VictorJuiz/thesis huggingface dataset:
Magnetic protein chips for detection of radiation exposure and neonatal diseases [electronic resource]

This dissertation presents the basic principles of the magnetic protein chip immunoassay and applications of the magnetic protein chip for the detection of protein biomarkers. The magnetic protein chip is based on the giant magnetoresistive (GMR) spin-valve sensors, and electrical resistance changes of the sensors are measured as signals. Immunoassays were developed using the magnetic protein chips to quantitate protein biomarkers with high sensitivity. The magnetic protein chip immunoassay has several advantages over conventional non-magnetic techniques, such as multiplex capability, smaller sample volume requirement, enhanced signal-to-noise ratio, and facile integration with electronics. Ionizing radiation is high energy radiation that can remove electrons from atoms, and it causes various cellular damages some of which are lethal. Using an in vivo mouse radiation model, we developed protocols for measuring fms-related tyrosine kinase 3 ligand (Flt3lg) and serum amyloid A1 (Saa1) in small amounts of blood collected during the first week after X-ray exposures of sham, 0.1, 1, 2, 3, or 6 Gy. Flt3lg concentrations showed excellent dose discrimination at ≥ 1 Gy in the time window of 1 to 7 days after exposure except 1 Gy at day 7. Saa1 dose response was limited to the first two days after exposure. A discriminant analysis using both proteins could show improved dose classification accuracy. Our magnetic protein chip immunoassay demonstrated the dose and time responses and low-dose sensitivity that have important advantages in radiation triage biodosimetry. Necrotizing enterocolitis (NEC) is an inflammatory bowel disease often observed in pre-term babies and has high mortality rate. However, timely diagnosis of NEC has been hampered due to its unspecific symptoms and ineffective clinical tests currently available. We developed a magnetic protein chip immunoassay for the validation of NEC biomarkers. Three biomarkers, C-reactive protein (CRP), matrix metalloproteinase-7 (MMP7), and epithelial cell adhesion molecule (EpCAM) were quantitated using a small amount of blood samples. Receiver operating characteristic (ROC) curve analysis combined with bootstrapping technique showed excellent discrimination of NEC from healthy control and NEC from sepsis. Given the generality of the detection scheme used in the magnetic protein chip immunoassay, the magnetic protein chips are expected to hold great potential for medical diagnosis and clinical research.

Keywords: Materials Science and Engineering.
Advisor: Wang Shan primary advisor. Thesis advisor
Melosh Nicholas A. advisor. Thesis advisor
Sylvester Karl advisor. Thesis advisor
Magneto-optical studies of high-temperature superconductors using Sagnac interferometry [electronic resource]

While discovered in 1986, high-temperature superconductivity in cuprates remains theoretically not understood yet. In this thesis I will describe new physical properties of the normal state properties of cuprates from which the superconducting state evolves. In particular we study the symmetries of the normal state because of the central role symmetries play in any natural phenomena. We use a high-resolution zero-area loop Sagnac interferometer to measure magneto-optic Kerr effect (P-MOKE) on high-temperature superconductors. In this measurement the polarization of normal-incidence-light reflected from the surface of a material will be analyzed against the polarization of the initial beam. Non-zero Kerr effect has usually been observed in association with magnetism, and thus interpreted as a signature for broken time-reversal symmetry. However, it was recently recognized that gyrotropic materials, that is, materials that breaks spatial inversion and all mirror symmetries can also exhibit P-MOKE signal in the presence of absorption. Our results for single crystals of several high-temperature superconductors provide further evidence to the uniqueness of the electronic state in the normal state of the cuprates. First we show that the inability to train the Kerr signal with an applied magnetic field while cooling the sample through the Kerr effect onset temperature. Second we show that when measured on parallel, opposite surfaces of the same sample, the Kerr signal shows the same onset temperature, similar magnitude and the same sign. Arguing that for all measured crystals the Kerr signal also coincides with some form of charge ordering, we propose that the high-temperature superconductors posses a ``gyrotropic'' order in the normal state.

