VictorJuiz/thesis huggingface dataset:
Design and Applications of Anti Albumin-Adduct Antibodies to Assess Human Exposure to Aromatic Hydrocarbons

Aromatic hydrocarbons are ubiquitous pollutants. Many of the hydrocarbons such as benzene and benzo[a]pyrene are genotoxic and are known risk factors for cancers. The genotoxicity comes from the metabolic activation of the parent compound to a reactive electrophilic form, which binds to the nucleophilic DNA and albumin to form stable adducts. Because adduct represents the biologically effective dose and albumin has relatively long half-life (~ 1 month) and is abundant in blood (~45 mg/ml), albumin adduct becomes a promising candidate to assess exposure to aromatic hydrocarbons in cancer epidemiology. This dissertation can be roughly divided into two parts. In the first part, an antibody was used to quantitatively assess benzo[a]pyrene exposure. A sandwich enzyme-linked immunosorbent assay (ELISA), using a commercially available antibody, was developed to measure benzo[a]pyrene diol epoxide - albumin adduct (BPDE-HSA). The assay is much simpler and faster to use and is 10 times more sensitive than the traditional competitive ELISA to detect BPDE-HSA. The method was further revised to be directly compatible with plasma, hence eliminated all the tedious HSA isolation and purification steps. Finally, the revised assay was validated with two different sets of archived plasma samples. In the second part, another antibody was used in an enrichment step for the albumin adductomics. To characterize albumin adducts with liquid chromatography - mass spectrometry, they have to be digested and detected as peptide adducts. Cysteine (Cys34) is a known nucleophilic hotspot on the albumin that scavenges reactive aromatic electrophiles in blood (such as benzoquinone and naphthoquinones), therefore a semi-targeting antibody was designed to capture all peptides with electrophiles bound on the Cys34 (T3 adducts). After incorporating the antibody enrichment step into the adductomic workflow, results shown that the antibody enrichment has huge potential to increase the detection rate of low abundant T3 adducts. The major significance from this study is that the innovations are applicable to the exposure to other reactive chemicals. With a suitable capture antibody, the sandwich ELISA can be used to assess other exposures such as aflatoxin (in form of aflatoxin albumin adduct), while the semi-targeting antibody can be tailored to capture albumin peptide with a different locus of exposure significant, such as lysine.

Advisor: Rappaport, Stephen M
Energy systems transformation and the political economy of climate change

Climate change mitigation requires immediate and enduring cuts to greenhouse gas emissions, achievable only through the transformation of today's fossil fuel energy systems. Those systems today provide high-quality, inexpensive, and dependable energy to industrial societies. The low-emissions renewable energy systems that would replace them are, as of 2013, still more expensive, more complex, and unproven./nThis combination of factors makes the political economy of climate change mitigation immensely difficult. Achieving real emissions reduction will impose very large material costs powerful interests, in pursuit of distant--if potentially massive--environmental benefits. These conditions are not auspicious for adopting, much less sustaining, effective climate policy./nYet an increasingly large number of countries have taken explicit or implicit action to reduce greenhouse gas emissions. These actions include emissions pricing schemes, renewable energy research and development, energy efficiency mandates, technological research and development, and a host of other policies. The list of states pursuing such policy is as diverse as the policies themselves: the European Union, South Korea, India, and even China have adopted some or all of the provisions outlined above./nThis dissertation addresses how states have overcome the apparently sizable barriers to climate change mitigation. It argues that successful states have made progress by choosing policies that target environmental ends with economic gains. Those gains comes through benefits derived from the transformation of national energy systems--transformations that improve energy security, increase economic competitiveness, improve technological leadership, or target other opportunities and challenges in the legacy energy infrastructure. By targeting such areas explicitly, these policies create new constituents with a material stake in long-term policy stability. Those constituents act as valuable political allies in the political fight over the scale and distribution of costs for emissions reduction./nBut while such policy strategies have proven successful to date, they do not resolve the underlying problem of cost that has plagued climate change mitigation to date. Massive emissions reduction still poses net economic costs, even if it yields huge positive environmental benefits. The benefits created by a low-emissions energy systems transformation can offset those costs, and if targeted can create supportive economic constituents. But the low-emissions energy systems of the future still do not, as of this writing, offer any novel economic or technological improvements over the reliably and ubiquitous energy we enjoy today. Hence these policies remain at risk of disruption from outside forces. The recent policy stagnation in the United States and Europe point to the risks posed by this inherent policy vulnerability.

