VictorJuiz/thesis huggingface dataset:
The Role of Pubertal Development in Adolescent Risky Decision-Making

Adolescence is a period in development characterized by a greater tendency to engage in risky behaviors. The onset of adolescence is marked by puberty, which involves a dramatic rise in sex steroids. Existing neurobiological models have proposed that the rise in sex steroids during puberty influences the development of the adolescent brain, in particular the brain regions involved in the processing of socio-emotional information. According to these models, adolescents engage in more risk taking compared to children and adults because they process rewards differently and are more sensitive to their social environment. In a separate line of research, it has been hypothesized that changes in sleep during adolescence also contribute to the greater tendency to take risks. In this dissertation, we explored the role of pubertal hormones, social information, and sleep in adolescent risky decisions. To measure risk taking, we designed a child-friendly probabilistic decision-making game called the Jackpot task. In this task, participants could choose to take a risk or play it safe based on explicitly provided information about the risk level and stakes involved in their decision, and the type of cumulative performance feedback (social or monetary) they received. This task was administered in two independent samples of adolescents while they were lying in an MRI scanner, which allowed for examination of the reward-related brain processes associated with their risky choices. Pubertal hormone levels were measured based on saliva provided by the participants. Sleep was measured using a self-report questionnaire that was administered across five days. Participants also filled out various measures to capture individual differences in personality. While we did not find evidence for a peak in reward-related brain activation during adolescence, we did find large individual differences among adolescents in their behavior as well as their neural responses to rewards and social information. Reward-related brain responses associated with risk taking corresponded with higher levels of testosterone and stronger self-reported approach tendencies. The influence of social feedback, in the context of risky decisions, was stronger in girls with higher levels of estradiol and girls who reported greater susceptibility to peer influence. Adolescent girls with a preference for later bedtimes and with more irregular sleep patterns tended to make more risky decisions. These findings provide insight into some of the factors that contribute to adolescent risk taking and highlight the importance of using an interdisciplinary approach to investigate adolescent behavior.

Advisor: Dahl, Ronald E
Bunge, Silvia A
Beyond Compliance: Toward Effective Principal Leadership of English Language Development Instruction

English Language Development instruction (ELD) is at the forefront of scrutiny in many schools and districts at-large. Within the Bay Vista Unified School District (BVUSD), a storied history, highlighted by a class-action lawsuit and resulting consent decree, has set the context for large scale decision making around language instruction and how schools are held accountable. Lau v. Nichols (1974) began with a group of Chinese-American families alleging that the school district failed to provide the necessary language instruction to provide access for English learners to the core curriculum, much of which was presented in English. The result of the litigation was a lengthy consent decree mandating that BVUSD provide a minimum number of minutes of daily focused ELD instruction. District officials worked under the intense monitoring of a federal court judge to hold all schools accountable for the provision of this ELD instruction daily. Principals quickly became tasked with formulating a structure at school for leveled ELD instruction and a system to monitor its implementation. Items to be monitored heavily involved classroom environmental tenets of “quality” instruction./nForty years later, Lau is still alive in BVUSD and principals, among the many other roles they play, are still responsible for this compliance-driven task of monitoring ELD instruction. The prevailing principal support, at the district level, is in the professional development on how to use the district’s monitoring tool to assess the level of implementation of ELD in classrooms./nThe following design development study aimed to shift principal practice beyond simply monitoring for compliance into a practice of understanding the instructional indicators of effective ELD instruction and how to observe for them, thus building the capacity to acknowledge compliance, but observe and offer feedback to teachers on the highest leverage instructional tenets of truly high quality ELD instruction. The three dimensions of this design include an awareness of compliance orientation, a shared understanding of the principals’ loci of control, and the technical competence necessary to move practice forward, from environmental/compliance driven observations to instructionally sound ones. The intervention design involves ten one-hour sessions designed to have principals engage in a reflection on their reliance on compliance, come to a shared understanding of the principal locus of control, goal setting, skill building, and working toward efficacy. Through these design features and intervention activities, principals became aware of their reliance on compliance, what they, themselves, could actually impact in instruction, were able to engage in goal setting, and actually engaged in observations though the lenses of an acknowledgment of compliance and focus on instructional effectiveness.

