VictorJuiz/thesis huggingface dataset:
Illness and indicators of beach water quality on the California coast [electronic resource] : an interdisciplinary study in oceans and human health

This work takes a multi-disciplinary approach to ocean and human health research by investigating illness/climate relationships through time series modeling and evaluating two microbial source tracking tools for human specificity. In each case the subject of the work is the California coast. In the first project, associations were characterized and modeled between four gastrointestinal illnesses and a number of climate factors across an eleven-year time series of data from Orange County, CA. The results suggest that incidence of gastrointestinal illness in Orange County may increase as a result of rising temperatures due to global climate change. The second project evaluated the use of Enterococcus species differentiation as a microbial source tracking tool in California recreational waters. The results indicate that no single Enterococcus species is a reliable indicator of the host fecal source; however, Enterococcus species composite 'fingerprints' may offer auxiliary evidence for bacterial source identification. The third project evaluated the distribution of the enterococcal surface protein (esp) gene in E. faecium in the Pacific coast environment as well as the distribution and diversity of the gene in Northern California animal hosts. The gene was found to be widespread in non-human animal feces and DNA sequence analysis revealed that esp gene sequences were not divergent between hosts. Overall, the work presented here indicates that gastrointestinal illness rates in California may increase over time, and that Enterococcus-based microbial source tracking methods are insufficient tools to assess risk from recreational water exposure.

Advisor: Boehm Alexandria primary advisor. Thesis advisor
Criddle Craig advisor. Thesis advisor
Francis Christopher advisor. Thesis advisor
The immoral road not taken [electronic resource] : using counterfactual transgressions to secure a virtuous identity and to regulate one's moral behavior

A series of studies supported the hypotheses that (H1) reflecting on immoral alternatives to one's past behavior can license one to act less virtuously in the future, and that (H2) the motivation to feel or appear virtuous can lead one to invent immoral alternatives to one's past behavior. Supporting H1, when White participants performed a behavior that did vs. did not have a racist alternative, they felt that they had obtained evidence of their morality (Pilot Study), they expressed less racial sensitivity (Study 1), and, if they had relatively prejudiced racial attitudes, they were more likely to state a preference for hiring Whites instead of Blacks for a particular job (Study 2). Supporting H2, when White participants were motivated to feel non-racist, they remembered a prior task as having afforded more racist alternatives to their behavior (Studies 3-5). Additional support was obtained in the domain of weight-loss. In support of H1, reflecting on unhealthy alternatives to their recent behavior licensed participants to express weaker intentions to pursue their weight-loss goals (Study 6), and, if they habitually placed little restraint on their eating, to consume more of an unhealthy food (Study 7). Supporting H2, the desire to eat an unhealthy food without compunction led participants to construe alternatives to their prior food choices as having been unhealthier (Study 8). Discussion focuses on moral behavior, self-control, identity concerns, and the motivated rewriting of one's moral history.

Keywords: Psychology
Advisor: Miller Dale T. primary advisor. Thesis advisor
Monin Benoît
Ross Lee advisor. Thesis advisor
Impact of hydrogen on the forming and switching behaviors of Pr(0.7)Ca(0.3)MnO(3) thin films for resistance change random access memory [electronic resource]

The continued scaling of NAND Flash memory technology is facing significant physical, electrical, and reliability challenges. Beyond the 16 nm technology node, the issues associated with these challenges may offset or even counteract the benefits of increased density. An increased appetite for high-capacity memory devices motivates the need to investigate new functional devices and materials for next-generation memory technology. One promising solution is Resistance-change Random Access Memory (RRAM), which offers the advantages of low cost, simple device structure, low power write and erase, high-speed switching, and integration into monolithic memory. Despite these advantages, some barriers must be overcome. Resistance-change films typically require "electroforming" - a one-time voltage application that induces a change in the film conductivity - before resistance switching can be accessed. Moreover, RRAM devices often display great variation, which partly arises from the lack of thorough understanding of the resistance switching mechanism. Filament formation through oxygen vacancies is typically cited as the underlying mechanism; however, the finer details remain hotly contested. Understanding these details may provide insight into overcoming the aforementioned hurdles. In this work, hydrogen contamination of RF-sputtered Pr(0.7)Ca(0.3)MnO(3) (PCMO) thin films is investigated as a reason for large device-to-device variation. Significant hydrogen is shown to enter the films during standard deposition and processing steps. Its effects on electroforming, switching, dielectric loss, and optical absorption are presented. These measurements are considered together to devise a comprehensive model for hydrogen-assisted electroforming and switching in PCMO.