Advisor: Zysman, John
Corporate Finance and the San Francisco Mining Share Market, 1860-1877

Throughout history, capital markets have been central to innovation and the development of new industries, job creation, low unemployment, wealth accumulation, reducing income inequality, improving living standards, and promoting economic growth. In perfect capital markets, firms can easily raise funds for profitable investments. However, market frictions, such as agency costs, liquidity constraints, and asymmetric information, can lead to underinvestment. In this dissertation, I study the financing decisions of firms in a young industry in an environment where securing capital was difficult./nFollowing the 1859 discovery of gold and silver in Nevada, mine owners incorporated in San Francisco and issued stock. Interestingly, firms had the right to levy assessments on their shareholders. An assessment is a request for additional capital and failure to pay resulted in the loss of shares. Firms relied heavily on assessments to finance their operations. I claim that assessments were more than a peculiar feature of stock ownership; the method of financing addressed particular challenges, making it easier to secure capital. To evaluate my claim, I construct a dataset of assessments levied, daily stock prices, and other relevant data. I use regression analysis and narrative evidence from a credible local newspaper to determine which variables influenced levies and how assessments addressed financing frictions. Collecting capital over several periods and limiting the loss to share ownership helped in reducing the agency costs of free cash and making mining securities attractive investments./nFor investors of the San Francisco mining share market, private information and assessments may also affect stock ownership. Because firms voluntarily provided reports to local newspapers, some investors may have information on the prospects of the mine prior to publication. An investor's willingness to pay assessments may also influence the timing of purchase or sale. I use stock transfer data from a major mining company to measure the effect that assessments and private information had on the propensity to sell. Share ownership was geographically diverse, the propensity to sell varied across investors, and there is some evidence that the timing of sales by investors from the Bank of California may be driven by private information./nIn addition, I examine whether the market predicted reasonable returns in a setting where active trading in mining securities was fairly new and investors are more likely to speculate. One interesting feature of the firms in my sample is that they owned adjacent mining claims along the vein of the Comstock. I consider the effect of reported strikes on the stock price of firms with adjacent and non-adjacent mines. The results suggest that, on average, the market predicted returns consistent with rational behavior.

Advisor: Hermalin, Benjamin E.
Pebble Games and Complexity

We study the connection between pebble games and complexity./nFirst, we derive complexity results using pebble games./nIt is shown that three pebble games used for studying computational complexity are equivalent: namely, the two-person pebble game of Dymond-Tompa, the two-person pebble game of Raz-McKenzie, and the one-person reversible pebble game of Bennett have the same pebble costs over any directed acyclic graph./nThe three pebble games have been used for studying parallel complexity and for proving lower bounds under restricted settings, and we show one more such lower bound on circuit-depth./nSecond, the pebble costs are applied to proof complexity./nConcerning a family of unsatisfiable CNFs called pebbling contradictions, the pebble cost in any of the pebble games controls the scaling of some parameters of resolution refutations./nNamely, the pebble cost controls the minimum depth of resolution refutations and the minimum size of tree-like resolution refutations./nFinally, we study the space complexity of computing the pebble costs and of computing the minimum depth of resolution refutations./nIt is PSPACE-complete to compute the pebble cost in any of the three pebble games, and to compute the minimum depth of resolution refutations.

