdown to anaphase that is partially rescued by inhibiting the spindle assembly checkpoint and not affected by inhibiting protein synthesis. Chapter 3 presents possible future directions for these studies. It contains preliminary data on the effect of shortened G2 on microtubule-kinetochore attachment, repair of DNA damage, and the centrosome.
Transactions for software defined networks [electronic resource]
Keywords: Electrical Engineering.

Computer networks have evolved tremendously over the past fifty years, evolving from their humble beginnings as interconnections for only several dozen academic hosts in the 1970s to vast hundred million dollar pieces of infrastructure supporting commerce and communication and communication services fundamental to our modern way of life. A major goal of the networking community is to build services, tools, and systems to manage these large, important networks efficiently while enforcing target policies — e.g., filtering packets from black-listed sources or preventing congestion on target links. Software defined networking (SDN) has been a transformative architecture for building management services that ensure such policies. We propose and implement a new transactional execution model for software defined networks. This execution model explicitly guarantees that either all management commands execute and their changes take effect or none do, resolving serious bugs discovered in existing software defined networking systems. Using fine-grained locking, a split execution model, and a sharded architecture, a transactional execution model can scale to provide tens of thousands of transactions per second. Finally, we show that a transactional model provides the versatility to express almost all network policies achievable in non-transactional systems, and allows new classes of debugging applications for software defined networks.
Transcriptional regulation of epidermal differentiation by ZNF750 [electronic resource]
Keywords: Biology.

The epidermis is a continuously self-renewing tissue that forms a critical barrier between the inside of the body and the outside world. Self-renewing progenitor keratinocytes are located in the basal layer of the epidermis, and a subset of their progeny will differentiate and migrate outwards to form the epidermal permeability barrier. The process of epidermal differentiation is tightly regulated and disruption of this process can lead to skin cancer or other skin disorders. Thus, we sought to identify and functionally characterize novel regulators of epidermal differentiation. To identify novel regulators of epidermal differentiation, we searched for genes whose expression changed during this process. ZNF750 was identified by its significant increase in expression during epidermal differentiation. ZNF750 was completely uncharacterized, with the exception of several studies linking mutations in ZNF750 to psoriasis. Depletion of ZNF750 in organotypic epidermal tissue results in decreased expression of late epidermal differentiation genes. Enforced expression of ZNF750 in progenitor keratinocytes is sufficient to induce epidermal differentiation, and ZNF750-driven epidermal differentiation depends on a single C2H2 motif. The transcription factor p63 binds to the ZNF750 promoter and induces ZNF750 expression. ZNF750 then binds to the KLF4 promoter and induces KLF4 expression. To further understand how ZNF750 regulates epidermal differentiation, we identified ZNF750 direct target genes and interacting proteins. ZNF750 binds near differentiation genes it activates and progenitor genes it represses at a sequence-specific DNA motif. ZNF750-interacting proteins were identified to include KLF4, RCOR1, KDM1A, and CTBP1/2. ZNF750 protein-protein interactions occur through two PLNLS motifs and ZNF750 binds DNA through its C2H2 motif. KLF4 co-localizes ~10bp from ZNF750 near differentiation genes to facilitate their activation, but is unnecessary for progenitor gene repression. In contrast, KDM1A co-localizes with ZNF750 at progenitor genes to facilitate their repression. RCOR1 and CTBP1/2 are required for both effects. Thus, ZNF750 as a p63 target gene that interacts with KLF4, RCOR1, and CTBP1/2 to induce epidermal differentiation genes and interacts with KDM1A, RCOR1, and CTBP1/2 to repress epidermal progenitor genes.
The tribune and the people [electronic resource] : revolutionary leadership in France, 1789-1871
Keywords: French and Italian.