Keywords: Applied Physics
Advisor: Harris J. S. (James Stewart)
Nishi Yoshio
Wong Hon-Sum Philip
The impact of III-V and GE devices on circuit performance [electronic resource]

Because the performance enhancement from scaling in accordance to Moore's law encounters difficulties, recent research has focused on finding new device materials with higher intrinsic carrier mobility. III-V and Ge MOSFETs have been, especially, studied as potential replacements for Si MOSFETs. This dissertation addresses the building of spice-compatible models for such new devices, the estimation of the delay and energy of digital circuits, and the performance comparison of various digital blocks and SRAM cells with different combinations of Si, III-V, and Ge devices. This work, first, develops spice-compatible III-V nFET and Ge pFET models in order to estimate the actual gain of using these devices in digital circuits. A compact model is employed for modeling the III-V nFET, a modified BSIM library is used for describing the Ge pFET, and a RC model is adopted for counting the effect of wires. With these models, various common digital blocks are explored. This thesis covers the modeling and simulations of the delay and energy of digital logics, including inverters, 32-bit adders, interconnect drivers as well as FPGAs. The driving capability of the nFET and pFET should be matched for optimum noise margin and performance, in typical digital design. Both capacitance and driving current are important for performance. The combination of III-V nFET with a thick barrier layer and Ge pFET achieves the best delay-energy performance for many digital logic circuits. The advantages of small capacitance and high driving capability disappear with long wire interconnect. FPGA design does not benefit from advanced device because the delay-energy performance is dominant by wires. An SRAM cell is also studied. This work addresses the trade-offs between performance specifications including noise tolerance of SRAM cells comprising Si, III-V, and Ge device. The read margin of SRAM is maximized with the Si passgate, the III-V nFET pull-down, and the Ge pFET pull-up transistor. The write margin of SRAM, on the other hand, is maximized with the III-V passgate, III-V nFET pull-down, and Ge pFET pull-up transistor. There is a tradeoff between read and write margin. The modeling and simulation methodology and insights provided in this thesis enable us to determine the actual gain of digital circuits with advanced devices. The results offer suggestions for the direction of future device development.

Keywords: Electrical Engineering
Advisor: Wong S. primary advisor. Thesis advisor
Mitra Subhasish advisor. Thesis advisor
Wong Hon-Sum Philip
The impact of traditional textbook and epistemologically transparent text accounts on high school biology students' interest, comprehension, learning, and epistemology [electronic resource]

Textbooks are highly influential in defining both the curriculum and instruction of high school biology classrooms, yet most widely-used textbooks have been criticized for their extensive focus on declarative knowledge that fails to reflect the nature of the discipline. This study compares the impact of traditional textbook accounts and alternative "epistemologically transparent" accounts on students' interest, comprehension, learning, and epistemological perspectives. Unlike traditional textbooks that provide scientific facts and concepts with no justification, these alternative texts incorporate narratives of historical experiments that include authentic research questions, methods, and data that support scientists' claims. This study included two components -- four replications of a randomized experiment involving approximately 235 students and a think aloud/interview protocol with 24 students. Results of the experiment showed that text type did not have a differential impact on student interest or comprehension. Students in the treatment condition did show instances in which they transferred biological concepts and experimental designs to novel situations at a statistically higher rate than students in the control group. Students in the treatment group also exhibited more sophisticated epistemological perspectives than students in the control group. Think alouds and interviews with a small sub-set of students indicated that the epistemic elements embedded in the treatment text positively affected students' interest, comprehension, and trust in the text's claims. These results suggest that epistemologically transparent texts may function as helpful supplements to traditional textbook accounts in order to help students both learn biological concepts and how the discipline justifies these concepts.

Keywords: Education.
Advisor: Brown Bryan Anthony primary advisor. Thesis advisor
Osborne Jonathan advisor. Thesis advisor
Shavelson Richard J.
Improved quantification of in vivo metabolic kinetics using hyperpolarized 13C magnetic resonance spectroscopic imaging [electronic resource]