Advisor: Mossel, Elchanan
Trevisan, Luca
Galactic Winds and Structure of z~2 Star-forming Galaxies

Galactic-scale outflows are a key driver of galaxy evolution through their feedback effect on star-formation and their ejection of metals and energy into the inter-galactic medium (IGM). While it is known that outflows likely play an important role in the quenching of star-formation - transforming actively star-forming, blue galaxies into their `red and dead' counterparts - this role is currently not well understood. In particular, at z~2, during the most active epoch of star-formation, the mass and energy in these outflows is poorly constrained, as is the mechanism for launching them. Furthermore, active-galactic nuclei (AGN) in the centers of massive star-forming galaxies (SFGs) likely play an important role in star-formation quenching, but we do not have a clear understanding of how this AGN feedback compares with that of star-formation driven feedback, and it is not known how many of these massive SFGs at z~2 even have AGN. This issue is complicated by the fact that many high-z AGN are likely highly obscured, and have strong nebular emission line contributions from both star-formation and the AGN./nIn this dissertation, I explore these issues using high-spatial and spectral resolution integral field unit spectroscopic data of z~2 SFGs. The observations are obtained with the instrument SINFONI on the European Southern Observatory (ESO) Very Large Telescope (VLT) at Cerro Paranal. These high-quality data allow spatially-resolved studies of the gas-phase kinematics of these galaxies, as well dynamical information on their outflows. In this work, I explore outflow properties in one galaxy with exceptionally deep data, allowing detailed examination of the outflow energetics, spatial extent and underlying ISM properties, as well those from a larger sample of galaxies. I also probe the fraction of SFGs in our sample which contain (possibly obscured) AGN, and study how this affects our determination of galaxy properties, such as gas-phase metallicity. Finally, I study a subsample of z~2 galaxies whose turbulent velocities dominate the kinematic signature, and examine the link between the overall evolution of z~2 galaxies and the systems we see today. Together this body of work explores how galactic-scale outflows in z~2 SFGs are launched, effect the IGM and eventually shape the evolution of their host galaxies.

Advisor: Genzel, Reinhard
On the Development of Compact Electronic Gamma and Neutron Sources

The development of compact electronic gamma and neutron sources utilizing several deuteron-induced nuclear reactions on low-Z compounds are presented in this study. These systems feature a compact high current density RF inductive discharge plasma source to provide the ion current necessary for a high yield gamma or neutron source. The first part of this project studied an electronic gamma source that utilized low-energy (d,ng) nuclear reactions to generate mono-energetic gamma rays (0.5 to 1.5 MeV) having energies similar to existing radiological sources used in the field (e.g. 60Co, 137Cs, 192Ir). The source incorporates a novel compact pyroelectric crystal powering system that produces the high voltage needed by thermal cycling the crystal in the room temperature range. Experiments were carried out and an analysis was performed to determine the gamma source performance requirements to provide equivalent or improved functionality for the user community, while being less susceptible to malevolent use./nThe second part of this project studied the next generation of compact high flux electronic neutron generators that utilized the deuteron-deuteron (D-D) reaction to produce 2.45 MeV neutrons. The maximum flux level for a 120 keV - 1 ampere D+ beam bombarding titanium is expected to approach 1011 n*cm-2*s-1, which is close to the levels available in research reactors and large accelerator facilities. Analysis and experiments with the neutron generators show promise for utilization in traditional applications that require reactor neutrons such as the 39Ar/40Ar geochronology dating technique and boron-neutron-capture therapy (BNCT).