Keywords: Applied Physics.
Advisor: Kapitulnik Aharon primary advisor. Thesis advisor
Beasley Malcolm advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
The making of the kilogram, 1789-1799 [electronic resource]

When France's leading academicians—Lavoisier, Coulomb, Laplace, Condorcet and Lagrange amongst them—set about defining and then implementing a new system of weights and measures in the 1790s, they did so with gusto and pride. Their purpose was not merely to unify the country's weights and measures, but to present to the world a system of measurement that was "perfect", "taken from nature" and "in no way arbitrary". It was deemed necessary to perform fresh scientific experiments, witnessed by international observers, to determine the value of the metre and its off-shoot, the kilogram. The creators of the metric system were anticipating the day when every public measurement, whether for commercial or scientific use, would be made with the new metric measures. The expectation was wild, generated in the fervour of the French Revolution, but it did come true. At the turning of the twenty-first century, the kilogram and the metre are the scientific community's measures of mass and length respectively, and used (even if indirectly) in almost all societal circles. The history of the kilogram has played second fiddle to that of the metre. I chart here how, ten years after the French people called upon its government to deliver a single weight for the entire nation, the first kilogram prototype came to be delivered to its vault. Along the way, I examine experiments that were performed to calibrate the new weight against the old, the metrological ideals that drove the project forward and the craftsmanship with which the first kilogram prototype was fabricated from platinum. My historical research has been guided by philosophical questions. What does it take for a scientific measure to be objective? What is the difference between a calibration and an experiment? Once we know all there it to know about how to measure mass, do we know all there is to know about mass? Without fully addressing questions like these, this thesis provides a commentary relevant to topics in the foundations of measurement: the nature of experimental calibration, the naturalness of scientific measures and the significance of a measure's definition are considered here, but from the perspective of the experimental and technological history of metrology.

Keywords: Philosophy.
Advisor: Friedman Michael primary advisor. Thesis advisor
Ryckman Thomas advisor. Thesis advisor
Smith George E. (George Edwin)
Suppes Patrick
Managing personal information with private, accountable crowdsourcing [electronic resource]

Crowd-powered systems combine the power of human judgment and creativity with the speed and precision of computers. These systems can efficiently help people be more productive in ways that no single human assistant or computer program could accomplish alone. To provide help with personal information management, crowd-workers need access to people's personal information. However, people are understandably reluctant to share their entire private dataset with online workers. I introduce privacy and accountability techniques for parsimoniously sharing private data with online workers and provide experimental evidence that people can be more productive with assistance from the crowd. These techniques develop crowdsourcing as a platform trustworthy and responsive enough to be integrated into personal information management. This thesis develops these ideas through two crowd-powered systems. The first, TaskGenies, is a task list that automatically breaks down users' tasks into actionable steps that can be completed one at a time. These action plans are created through crowdsourcing and reused through natural language processing when possible. The second system, EmailValet, is a web-based email client that introduces valet crowdsourcing. With EmailValet, users can share a limited subset of their inbox with online human assistants who extract embedded tasks from these emails. The system mediates and logs assistant access to establish accountability. These systems point to a future in which people are personally empowered by the crowd and people's private data can be entrusted to crowdsourcing.

Keywords: Electrical Engineering.
Advisor: Klemmer Scott primary advisor. Thesis advisor
Rosenblum Mendel primary advisor. Thesis advisor
Lam Monica S. advisor. Thesis advisor
Managing radio resources in dense wireless areas [electronic resource]

Smartphone proliferation has created the demand for ubiquitous access to wireless data anywhere and at any time. This demand is particularly perceived in crowded venues such as concert halls, conference halls and sports stadiums, where a large number of mobile devices contend for limited spectrum. This dissertation focuses on highly dense wireless areas, where all users must communicate simultaneously with a common destination node, such as a cellular base-station. The research identifies a solution of multiple, small, dynamic user hotspots to better distribute the limited radio resources. This is achieved by taking advantage of reduced pathloss, communicating over locally available spectrum, and reuse of spectrum over spatially separated links. This dissertation presents two different methods of selecting hotspots, routing data and allocating resources in dense wireless areas. The first part of this dissertation focuses on improving network performance by creating a clustered configuration of nodes where the nodes within each cluster can operate over locally available spectrum (white-spaces). A single node within each cluster is designated as the hotspot, and all the other nodes communicate with the destination node through the hotspots. A semi-distributed algorithm, that clusters the nodes and coordinates the hotspots to tether over locally available white-spaces is proposed. In addition to providing simultaneous service to more users than conventional direct communication in cellular networks, simulation results show that the proposed method can increase the average battery life of devices by 30%. The second part of this dissertation aims at improving network performance in dense wireless areas through multiple hops and spatial reuse of spectrum. The proposed method groups nodes based on their location and creates a structured multi-hop configuration in which each group can forward its neighbor's data. Employing the large number of active radio nodes as relays, and exploiting the common direction of communication toward the single destination allows spatially separated groups to reuse limited spectrum resources. Resource allocation and routing among users is formulated as a convex cross-layer optimization problem. Furthermore, exploiting the structure of such problem leads to a semi-distributed optimization algorithm. As such, each node can optimize its resources independently based on local channel information.

