VictorJuiz/thesis huggingface dataset:
High-performance service-oriented computing [electronic resource]

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.

Keywords: Electrical Engineering.
Advisor: Dally William J. primary advisor. Thesis advisor
Davis A. (Alan Lynn)
Ousterhout John K. advisor. Thesis advisor
High-throughput allogeneic antibody detection using protein microarrays

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.

Keywords:  Department of Biology
Biology
Protein microarray
HY antigen
Hematopoietic cell transplantation
Chronic graft versus host disease
Alloantibody
Thesis
Advisor: Miklos David
Jones Patricia
Cyert Martha
HIV and Motherhood in Ho Chi Minh City, Vietnam: Caregiving of HIV Positive Children as a Moral Mode of Disease Engagement

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.

Keywords:  Department of Anthropology
HIV
AIDS
Vietnam
motherhood
care-giving
Thesis
Advisor: Garcia Angela
Lurhmann Tanya
Hosting: The Choice of Authoritarian States to Bid for the Olympic Games & the Impact on Their Governments

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.

Keywords: Olympics
Sochi
Authoritarian Governments
IOC
Russia
Beijing
Berlin
International Relations
Stanford University
Honors Thesis
Thesis
Advisor: Weiner Amir
How does the brain detect visual motion? [electronic resource]

The ability to detect visual motion is critical to the survival of many organisms. Motion detecting circuits must tightly regulate and correlate signals across space and time, a general feature of many neural computations. Thus, this experimentally tractable and relatively simple visual computation is a powerful context in which to dissect how brains compute. What are the circuit algorithms that allow the brain to extract such behaviorally vital motion cues? How are these algorithms actually implemented within biological hardware? The work presented within this dissertation tackles these questions focusing on the visual system of the fruit fly, Drosophila melanogaster. Using a combination of 2-photon calcium imaging, pharmacology, behavioral analysis and genetic manipulations, my work has contributed to the dissection of elementary motion detection at the molecular, cellular and algorithmic level.

Advisor: Clandinin Thomas R. (Thomas Robert)
Baccus Stephen A. advisor. Thesis advisor
Hestrin Shaul
Luo Liqun
How employers hire (women, immigrants, and the educationally elite) [electronic resource] : meritocracy, egalitarianism, and cultural fit in a Silicon Valley high technology firm

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.

Keywords: Sociology.
Advisor: Grusky David B. primary advisor. Thesis advisor
Fields Corey advisor. Thesis advisor
Jiménez Tomás R. (Tomás Roberto)
Hoxb5 marks the long-term hematopoietic stem cell and reveals a near homogenous perivascular niche and prospective isolation and differentiation of the mouse skeletal stem cell [electronic resource]

The hematopoietic stem cell (HSC) is arguably the most extensively characterized tissue stem cell and has served as a model for understanding numerous aspects of stem cell biology. Since its identification by prospective isolation, complex multi-parameter flow cytometry has facilitated studies on many aspects of HSC biology, including, self-renewal, differentiation, aging, niche, and diversity. However, due in part to its rarity, complexity of isolation, and lack of HSC-specific lineage tracing, many findings still remain controversial. Here we demonstrate by unbiased multiple-step screening, identification of a single gene, Hoxb5 (homeobox B5 also known as Hox-2.1), whose expression is limited to the long-term HSC (LT-HSC) in mice; linking of Hoxb5 to fluorescent proteins allows identification, isolation, and localization of the LT-HSC. In a single-color tri-mCherry reporter mouse driven by endogenous Hoxb5 regulation, only 20% of total immunophenotypic HSCs are labelled by the fluorescent protein. Critically, only the Hoxb5-positive HSCs show long-term reconstitution capacity after transplantation—i.e., > 16 week hematopoietic reconstitution in primary transplant recipients, and reconstitution in secondary recipients. Bone marrow (BM) analysis of recipient mice also reveals that Hoxb5-positive HSCs can give rise to Hoxb5-negative multipotent and oligopotent hematopoietic progenitors, but not vice versa (Hoxb5-negative cells do not give rise to Hoxb5-positive hematopoietic cells), indicating Hoxb5-positive LT-HSC are at the top of the hematopoietic hierarchy. Only 7--35% of various previously defined immunophenotypic HSCs are LT-HSCs. Finally, by in situ imaging of mouse bone marrow, we show that > 94% of LT-HSCs (Hoxb5+) are directly attached to VE-cadherin+ cells, implicating the perivascular space as a near-homogenous location of LT-HSCs. Prospective isolation and transplantation has been critical to the identification of the the hematopoietic stem cell and its downstream progenitors. Here we utilize this same approach to help identify the stem and progenitors of the skeletal lineage. Transcriptional profiling of these candidate stem and progenitor fractions revealed differential expression of CD24a and CD200, two cell surface molecules that we demonstrate can be utilized to separate chondrocyte progenitors from bone progenitors. Using modulation of the BMP2 and VEGF signalling pathways allowed us to direct differentiation of these stem and progenitor fractions to the formation of bone or cartilage. Lastly, we compared the transcriptome of our stem and progenitor fractions to the lineage tracing experiments using Mx-1, Sp7 (Osterix), and Bglap.

