VictorJuiz/thesis huggingface dataset:
High speed links for flexible optical networks [electronic resource]
Keywords: Electrical Engineering.

Web-based applications, content streaming, and cloud computing have been driving the need for large-scale high-bandwidth datacenter networks. Optical links from ultra-long-distance links between datacenters to short-reach Ethernet links inside a warehouse are critical for scaling datacenter networks. In this dissertation, we study spectrally efficient and high-speed optical links for various types of optical networks such as intra-datacenter networks as well as wide-area networks interconnecting datacenters. In the first part of this dissertation, we study short-reach intra-datacenter networks. More specifically, we investigate various schemes to scale these links to 100 Gbit/s per-wavelength using multi-level intensity modulation and direct detection, relying on digital signal processing to compensate for component bandwidth limitation. Moreover, we discuss the complexity and requirements for different components of the system. We further show that 100 Gbit/s per-wavelength links are constrained in their optical power budget and study the benefits and challenges of using semiconductor optical amplifiers to improve the power margin. Extra margin can enable future datacenter architectures based on high number of wavelength-division multiplexed channels and optical circuit switching. In the second part of this dissertation, we propose a modular architecture for long-haul optical networks interconnecting datacenters that can support spectrally efficient superchannels with variable bandwidth. In the proposed architecture, multiple synchronized transceivers can cooperate to modulate/detect a superchannel comprising of multiple subcarriers, enabling transmission at bit rates beyond 1 Tbit/s. We analyze and simulate the performance of the proposed system in the presence of linear fiber impairments and synchronization errors and establish design requirements for practical deployment of such an architecture.
High-k gate dielectric interfaces with germanium and silicon-germanium substrates [electronic resource]
Keywords: Electrical Engineering.

As transistors scale to their physical limits, germanium and silicon-germanium (SiGe) alloys are both promising candidate metal-oxide-semiconductor field effect transistor (MOSFET) channel materials to extend the roadmap. In this work, I used carefully-controlled atomic layer deposition (ALD) processes and a simple forming gas anneal (FGA), to form TiO2/Al2O3/Ge gate stacks with 0.65 nm EOT and low interface trap densities. For the first time, I applied bilayer gate dielectric stacks to Ge pMOSFETs with sub 1-nm EOT and a subthreshold swing (SS) as low as 71 mV/dec. For the first time, soft x-ray and hard x-ray photoelectron spectroscopy were used to rigorously study the formation of a GeO2 interface layer between an atomic layer deposited gate dielectric and a Ge(100) substrate during forming gas anneal (FGA). A new and simple method was demonstrated to selectively passivate interface traps with energies in the top half of the Ge band gap under annealing conditions that produce a GeO2 interface layer. I also describe how the sensitivity of the interface trap density in metal/Al2O3/Ge MOSCAPs is related to the nature of the H2/N2 anneal and the presence of a gate metal such as Pt that is effective in dissociating H2 to atomic hydrogen. The third part of this work focuses on SiGe substrates. Experiments show that, even though the native oxides of the SiGe channel are removed by 2% HF(aq)/ H2O cyclic cleans, a SiOx/GeOx interfacial layer is formed during Al2O3 ALD. Using Al as the gate metal instead of Pt, Al2O3/SiGe MOSCAPs show C-V curves with minimal frequency dispersion and much smaller Dit response. Experiments reveal that the Al-gate scavenges oxygen from the underlying GeOx, producting a SiOx/SiGe interface with much-reduced Dit.
High-performance service-oriented computing [electronic resource]
Keywords: Electrical Engineering.

This dissertation presents Sikker, a highly-scalable high-performance distributed system architecture for secure service-oriented computing. Sikker includes a novel service-oriented application model upon which security and isolation policies are derived and enforced. The workhorse of Sikker is a custom network interface controller, called the Network Management Unit (NMU), that enforces Sikker's security and isolation policies while providing high-performance network access. Sikker's application model satisfies the complex interactions of modern large-scale distributed applications. Experimental results show that even when implemented on very large clusters, the NMU adds a negligible message latency of 41 ns under realistic workloads and 91 ns at the 99.99th percentile of worst-case access patterns. Analysis shows that the NMU can support many hundreds of Gbps of bandwidth with common VLSI technologies while imposing zero overhead on the CPU. Integrated into Sikker and the NMU is a novel service-oriented, distributed rate-control algorithm, called Sender-Enforced Token and Rate Exchange (SE-TRE), that is able to regulate service-to-service aggregate rates while imposing zero latency overhead at the 99.99th percentile, less than 0.3% bandwidth overhead, and zero overhead on the CPU. Sikker's service-oriented security and isolation methodology removes high overheads imposed by current systems. Sikker allows distributed applications to operate in an environment with fine-grained security and isolation while experiencing supercomputer-like network performance.
High-throughput allogeneic antibody detection using protein microarrays
Keywords:  Department of Biology
Biology
Protein microarray
HY antigen
Hematopoietic cell transplantation
Chronic graft versus host disease
Alloantibody
Thesis