Advisor: Greif, Ralph
Mao, Samuel S
Racial Discourse in Mathematics and its Impact on Student Learning, Identity, and Participation

Discussions of race in educational research have focused primarily on performance gaps and differential access to advanced coursework. Thus, very little is known about how race mediates the learning process, particularly with respect to classroom participation and student identity formation. This dissertation examines mathematics learning as a context for illuminating the racial dynamics of learning in everyday classroom activity./nAlthough mathematics and race may seem strange bedfellows, a poststructural analysis reveals specific linkages between them that suggest that their discourses are actually well aligned. To conceptualize this alignment, this dissertation introduces the theoretical frame of racial-mathematical discourse, which establishes the groundwork for the empirical investigation reported here. Observations took place in four mathematics classrooms at a racially diverse high school over the course of a school year. Interviews (n=35) were conducted with students from the focal classrooms. Data were analyzed to explore how students make sense of racial-mathematical discourse, and to gauge the discourse's impact on learning./nFindings indicate that racial-mathematical narratives were central to students' sense making. All students reported awareness of the "Asians are good at math" narrative, as part of a web of racial ideology. Importantly, students linked it to narratives about other groups' mathematical inferiority (e.g., "Blacks are bad at math"). They also connected racial-mathematical narratives to broader racialized discourses outside mathematics (e.g., perceptions of intelligence). Students observed the presence of these narratives in locations outside the school setting, such as media imagery and international comparisons./nData further suggest that racial-mathematical discourse is not a static belief system. Rather, it emerges and is reified as students engage in typical classroom practices, such as noting which classmates get asked for help. This is consequential for learning, in that the deployment of racial narratives in social interaction frames students' opportunities to build identities as capable learners. This dissertation develops a framework leveraging insights from sociocultural and poststructural theory to trace the impact of racialized classroom episodes on students' identity formation. It highlights critical issues that need to be taken into account in the design of equitable learning environments, especially for students of color from persistently marginalized backgrounds.

Advisor: Schoenfeld, Alan H
Essays on Causal Inference in Randomized Experiments

This dissertation explores methodological topics in the analysis of randomized experiments, with a focus on weakening the assumptions of conventional models./nChapter 1 gives an overview of the dissertation, emphasizing connections with other areas of statistics (such as survey sampling) and other fields (such as econometrics and psychometrics)./nChapter 2 reexamines Freedman's critique of ordinary least squares regression adjustment in randomized experiments. Using Neyman's model for randomization inference, Freedman argued that adjustment can lead to worsened asymptotic precision, invalid measures of precision, and small-sample bias. This chapter shows that in sufficiently large samples, those problems are minor or easily fixed. OLS adjustment cannot hurt asymptotic precision when a full set of treatment-covariate interactions is included. Asymptotically valid confidence intervals can be constructed with the Huber-White sandwich standard error estimator. Checks on the asymptotic approximations are illustrated with data from a randomized evaluation of strategies to improve college students' achievement. The strongest reasons to support Freedman's preference for unadjusted estimates are transparency and the dangers of specification search./nChapter 3 extends the discussion and analysis of the small-sample bias of OLS adjustment. The leading term in the bias of adjustment for multiple covariates is derived and can be estimated empirically, as was done in Chapter 2 for the single-covariate case. Possible implications for choosing a regression specification are discussed./nChapter 4 explores and modifies an approach suggested by Rosenbaum for analysis of treatment effects when the outcome is censored by death. The chapter is motivated by a randomized trial that studied the effects of an intensive care unit staffing intervention on length of stay in the ICU. The proposed approach estimates effects on the distribution of a composite outcome measure based on ICU mortality and survivors' length of stay, addressing concerns about selection bias by comparing the entire treatment group with the entire control group. Strengths and weaknesses of possible primary significance tests (including the Wilcoxon-Mann-Whitney rank sum test and a heteroskedasticity-robust variant due to Brunner and Munzel) are discussed and illustrated.