With signal-to-noise ratio enhancements on the order of 10,000-fold, hyperpolarized 13C MRSI allows the study of both the injected substrate and downstream metabolic products in vivo within the target organ, with the appearance of the 13C labels on the various metabolites resulting from a combination of isotopic exchange and metabolic flux. Although hyperpolarized [1-13C] pyruvate has been extensively researched as an in vivo biomarker for disease diagnosis and response to therapy, efficient and robust quantification still remains important areas of investigation. Recently, a new quantification paradigm called the saturable kinetics of 13C labeling process was proposed. This method utilized a Mechaelis-Menton-like mathematical formulation with the estimated apparent Vmax to directly quantify the dose dependence (i.e., the saturation effects) of lactate and alanine reaction velocities following one hyperpolarized 13C pyruvate injection. However, to obtain the apparent Vmax, the current quantification method repeats the multi-site exchange model fitting with different pyruvate doses and each data point corresponds to one independent pyruvate injection. Therefore, the process needs multiple injections and multiple subjects to obtain one single saturation curve. Such an intense injection pattern is almost impossible for clinical trials. Also, the estimated apparent Vmax inevitably involves the inter-subject variability due to the multi-subject requirement. Therefore, it is necessary to have an efficient quantification method for the saturable kinetics and apparent Vmax measurement. First, we developed an inflow-based single-slice quantification method which can measure saturable kinetics in one slice efficiently. The experiment time can be reduced from multiple injections with multiple animals to one injection. We demonstrated our quantification method on healthy models (rat kidney and liver) and disease models (mouse prostate tumor). Second, we applied our proposed inflow-based single-slice quantification method and demonstrated the relative change of apparent Vmax of the lactate 13C labels was well correlated with the gold-standard ALDH2 enzymatic activity in rat liver. It may serve as a potential noninvasive in vivo indicator for ALDH2 activity and provide an alternative way to research the related diseases including alcoholism and ischemia. Finally, we extended our proposed inflow-based quantification method to the 3D case so that the saturable kinetics in multiple slices can be measured efficiently following one single pyruvate injection. This extension further improved the quantification efficiency and is useful in the case of the heterogeneous in vivo saturable kinetics. We demonstrated our 3D quantification method in healthy rat models.

Keywords: Electrical Engineering
Advisor: Pauly John (John M.) primary advisor. Thesis advisor
Spielman Daniel (Daniel Mark) primary advisor. Thesis advisor
Pfefferbaum Adolf advisor. Thesis advisor
An in vitro CENP-A assembly assay reveals a role for CENP-C in CENP-A deposition [electronic resource]

Eukaryotic chromosomes segregate by attaching to microtubules of the mitotic spindle through a chromosomal microtubule-binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant centromere protein A (CENP-A). CENP-A nucleosomes are believed to epigenetically specify centromere identity, thus understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segregation mechanisms. CENP-A nucleosome assembly requires the Mis18 complex and the CENP-A chaperone HJURP. HJURP binds to pre-nucleosomal CENP-A and facilitates the deposition of new CENP-A nucleosomes into centromeric chromatin. The mechanistic roles of the Mis18 complex in CENP-A assembly and maintenance are not well understood. The Mis18 complex and HJURP localize to centromeres in telophase/G1, when new CENP-A chromatin is assembled. The molecular interactions that control their targeting are unknown. Several constitutive centromere proteins that remain associated with CENP-A chromatin throughout the cell cycle have also been implicated in CENP-A assembly, including CENP-C. Their functions in CENP-A assembly are unknown. The first chapter of this thesis work describes the development of an in vitro system for centromeric chromatin assembly in Xenopus laevis egg extracts. We show that CENP-A assembly in extract recapitulates the cell cycle dependence and HJURP requirement of CENP-A assembly in somatic cells. We then use this in vitro system to identify a novel role for CENP-C in recruiting CENP-A assembly factors to the centromere to promote CENP-A assembly, described in Chapter 2. We show that CENP-C is required to target the Mis18 complex protein M18BP1 to Xenopus sperm centromeres in metaphase. In the absence of CENP-C, M18BP1 and HJURP targeting to centromeres is disrupted and new CENP-A assembly into centromeric chromatin is inhibited. We find that CENP-C interacts directly with M18BP1 through conserved domains in the CENP-C protein. Thus, CENP-C provides a link between existing CENP-A chromatin and the proteins required for new CENP-A nucleosome assembly. Overall, this work extends our mechanistic understanding of how the pre-existing centromere directs the local assembly of new CENP-A nucleosomes to ensure stable propagation of the centromere. Furthermore, the ability to assemble centromeric chromatin in vitro will provide a valuable tool for dissecting the biochemical and cell cycle regulatory mechanisms that control new CENP-A assembly and ensure faithful centromere propagation.