Chronic graft-versus-host disease (cGVHD) often arises following hematopoietic cell transplantation (HCT), impeding the success of the treatment. Previous studies have shown that in sex-mismatched HCT between a female donor and a male recipient, the donor immune system will develop antibodies against certain proteins encoded on the Y chromosome that associate with cGVHD, called HY antibodies. Detection of these alloantibodies, meaning antibodies that are produced by the donor immune system, has traditionally been performed via an enzyme-linked immunosorbent assay (ELISA). However, ELISA requires a large amount of patient serum, is inefficient for testing multiple antigens concurrently, and is unable to detect antibodies against short peptides. Protein microarrays have the potential to overcome these shortcomings. Here, we optimize the protein microarray method for HY antibody detection. Six microarray surfaces were tested for their ability to bind recombinant protein and peptide antigens. Using normal male donors as a baseline, we quantified HY antibody levels in male patients with female donors and compared these measurements to those previously gathered by ELISA. Overall, the epoxide-based surface manufactured by Schott maximized positive signal detection and produced the most reproducible results against both peptide and protein antigens. Significant levels of HY antibodies as measured by microarray were found to associate with cGVHD, suggesting the platform’s clinical utility in predicting cGHVD development. Moreover, detecting antibodies against short peptides with microarrays will allow for the study of monoclonal HY-targeting B cell populations, providing a detailed understanding of the mechanism behind cGVHD and allowing for enhanced prophylactic treatments.
HIV and Motherhood in Ho Chi Minh City, Vietnam: Caregiving of HIV Positive Children as a Moral Mode of Disease Engagement
Keywords:  Department of Anthropology
HIV
AIDS
Vietnam
motherhood
care-giving
Thesis

Since the early 1990s, when the HIV virus first appeared in Vietnam, the epidemic has increased rapidly throughout the country and has indelibly influenced all levels of Vietnamese society – from the lives of individuals infected with HIV and their families to the policy and programmatic efforts of a diverse array of government bodies and local community organizations. In the Asia-Pacific region, Vietnam ranks fifth among countries with the highest number of people living with HIV: More than 260,000 people are living with HIV and an estimated 100 people become infected every day (Tuoi Tre News 2014). Ho Chi Minh City, according to a report by the Vietnam Administration of HIV/AIDS Control in 2013, is among the cities in Vietnam with the highest rates of HIV infections. Among the various groups of HIV patients in Vietnam, this paper zooms in on that of single HIV-positive mothers with HIV-positive children. As negative connotations are still deeply linked with HIV/AIDS, mothers perceive their own HIV positive status not only as burden to themselves, but also to their children. How, then, does such awareness contribute to their illness narratives and shape the mothers’ relationship with their children as well as other community members? Furthermore, what larger implications does this have on the effect of HIV/AIDS on notions of motherhood in the Vietnamese society?
This paper consists of three chapters. The first chapter traces the historic and social progression of HIV/AIDS scene in Vietnam. Here I examine how various social and cultural forces have rendered HIV/AIDS in Vietnam to be more of a moral than a biomedical discourse. The second chapter describes how the increasing availability and access of biomedical treatments have redefined the temporality of HIV, causing a shift in its portrayal from being an acute and rapidly deteriorating to a chronic lifelong condition. I further discuss the ways in which HIV positive mothers as well other people living HIV employ such chronicity discourse as part of a larger effort of disease normalization. The last chapter examines notions of motherhood and caregiving as they intersect with discourses of HIV. I focus on how HIV positive mothers see and live out her identity as a caregiver of HIV positive children.
Hosting: The Choice of Authoritarian States to Bid for the Olympic Games & the Impact on Their Governments
Keywords: Olympics
Sochi
Authoritarian Governments
IOC
Russia
Beijing
Berlin
International Relations
Stanford University
Honors Thesis
Thesis