Advisor: Weissman Irving L. primary advisor. Thesis advisor
Kim Peter
Nakauchi Hiromitsu
Shizuru Judith Anne advisor. Thesis advisor
Human induced pluripotent stem cell-derived cardiomyocytes model cardiovascular disease and predict chemotherapeutic cardiotoxicity [electronic resource]

Human induced pluripotent stem cells (hiPSCs) have emerged as a novel tool for drug discovery and therapy in cardiovascular medicine. These hiPSCs can be derived autologously without the ethical challenges associated with human embryonic stem cells. The use of hiPSC-derived cardiomyocytes (hiPSC-CMs) to explore cellular mechanisms of cardiovascular diseases in vitro has proven to be extremely valuable. Furthermore, patient-derived hiPSC-CMs are now providing new insights regarding drug efficacy and toxicity. In this thesis, I present novel applications of hiPSC-CMs for cardiac disease modeling in vitro and as a platform for drug validation. The first project presented in this thesis concerns viral myocarditis, a life-threatening illness that may lead to heart failure or cardiac arrhythmias. A major causative agent for viral myocarditis is the B3 strain of coxsackievirus, a positive-sense RNA enterovirus. I examined whether hiPSC-CMs could be used to model the pathogenic processes of coxsackievirus-induced viral myocarditis and to screen antiviral therapeutics for efficacy. The second project in this thesis concerns the cardiotoxicity of tyrosine kinase inhibitors (TKIs), which, despite their effectiveness as chemotherapeutic agents, are associated with cardiotoxic side-effects ranging from induced arrhythmias to heart failure. Advances in stem cell biology have enabled the development of human cardiac platforms for screening pharmacological cardiotoxicity in a high-throughput fashion in vitro. I utilized patient-specific hiPSC-CMs to screen FDA-approved TKIs in vitro for cardiotoxicities manifesting as alterations in cardiomyocyte viability, contractility, and intracellular signaling. With this data, we generated a "cardiac safety index" to assess the cardiotoxicities of existing TKIs. Therefore, hiPSC-CMs hold immense translational potential for cardiovascular disease modeling and drug screening.

Advisor: Wu Joseph M. primary advisor. Thesis advisor
Longaker Michael T.
Red-Horse Kristy
Human natural killer cell diversity [electronic resource]

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.

Keywords: Immunology.
Advisor: Blish Catherine primary advisor. Thesis advisor
Krams Sheri Michele advisor. Thesis advisor
Nolan Garry P. advisor. Thesis advisor
Parham Peter
Human navigation of information networks [electronic resource]

Network navigation constitutes a fundamental human behavior: in order to make use of the information and resources around us, we constantly explore, disentangle, and browse networks such as the Web, social networks, academic paper collections, and encyclopedias, among others. Studying the navigation patterns humans employ is important because it lets us better understand how humans reason about complex networks and lets us build more intuitively navigable and human-friendly information systems. In this dissertation, we study how humans navigate information networks by analyzing tens of thousands of navigation traces harvested from the human-computation game Wikispeedia, where participants are asked to navigate between two given Wikipedia articles in as few clicks as possible. We first shed light on human navigation strategies by describing the anatomy of typical human navigation traces. We then build on these results to develop models and tools for predicting the targets of human paths from only the first few clicks, learning to navigate automatically, and recommending the insertion of important missing hyperlinks. These are useful building blocks for designing more intuitively navigable information spaces and tools to help people find information. The navigation traces collected through the Wikispeedia game have the unique property of being labeled with users' explicit navigation targets. In general, however, humans need not have a precise target in mind when navigating the Web. Records of such navigation traces are abundant in the logs kept by any web server software. We demonstrate the value of passively collected web server logs by presenting an algorithm that leverages such raw logs in order to improve website hyperlink structure. The resulting system is deployed on Wikipedia's full server logs at terabyte scale, producing links that are clicked 12 times as frequently as the average link added by human Wikipedia editors.

Advisor: Leskovec Jurij primary advisor. Thesis advisor
Horvitz Eric J. (Eric Joel)
Jurafsky Dan
Hydromechanical and frictional faulting behavior of fluid-injection-induced earthquakes [electronic resource]

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.

Keywords: Energy Resources Engineering.
Advisor: Horne Roland N. primary advisor. Thesis advisor
Dunham Eric advisor. Thesis advisor
Zoback Mark D. advisor. Thesis advisor