Keywords: Electrical Engineering.
Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Cioffi John M. primary advisor. Thesis advisor
Farhadi Golnaz advisor. Thesis advisor
Mapping local disorder in graphene nanostructures [electronic resource]

Graphene has attracted substantial interest due to its relativistic band structure, ease of deposition, and almost ideal two-dimensional nature. While very high mobilities (even at room temperature) have been reported for graphene, its exposed nature as a single atomic layer of carbon makes it prone to disorder induced by processing steps during fabrication and other environmental conditions. In particular at low densities or small length scales, this disorder can dominate the properties of graphene. As a means of probing this disorder, I present scanning gate measurements of graphene constrictions with evidence of disorder related phenomena in transport. I also discuss means to minimize the disorder in graphene such as using boron nitride as an alternative substrate as well as a newly developed method for removing processing based organic contaminants.

Keywords: Applied Physics.
Advisor: Goldhaber-Gordon David
Moler Kathryn A. primary advisor. Thesis advisor
Reed Evan J. advisor. Thesis advisor
Mapping RNA protein interactions in Saccharomyces cerevisiae [electronic resource]

We are on the threshold of a new era in our understanding of that fantastic feat of regulation at the core of life itself—gene expression. The rapid pace of new developments in genome-wide, high-throughput technologies has allowed us unprecedented access to observe multiple stages of the gene expression program for nearly the entire genome. This has revealed a widespread discordance between mRNA abundance and protein abundance for many genes whose expression changes in response to environmental stimuli, and a significant coordination of post-transcriptional regulation for specific sets of related mRNAs at the levels localization, translation, decay, and the noise in gene expression. Despite this evidence suggesting the existence of a coordinated regulatory framework that potentially affects the fate of every mRNA in the cell, our efforts to discern the underlying structure and regulatory themes are hindered by an incomplete understanding of RNA-protein interactions. To advance our comprehension of post-transcriptional regulation, we developed new tools to identify which proteins bind to RNA, which of those bind concurrently, which RNAs are bound by a given protein, and where each protein binds on each RNA. Using our proteomic tools we discovered hundreds unexpected RNA binding proteins, uncovered new RNA binding domains, identified widespread, concurrent binding with several RNA binding proteins, and inferred functional information from the simultaneous binding partners of several RNA binding proteins. We used our genomic, sequencing-based tools to systematically interrogate a large set of diverse RNA binding proteins and we discerned new themes from the resulting data. This revealed significant differences in function, localization, and regulation among the proteins encoded by the targets of a given RNA binding protein based on binding position. These results suggest that the functional consequences of the RBP-RNA interaction are determined not only by whether an mRNA is bound by an RBP but also by the position of the binding site within the mRNA and its relation to the other RBPs that bind the same mRNA. Overall, we found evidence of an extensive regulatory framework involving hundreds of RNA binding proteins, encompassing nearly the entire transcriptome, and extending our understanding of the RNA-protein interactions at the heart of post-transcriptional regulation.

Keywords: Biochemistry.
Advisor: Brown Patrick O'Reilly
Herschlag Daniel advisor. Thesis advisor
Straight Aaron
Matching In Groups: A Theoretical and Empirical Study

We study the matching of workers to firms when workers have preferences over being matched with their colleagues. We extend existing results by considering that workers want to be matched in groups of friends, and these groups of friends partition the set of workers. Rather than agents having preferences over their own side of the market, they have a pre-determined set of agents with whom they want to be matched, and we want to keep these groups intact to whatever extent we can. We then propose several algorithms to match agents in groups, and we analyze the stability and other desirable properties of the matchings. We develop an algorithm to find a stable matching in the case of all workers in a group having the same preferences, all groups being the same size, and all firms having the same capacity. However, if any of these three conditions fail to hold, then there may not exist a stable matching for workers who want to be matched in groups. We include numerical results in the case of matchings that are almost stable. We examine an actual market to which we can apply our model and demonstrate how one of our algorithms does a better job of matching agents in groups.