The focus of this honors thesis is the 2014 Sochi Olympic Games and a retrospective look at how the Russian government used the Games as a platform upon which to propagate their political, economic and social agenda. In exploring the Russian use of the Sochi Games, the author compared it to the 1936 Berlin Olympic Games and the 2008 Beijing Olympic Games, as these three case studies reflect similar regime types and similar use of the media. The author explored the connection between the Olympics and the crucial times, economically and politically, during which these countries bid for and hosted the Games, and the relationship between the Games and the hosts’ deployment of new or existing political, economic and social policies. The author’s findings were that these authoritarian nations all bid for the Olympics during periods of high unemployment, in large part to as a counteractive measure to boost nationalism and to reconsolidate power under their existing leadership.
How employers hire (women, immigrants, and the educationally elite) [electronic resource] : meritocracy, egalitarianism, and cultural fit in a Silicon Valley high technology firm
Keywords: Sociology.

This dissertation, organized into three manuscripts, draws from a case study of the software engineering hiring process at InGen, a high technology firm in Silicon Valley. I use quantitative data primarily from in-person interview candidate evaluations and job offer decisions, and qualitative data primarily from semi-structured interviews with interviewers, recruiters, and management, and from participant observation of hiring deliberations. I first focus on the following puzzle: despite ample experimental evidence of cognitive bias in the evaluation of male-typed tasks, organizational studies fail to find a gender penalty in hiring rates for male-typed jobs. I argue that decision-maker discretion under equal opportunity norms helps to explain this puzzle. At InGen, decision-makers use their discretion to override mediocre technical evaluations, and then rationalize their discretion in terms of the candidates' near-future merit, resulting in gender equality in job offer rates. I next focus on the economic penalty that first-generation immigrants (those who attend a foreign university) incur in the U.S. economy. I argue that part of this economic penalty is due to perceived "cultural" differences between immigrants and organizational gatekeepers. At InGen, interviewers systematically perceive first-generation immigrants as socially distant to themselves due to perceived violations of national cultural norms, resulting in a penalty in job offers. Finally, I focus on how employers use and interpret elite educational credentials, taking seriously the systematic difference in perspective between management and peers (e.g., engineering interviewers) involved in the hiring process. I find that management and peers assign different meaning and importance to elite educational credentials according to the candidate uncertainty to which either group is oriented. To avoid internal conflict between the two groups, management establishes the formal rules for how to use elite educational credentials, routinizes recruiters to follow those rules, and segregates the peer review process from the rest of the hiring apparatus.
Human natural killer cell diversity [electronic resource]
Keywords: Immunology.

Natural killer (NK) cells are a unique lymphocyte lineage with remarkable agility in the rapid destruction of virus-infected cells. They are also the most poorly understood class of lymphocyte. A spectrum of activating and inhibitory receptors at the NK cell surface leads to an unusual and difficult-to-study mechanism of cellular recognition, as well as a very high capacity for diversity at the single-cell level. Here, we provide the first examination of human natural killer cell repertoire diversity. Using mass cytometry, we identify an unanticipated level of single-cell diversity within and among human subjects. In a study of monozygotic twins, we show that inhibitory receptor expression is determined primarily by genetics, while activating receptor expression is environmentally influenced. This study shows that the human NK cell repertoire is extremely diverse, with both genetic and environmental influences. We further show that this diversity is not limited to NK cells. NK receptors actually become less specific for NK cells as the immune repertoire matures. These receptors are also expressed on T cells, B cells, and monocytes, with cell type-specific changes observed upon maturation. NK cells acquire primarily inhibitory receptors when they mature, while CD8+ T cells acquire both activating and inhibitory receptors. These results show that the expression of NK receptors on multiple cell types is coordinately regulated. In a final study, we show that NK diversity is low at birth, increases by adulthood, and is stable over at least 6 months in healthy adults. It also increases in culture in response to interaction with virally infected cells. Furthermore, in a cohort of Kenyan women, a higher pre-infection level of NK diversity is predictive of a higher likelihood of HIV-1 acquisition. This data shows that NK cell diversity has functional significance and appears to be detrimental in the setting of viral acquisition. We conclude by reviewing outstanding questions in the nascent field of NK cell repertoire diversity. Finally, we look to the future, where emerging single-cell technologies will enable a new generation of rigorous and clinically relevant studies of NK cells accounting for all of their unique and diverse characteristics.
Hydromechanical and frictional faulting behavior of fluid-injection-induced earthquakes [electronic resource]
Keywords: Energy Resources Engineering.