Advisor: Sekhon, Jasjeet S
Speed, Terence P
Design and Analysis of Digitally Modulated Transmitters for Efficiency Enhancement

The last decade has witnessed a tremendous growth in wireless communications. Consumer demands for battery-operated mobile devices with versatile, high data-rate communication capabilities that are of low cost, small form-factor and long operating cycle have motivated the research on fully-integrated, back-off-efficient and coexistence-friendly wireless transceivers in CMOS VLSI technology. However, the full integration of an efficient CMOS power amplifier (PA) into such a transceiver is still among the most difficult challenges towards a true System-On-Chip (SOC) solution. This thesis investigates the PA efficiency enhancement techniques for a complete power transmitter system that is fully-integrated and coexistable. Direct digitally modulated transmitter architecture has been identified as one of the most promising solutions to the above challenges. Within such a transmitter, the PA efficiency is able to back off from a high peak efficiency at least with class-B characteristic; meanwhile, the transmit linearity can be more easily improved by digital predistortion due to the direct digital modulation scheme. To validate such a promising architecture, we have built a fully-integrated CMOS digital power transmitter for the IEEE 802.11g 54Mbps application. System-level considerations and design choices are presented with an aim for low out-of-band noise and good transmit linearity. As the core of the transmitter, the RF switching PA is designed for high efficiency with minimum number of on-chip passives that only exercise an accurate control over fundamental and second-harmonic terminations. The class-B efficiency back-off characteristic is further improved by a dynamic impedance modulator which boosts the PA drain impedance at a low instantaneous envelope level. Open-loop phase interpolator based topology is used for the polar phase modulator, which achieves wideband phase modulation with competitive power consumption. Digital baseband filtering is fully optimized at both the algorithm and the hardware level, which offers larger than 60dB attenuation on the close-in spectral images with reduced filter complexity. The prototype has been implemented in a 65nm bulk CMOS technology and has demonstrated a combination of good output power, overall efficiency and spectral purity with a very high level of system integration.

Advisor: NIKNEJAD, ALI M
Two Sides of the Same Coin? Behavioral and Cognitive Responses to Social Rejection on the Basis of Higher and Lower Socioeconomic Status

Two Sides of the Same Coin? Behavioral and Cognitive Responses to Social Rejection on the Basis of Higher and Lower Socioeconomic Status/nby/nMichelle Flythe/nDoctor of Philosophy in Psychology/nUniversity of California, Berkeley/nProfessor R. Mendoza-Denton, Chair/nExisting research shows that individuals seek to avoid painful and costly social rejection (Ayduk, Mendoza-Denton, Mischel, Downey, Peake, & Rodriguez, 2000; Mendoza-Denton, Downey, Purdie, Davis, & Pietrzak, 2002). Some of this past research has debated the nature of socioeconomic status-based rejection and whether there is similarity between the nature of lower and higher SES rejection (Johnson, Richeson, & Finkel, 2011; Exline & Zell, 2012). In my research, I tested whether SES-based rejection anxiety exists for both lower and higher SES individuals and whether anxiety over such rejection would predict context-specific behavioral changes, namely identity concealment. To this end, I developed a scale measuring an individual's anxiety over potential social rejection based on his or her socioeconomic status (RS-s anxiety). I hypothesized that individuals all along the SES continuum would be vulnerable to rejection anxiety and that anxiety would be positively related to concealment behaviors. I expected greater sensitivity and concealment among lower SES individuals than higher SES individuals. Lower SES individuals experience less control of their environment and are more likely to encounter social rejection (Gallo, Espinosa de los Monteros, & Shivpuri, 2009). I measured identity concealment across two environments: at the university and at home. In the measure development stage and across two studies, RS-s anxiety was reported by individuals of both lower and higher SES. Across two studies greater SES identity-based rejection anxiety was found to predict greater self-reported SES identity concealment in the university setting. This positive relationship emerged among both lower and higher SES participants (Study 1 and Study 2). Greater SES identity-based rejection anxiety also predicted greater self-reported identity concealment in the home setting, but only for participants who reported a strong sense of belonging to a lower SES group (Study 2). RS-s anxiety was positively associated with existing social comparison measures and negatively correlated with self-esteem measures (Study 2).

Advisor: Mendoza-Denton, Rodolfo