Keywords: Biochemistry
Advisor: Straight Aaron
Pfeffer Suzanne advisor. Thesis advisor
Theriot Julie advisor. Thesis advisor
India’s Red Stain: Explaining the Indian Government’s Ineffective Response to the Maoist-­Naxalite Insurgency Since 1967

Since 1967, the Maoist-Naxalite movement has grown from a local peasant rebellion to a violent insurgency that operates in more than 10 of India’s 28 states and is widely considered to be the single biggest threat to India’s internal security. For more than four decades, as Naxalite violence has killed an estimated 15,000 Indians, the government has failed to address the driving motivation of the insurgency, allowing the movement to spread geographically and increase its violent threat. Most of what has been written about the Naxalites offers only partial or murky explanations of India’s failure to effectively address the violence. This thesis examines the nature of the Naxalite movement since its inception and analyzes the response of the government over time to answer the question: What accounts for India’s failure to effectively address Naxalite violence from 1967 to the present? It concludes that India consistently adopted the wrong strategy at the wrong time toward the insurgency, and that it did so due to a combination of three factors: the shifting nature of the movement; inherent inefficiencies in center-state relations; and the presence of other security challenges on the nation’s agenda. India is increasingly the focus of global attention, as its economy today grows at a rate second only to that of China. Yet, its advancement is still constrained by the same socio-­economic grievances that inspired the Naxalites in 1967. The study concludes with the implications relevant for current and future Indian policymakers to consider in adopting a strategy against the threat posed by the Maoist-­Naxalite insurgency.

Keywords: Center for International Security and Cooperation
CISAC
India
Naxalite movement
Communist Party of India
insurgency
policy
Thesis
Advisor: Crenshaw Martha
Inducing event schemas and their participants from unlabeled text [electronic resource]

The majority of information on the Internet is expressed in written text. Understanding and extracting this information is crucial to building intelligent systems that can organize this knowledge, but most algorithms focus on learning atomic facts and relations. For instance, we can reliably extract facts like "Stanford is a University" and "Professors teach Science" by observing redundant word patterns across a corpus. However, these facts do not capture richer knowledge like the way detonating a bomb is related to destroying a building, or that the perpetrator who was convicted must have been arrested. A structured model of these events and entities is needed to understand language across many genres, including news, blogs, and even social media. This dissertation describes a new approach to knowledge acquisition and extraction that learns rich structures of events (e.g., plant, detonate, destroy) and participants (e.g., suspect, target, victim) over a large corpus of news articles, beginning from scratch and without human involvement. As opposed to early event models in Natural Language Processing (NLP) such as scripts and frames, modern statistical approaches and advances in NLP now enable new representations and large-scale learning over many domains. This dissertation begins by describing a new model of events and entities called Narrative Event Schemas. A Narrative Event Schema is a collection of events that occur together in the real world, linked by the typical entities involved. I describe the representation itself, followed by a statistical learning algorithm that observes chains of entities repeatedly connecting the same sets of events within documents. The learning process extracts thousands of verbs within schemas from 14 years of newspaper data. I present novel contributions in the field of temporal ordering to build classifiers that order the events and infer likely schema orderings. I then present several new evaluations for the extracted knowledge. Finally, I apply Narrative Event Schemas to the field of Information Extraction, learning templates of events with sets of semantic roles. Most Information Extraction approaches assume foreknowledge of the domain's templates, but I instead start from scratch and learn schemas as templates, and then extract the entities from text as in a standard extraction task. My algorithm is the first to learn templates without human guidance, and its results approach those of supervised algorithms.

Advisor: Jurafsky Dan
Manning Christopher D. advisor. Thesis advisor
Ng Andrew Y.
Inferring the Halo Mass Function from Galaxy Clusters: Accuracy Limits Due to Redshift-Space Distortions

Measuring the abundance of dark matter halos as a function of mass – termed the halo mass function – allows us to constrain cosmological parameters of interest. One way to infer the halo mass function is through measuring the abundance of galaxy clusters as a function of optical richness in redshift surveys. However, redshift-space distortions cause errors in cluster-finding and thus place a fundamental limit on the accuracy of this method. In particular, the velocity dispersion of member galaxies stretches out a galaxy cluster in redshift-space along the line of sight, in what is known as the 'fingers-of-God' effect. The main focus of this thesis is to estimate the contribution of this effect to the accuracy limit of the cluster mass function measured from optically-selected galaxy clusters.
This study uses Monte Carlo experiments to estimate the error rate in cluster-finding due to 'fingers-of-God' confusions in an idealized model. The trade-off between two types of error – fragmentation and overmerging – is studied in detail, and presented as an intermediate result. The model is then applied to a halo catalog from a cosmological simulation. Redshift-space confusions are found to tilt the measured halo mass function towards higher masses. Under the assumptions of our setup, the effects bias the best-fit cosmological parameters by a few percent, within the range that is relevant for inferring these parameters from upcoming surveys.

Keywords: Physics
Petrosian, Vahe
dark matter halos
halo mass function
fingers-of-God effect
Thesis