From 1789 Paris until today, revolutions have attempted to reach their goals all the while continuously re-thinking the relationship between leaders and followers in a popular movement. This project takes a look at the era that first defined and explored this dichotomy in revolutionary politics and rhetoric. By examining each key moment in the long century of French revolutions -- the revolution of 1789-1794, the July revolution of 1830, the events of February and June 1848, and, finally, the Paris Commune of 1871 -- I demonstrate the unstable and ever-developing nature of the relationship that the people in revolution has with those who claim to lead it. Presenting and analyzing debates on civic education, popular sovereignty, and revolutionary dictatorship as seen through emblematic novels and political thought of the period, I argue that the controversial figure of a "people's tribune" and its relationship to the people in revolution was central to the expiration of the revolutionary tradition in France.
"Tweeting for Tickets:” The Role of Social Media Marketing in Sports Franchises
Keywords:  Department of Economics
Stanford Department of Economics
Thesis

In recent years, social networks like Facebook and Twitter have become extremely useful marketing tools. Recent literature has shown that the use of social networks by corporations is important for building brand equity and consumer relationships. Additional research has shown that a consumer’s emotional connection to a product or brand can lead to more consistent habits from the consumer. While a general hypothesis that increased use of social media marketing by corporations will lead to higher sales is intuitive, testing this in many consumer-facing businesses is difficult because it is difficult to attribute sales from increased social media activity to a consumer’s emotional attachment to the brand. Additionally, identifying specific time windows to compare changes in social media use and sales is difficult. This study builds on the current literature by looking specifically at social media use in the world of sports, where “fandom”, an extreme form of emotional attachment, is present,
and ticket sales can be measured game-to-game, so there are clear time benchmarks between which we can analyze changes in social media activity. In particular, this paper looks to exploit these characteristics of the sports world by analyzing the Twitter activity of franchises in the National Basketball Association (NBA). The results of the analysis show significant association between game attendances and both short-term and long-term Twitter activity measures. These effects increase and remain significant when looking only at teams located in “small markets”, cities with a TV population less than 3 million. Collectively, these results suggest that social media activity is associated with sales through the construct of consumers’ emotional attachment with a brand.
Ultra high-throughput evolution towards the brightest monomeric green fluorescent protein
Keywords: fluorescent protein
evolution
Thesis

Since the first demonstration of exogenous Green Fluorescent Protein (GFP) expression in E.coli and C. elegans, fluorescent proteins have served as revolutionary molecular tools in the life sciences. The brightest fluorescent proteins enable super resolution imaging, a microscopic technique with resolution at the nanometer scale. Here, we engineered a green fluorescent protein for enhanced brightness using the ultra-high throughput μSCALE engineering platform. The μSCALE platform utilizes a glass array comprised of millions of densely packed 10um capillaries, enabling the screening and isolation of the brightest clones from libraries with nearly 106 variants. Starting from a single domain of a recently isolated four-domain Anthoathecata protein, a bright dimer with brightness exceeding five times the parent was evolved in only four rounds of evolution. The dimer was rationally monomerized through disruption of a hydrophobic interface to produce a monomer, the desired oligomeric status for a molecular imaging tool. The resulting monomer was again evolved for improved brightness, surpassing that of the parent while retaining monomeric character.
Ultrafast multifocal two-photon microscopy for brain imaging [electronic resource]
Keywords: Mechanical Engineering.

Two-photon fluorescence microscopy has extensive application in biological studies, but it is typically limited by low full-field frame rates of ∼10-20 Hz. We present a novel multifocal two-photon microscope design that can image 455 × 110 μm2 at 1 kHz frame rate and 455 × 306 μm2 at 400 Hz with micron-level resolution. We utilize an ultrashort-pulsed regenerative fiber laser amplifier as the excitation source, and use a micro-lens array to split the initial laser beam into a rectangular array of beamlets. The array of beamlets is tilted at a fixed angle along the major optical axis in the excitation path, and is scanned laterally along a single dimension with a laser-scanning mirror to cover the entire FOV at the x-y focal plane. We use a low-read-noise scientific CMOS camera to acquire multi-pixel images in the collection path of the microscope. We further demonstrate its ability to track single cell flow trajectories in cerebral arterial networks, capture cerebral bridging vein constriction events near the superior sagittal sinus, and estimate Purkinje cell Ca2+ spike timing, all with millisecond temporal resolution.
Ultrafast response of single ferroelectric nanoparticles [electronic resource]
Keywords: Electrical Engineering.