Keywords: Stanford Department of Economics
market design
sororities
microeconomics
deferred acceptance
two-sided matching
coalition formation.
Thesis
Advisor: Kojima Fuhito
Measurement of CP-violating asymmetries in B₀ --> ([rho pi])₀ using a time-dependent Dalitz plot analysis [electronic resource]

We present results for a time-dependent Dalitz plot measurement of CP-violating asymmetries in the mode B^0 --> pi^+ pi^- pi^0, dominated by B^0 --> rho^\pm pi^\mp (rho^\pm --> pi^\pm pi^0) decays. Our dataset is derived from the complete sample of 471 x 10^6 B-Bbar meson pairs collected by the BABAR detector at the PEP-II asymmetric-energy e^+e^- collider at the SLAC National Accelerator Laboratory, operating on the Upsilon(4S) resonance. We extract parameters describing the time-dependent B^0 --> rho pi decay probabilities and CP asymmetries, including C, DeltaC, S, and DeltaS, finding these measurements to be consistent with the results of previous analyses. Additionally, we present a two-dimensional likelihood scan of the direct CP-violation asymmetry parameters for B^0 --> rho^\pm pi^\mp decays, finding the results to be consistent with direct CP violation at ~ 2 sigma significance. Finally, we present information on the CP-violating parameter alpha, corresponding to an angle in the unitarity triangle associated with the CKM quark-mixing matrix. We perform a likelihood scan of alpha that incorporates constraints from B^\pm --> rho pi measurements by means of isospin relationships. A robustness study assessing the reliability with which alpha is extracted provides important insights into the interpretation of this result.

Keywords: Physics.
Advisor: Burchat P. (Patricia) primary advisor. Thesis advisor
Quinn Helen R.
Su Dong
Mechanical stimulation and non-destructive functional assessment of cardiovascular cells in vitro [electronic resource]

The heart is a complex integrated system that leverages mechanoelectrical signals to synchronize cardiomyocyte contraction and push blood throughout the body. Due to the heart's limited regenerative capacity and the wide variety of cardiovascular pathologies, heart disease is often studied in vitro. However, it is difficult to accurately replicate the cardiac environment outside of the body. In this dissertation, I describe an integrated strain array for cell culture that mimics the mechanical movement of the heart and enables high-throughput mechanotransduction studies. Along with mechanical strain, substrate stiffness is an important mechanical stimulus. The heart and vasculature, along with other organs, remodel in both development and disease, changing their mechanical properties. I successfully implement a method that can simultaneously tune both substrate stiffness and mechanical strain in normal and pathological ranges. Polyacrylamide gels, attached to stretchable silicone platforms by interpenetrating networks, can be stretched up to 50% without delaminating. To fully harness the potential of studying heart disease in vitro, better techniques for studying heart cell contractions are required in addition to biomimetic dynamic culture. In this dissertation, I also describe two successful new approaches to quantifying cardiomyocyte contractility using simple phase contrast videos: one for single cells plated on soft gels and one for cell monolayers attached to glass or plastic. Together, these innovations provide a suite of tools to stimulate and assess cardiovascular cells and advance our collective knowledge of cardiovascular health and disease.

Keywords: Mechanical Engineering.
Advisor: Pruitt Beth primary advisor. Thesis advisor
Kenny Thomas William advisor. Thesis advisor
Nelson W. J. (W. James) advisor. Thesis advisor
Mechanics of the mitral valve - an in vivo/in silico approach [electronic resource]

The mitral valve is one of four heart valves that ensure unidirectional blood flow through the heart. Due to mitral valve failure approximately 44,000 people in the US alone undergo open heart surgery every year. Current treatment options include mitral valve replacement and mitral valve repair, neither of which have shown satisfying long-term success. A deepened understanding of mitral valve mechanics may help in improving current medical device designs and treatment options for mitral valve regurgitation. Here I provide an in depth analysis of the in vivo mechanics of the mitral valve using the theory of finite kinematics and based on this data develop non-linear in silico models of the mitral valve employing the finite element method. Using mechanical metrics such as strain and curvature I reveal the in vivo deformation of the mitral annulus and the mitral leaflet in the healthy, diseased, and repaired mitral valve. Furthermore, in silico I explore the effects of prestrain as well as growth and remodeling on the mechanics of the mitral valve. The results of my in vivo studies extend our current understanding of the healthy mitral valve, reveal new insight into disease characteristics and progressions, and evaluate the efficacy of current device designs. Furthermore, results from the in silico studies provide improved means to simulate mitral valve mechanics and predict long term adaptation for basic science research and medical device design. In conclusion, with the current work I take a large step toward a deepened understanding of mitral valve mechanics that may help to optimize medical device designs and treatment options.

Keywords: Mechanical Engineering.
Advisor: Kuhl Ellen
Delp Scott advisor. Thesis advisor
Pinsky Peter M. (Peter Michael)