This work serves to advance a fundamental understanding on the role of the coupled interaction between hydromechanical and frictional processes that influence fluid-injection-induced earthquakes. An analysis of the hydraulic stimulation and fluid circulation experiments at the Fenton Hill Enhanced Geothermal System test site supported the hypothesis that permeability enhancement occurred though a mixed-mechanism combination of mechanical opening of fractures and propagation of hydraulic splay fractures from the tips of preexisting natural fractures. A novel field test, called microseismic depletion delineation, was demonstrated to provide useful reservoir engineering information about production trends near horizontal wells in unconventional hydrocarbon reservoirs. An investigation of the 2011 Mw 5.6 Prague, Oklahoma earthquake sequence suggested that an initial undrained response resulting from elastic stress transfer from the foreshock followed by transient fluid flow along the fault may have influenced the timing of the main shock. The relationship between wastewater disposal well operational data and statistics of earthquake sequences that inform seismic hazard analyses was investigated using a coupled fluid flow and rate-and-state earthquake model.
Hydromechanical modeling framework for multiscale porous materials [electronic resource]
Keywords: Civil and Environmental Engineering.

Hydromechanical interactions between fluid flow and deformation in porous geomaterials give rise to a wide range of societally important problems such as landslides, ground subsidence, and injection-induced earthquakes. Many geomaterials in these problems possess two-scale porous structures due to fractures, particle aggregation, or other reasons. However, coupled hydromechanical processes in these multiscale porous materials, such as ground deformation caused by preferential flow, are beyond the modeling capabilities of classical frameworks. This thesis develops theoretical and computational frameworks for fully coupled hydromechanical modeling of geomaterials with two-scale porous structures. Adopting the concept of double porosity, we treat these materials as a multiscale continuum in which two pore regions of different scales interact within the same continuum. Three major developments are presented. First, we build a mathematical framework for thermodynamically consistent modeling of unsaturated porous media with double porosity. Conservation laws are formulated incorporating an effective stress tensor that is energy-conjugate to the rate of deformation tensor of the solid matrix. Based on energy-conjugate pairs identified in the first law of thermodynamics, we develop a constitutive framework for hydrological and mechanical processes coupled at two scales. Second, we introduce a novel constitutive framework for elastoplastic materials with evolving internal structures. By partitioning the thermodynamically consistent effective stress into two individual, single-scale effective stresses, this framework uniquely distinguishes proportional volume changes in the two pore regions under finite deformations. This framework accommodates the impact of pore pressure difference between the two scales on the solid deformation, which was predicted by thermodynamic principles. We show that the proposed framework not only improves the prediction of deformation of two-scale geomaterials, but also simulates secondary compression effects due to delayed pressure dissipation in the less permeable pore region. Third, we develop a finite element framework that enables the use of computationally efficient equal-order elements for solving coupled fluid flow and deformation problems in double-porosity media. At the core of the finite element formulation is a new method that stabilizes twofold saddle point problems arising in the undrained condition. The stabilized finite elements allow for equal-order linear interpolations of three primary variables—the displacement field and two pore pressure variables—throughout the entire range of drainage conditions.
Iceberg profiling using autonomous underwater vehicles [electronic resource]
Keywords: Aeronautics and Astronautics.

An improved method for creating 3D reconstructions, or profiles, of the submerged portion of free-drifting icebergs using autonomous underwater vehicles (AUVs) and simultaneous localization and mapping (SLAM) is presented. These 3D reconstructions provide context for scientific data collected around icebergs, and can aid in navigating back to points of interest on the iceberg for further study. Additionally, these reconstructions can be used to assess risk to infrastructure like oil rigs and pipelines. However, the motion of the iceberg during data collection complicates the mapping process by introducing warping and inconsistency into the reconstruction. This motion must be accounted for in order to obtain an accurate profile. The work presented here improves upon prior work in three areas. First, it enables profiling the full iceberg depth, including multiple swaths of data and many loop closure events. Second, it reformulates the motion estimation problem entirely in an iceberg-fixed frame of reference. This choice of reference frame yields computational speed increases of several orders of magnitude, and removes the need to provide an explicit estimate of the vehicle's world-relative position, which can be difficult to determine accurately. Third, it presents a method for automating the data correspondence problem, a crucial component of SLAM that is challenging in any underwater mapping task, and made even more so by the motion of the iceberg. Both simulation and field results are presented. For the simulation, a 150 meter long iceberg was modeled to an accuracy of 0.8m rms error. For the latter case, data recorded at an underwater sea cliff in Monterey Canyon was used as an analog for the vertical walls of a tabular Antarctic iceberg. The vehicle's navigation data was corrupted to simulate the effects of iceberg motion.