Ferroelectric nanowires represent fundamental building blocks of complex functional devices due to their large nonlinear optical and piezoelectric responses, related to the large built-in electric polarization of the ferroelectric material. The coupling of light to nanoscale ferroelectrics enables novel means of engineering and manipulating their coupled degrees of freedom and inducing new functionality, including photo-ferroelectric effects and other opto-mechanical responses.Because one dimensional nanowires with subwavelength diameters exhibit modified light-matter interactions, they represent an unexplored means of coupling to these degrees of freedom all-optically. Here we present ultrafast nonlinear-optical measurements of light induced structural and electronic dynamics within single ferroelectric nanowires driven by above band gap femtosecond light pulses. By utilizing second harmonic generation (SHG) processes, which are sensitive to the non-centrosymmetry of the unit cell, we can probe the structural and polarization response in real-time. We can also identify the crystallographic orientation of the nanowire by SHG. In this thesis, the results for single barium titanate nanowires and potassium niobate are discussed. We observe ultrafast modulations in SHG, associated with both photo-refractive effects and polarization rotation under light excitation from single barium titanate nanowires. Then the nonlinear optical measurements probing the dynamics of single potassium niobate nanowires integrated into an optical tweezers setup is discussed. We observe large-amplitude, reversible modulations of the nonlinear optical properties and the associated ferroelectric polarization developing within a few picoseconds, and probe the enhanced coupling of the light into the nanowire. These measurements open up new possibilities for both all-optical manipulation of the nonlinear optical properties of single nanowires and for ultrafast microscopy at sub-wavelength resolution.
Ultrasound-guided robotic needle steering for percutaneous interventions in the liver [electronic resource]
Keywords: Mechanical Engineering.

Liver cancer is a significant health concern worldwide. Percutaneous ablation of liver tumors is a common treatment that suffers from significant limitations, primarily the inability to treat larger tumors and tumors in certain regions of the liver. Robotic needle steering is a technique for inserting flexible needles along controlled, curved paths through tissue. Applying robotic needle steering in percutaneous ablation of liver tumors could potentially allow clinicians to correct for errors during insertion, steer around obstacles to previously unreachable targets, and reach multiple targets from a single insertion site. To date, however, robotic needle steering has largely been limited to artificial tissues and tightly controlled bench-top settings. The goal of this dissertation was to move robotic needle steering closer to the clinical domain, by solving several technical problems specific to percutaneous ablation of liver tumors. Clinical application of robotic needle steering necessitates real-time medical imaging methods, steerable needles that can curve tightly and reach the majority of the liver volume, and a control approach that allows the clinician to define targets and provide feedback using medical imaging. First, a method for automatically segmenting a steerable needle from 3D ultrasound data is proposed, which uses mechanical vibration of the steerable needle to make it visible in power Doppler images. Second, finite-element and experimental studies of steerable needle insertion are described, and demonstrate that average radius of curvature of approximately 50 mm can be achieved in liver tissue through optimization of bent-tip geometry. An articulated-tip design, which uses a miniaturized rotary joint to articulate a distal section is also presented. Third, to allow closed-loop control of a needle steering robot using ultrasound measurements, an estimation scheme based on an unscented Kalman filter is proposed. Finally, a complete pre-clinical system for image-guided needle steering is presented, which combines the described methods for imaging, needle design and control. Validation testing in a porcine cadaver is described, in which simulated targets are introduced into the liver, and the system is used to place the steerable needle tip at the target.
Understanding and affecting students' path to success in community colleges [electronic resource]
Keywords: Education.

In the four papers of this dissertation, I examine the question of how structural policies and practices affect student outcomes in community colleges. Together, these papers aim to deepen our understanding of how students make decisions in community colleges with an eye toward how such an understanding could influence policy and practice. In papers 1 and 2, I examine the effects of two structural interventions (a more streamlined transfer process from two- to four-year schools and requiring students to declare a major intent when applying) on student course taking behavior. In papers 3 and 4 I use a multi-stage model of choice (observing awareness, consideration and choice) to examine how different groups of students make programmatic and major-choice decisions to gain a more nuanced understanding of how of how this important decision process unfolds.
Understanding antibiotic resistance in bacteria through molecular dynamics simulations [electronic resource]
Keywords: Chemistry.

An atomic level understanding of how biological molecules and proteins function is an ongoing challenge in chemical biology. Spectroscopic methods are useful for providing information about stable states and overall transition processes but it is impossible to directly observe these processes at an atomistic level of detail. Here, computational techniques are used to supplement experimental measurements in order to provide a more complete picture of a bacterial resistance to antibiotics at the atomic scale. Markov Models are used to analyze Molecular Dynamics simulations in order to propose an activation pathway for the conformational change in a key bacterial signaling protein NtrC. Similar techniques are applied again, in combination with a novel clustering algorithm, to compute the binding affinity of vancomycin to its targets. In sum, the present work demonstrates how simulations can contribute to a better understanding of important biological systems.
Understanding charge transport in semiconducting polymers for applications in organic electronics and bioelectronics [electronic resource]
Keywords: Materials Science and Engineering.

Organic electrochemical transistors (OECTs), in recent years, have emerged as promis- ing devices for fabricating biosensors using semiconducting polymers. Although in- organic materials have long dominated the semiconductor market, organic semicon- ductors have been found to be much better candidates for interfacing with biological systems due to their high chemical variability, low elastic moduli and ability to per- form both electronic and ionic transport. Because ionic species can penetrate highly porous polymer films leading to large interfacial areas, OECT devices typically ex- hibit extremely large capacitances and display among the highest transconductance values in published literature. Despite great technological advancements in device fabrication and designs over the last decade, there still lacks a thorough understanding of electronic transport, molec- ular doping, and device physics in these systems. My doctoral research focused on developing a more complete picture of these fundamental processes in OECTs. The first few chapters of this thesis will be dedicated to our work in characterizing poly- mer crystal structures, film formation and microstructures, and charge percolation in semiconducting polymer thin films. Subsequently, I will discuss how we can control- lably dope polymer thin films, and the physical and chemical properties that affect the doping process. In the last parts, I will present our electrical model for predicting OECT device responses and how we can extract useful device and biological properties in sensing experiments. Our findings provide important, fundamental insights into physical and electronic processes in semiconducting polymers, and are indispensable for designing better materials and biosensors.
Understanding the functional link between adherens junctions and the cytoskeleton [electronic resource]
Keywords: Biology.

This thesis focuses on understanding the functional link between the Adherens Junction (AJ) and the cytoskeleton. In order to control tissue integrity, the AJ complex links to the cytoskeleton, including actin and microtubules, and thereby controls intercellular adhesion, cell migration and the orientation of cell division. However, how AJ connection to the cytoskeleton is established and regulated is not well understood. Formation of the AJ is directed by the cadherin-catenin complex (CCC), which in epithelial cells comprises E-cadherin that binds β-catenin, which in turn recruits the F-actin binding and bundling protein αE-catenin. αE-Catenin is essential for cell-cell adhesion, and at cell-cell junctions is thought to link the CCC to F-actin either directly when under force, or indirectly by recruiting additional actin binding proteins (reviewed in Chapter 1). Mammalian αE-catenin also forms a homodimer in the cytosol, which is mutually exclusive with β-catenin binding in the CCC. However, even though the αE-catenin homodimer binds readily to F-actin and has been shown to inhibit Arp2/3 and cofilin activities, its role in cell-cell adhesion remains poorly understood. In Chapter 2 we directly test whether αE-catenin bound to β-catenin in the CCC is sufficient to induce intercellular adhesion, and results from this work show that both junctional monomer and cytosolic homodimer pools of αE-catenin act together to induce strong cell-cell adhesion. However, understanding the specific function of the αE-catenin homodimer and its role in locally controlling actin dynamics at cell-cell junctions has been technically challenging because the N-terminus of αE-catenin mediates both homodimerization and β-catenin binding. Thus, removing the homodimerization domain of αE-catenin also disrupts αE-catenin binding to β-catenin in the CCC. Chapter 3 describes the design of a locked-monomer αE-catenin mutant that uncouples homodimerization from αE-catenin binding to β-catenin. Expression of this mutant in an αE-catenin-/- generated cell line, we show that the αE-catenin homodimer pool is essential for regulation of epithelial intercellular adhesion and cell migration. Finally, in Chapter 4, we identify a link between the AJ complex and the microtubule cytoskeleton in mitosis. Epithelia cells divide parallel to the epithelial plane in order to maintain tissue architecture. Although E-cadherin has been implicated in this, the underlying molecular mechanism remains unclear, and here we identify how E-cadherin is linked to the mitotic spindle in order to instruct the orientation of cell division.