Advisor: Mintrop, Heinrich
Aspects of Particle Physics Beyond the Standard Model

This dissertation describes a few aspects of particles beyond the Standard Model, with a focus on the remaining questions after the discovery of a Standard Model-like Higgs boson. In specific, three topics are discussed in sequence: neutrino mass and baryon asymmetry, naturalness problem of Higgs mass, and placing constraints on theoretical models from precision measurements.\/nFirst, the consequence of the neutrino mass anarchy on cosmology is studied. Attentions are paid in particular to the total mass of neutrinos and baryon asymmetry through leptogenesis. With the assumption of independence among mass matrix entries in addition to the basis independence, Gaussian measure is the only choice. On top of Gaussian measure, a simple approximate $U(1)$ flavor symmetry makes leptogenesis highly successful. Correlations between the baryon asymmetry and the light-neutrino quantities are investigated. Also discussed are possible implications of recently suggested large total mass of neutrinos by the SDSS/BOSS data.\/nSecond, the Higgs mass implies fine-tuning for minimal theories of weak-scale supersymmetry (SUSY). Non-decoupling effects can boost the Higgs mass when new states interact with the Higgs, but new sources of SUSY breaking that accompany such extensions threaten naturalness. I will show that two singlets with a Dirac mass can increase the Higgs mass while maintaining naturalness in the presence of large SUSY breaking in the singlet sector. The modified Higgs phenomenology of this scenario, termed ``Dirac NMSSM'', is also studied.\/nFinally, the sensitivities of future precision measurements in probing physics beyond the Standard Model are studied. A practical three-step procedure is presented for using the Standard Model effective field theory (SM EFT) to connect ultraviolet (UV) models of new physics with weak scale precision observables. With this procedure, one can interpret precision measurements as constraints on the UV model concerned. A detailed explanation is given for calculating the effective action up to one-loop order in a manifestly gauge covariant fashion. This covariant derivative expansion method dramatically simplifies the process of matching a UV model with the SM EFT, and also makes available a universal formalism that is easy to use for a variety of UV models. A few general aspects of RG running effects and choosing operator bases are discussed. Mapping results are provided between the bosonic sector of the SM EFT and a complete set of precision electroweak and Higgs observables to which present and near future experiments are sensitive. Many results and tools which should prove useful to those wishing to use the SM EFT are detailed in several appendices.

Advisor: Murayama, Hitoshi
III-V Nanolaser Integration with CMOS Electronics and Silicon Photonics

Using optical signal rather than electrical signal to transmit information on silicon-based computer chips, also known as intra-chip optical interconnect, can potentially boost computation speed and reduce energy consumption. This requires a laser source on silicon, which is a challenging task. Almost all commercial semiconductor lasers are made of III-V material because silicon is an inefficient emitter due to its indirect bandgap. Therefore, integration of III-V laser on silicon is a must towards practical optical interconnect. However, both lattice constant and thermal expansion coefficient mismatch between III-V and silicon fundamentally restricted high quality III-V thin film growth on top of silicon substrates. III-V nanostructures on silicon, on the other hand, can overcome this issue thanks to their small footprint and fully relaxed strain from lattice mismatch. As a result, III-V nanolaser becomes a promising candidate as the on-chip light source for optical interconnect./nIn this dissertation, our III-V nanopillar lasers experimentally demonstrate integration capabilities with silicon-based electronics and photonics. The nucleation and growth mechanism of InGaAs and InP nanopillars is first studied with characterization observations, unveiling the reason accounting for the high quality nanopillar. The superior crystal quality, together with unique 3D whispering gallery mode, enables the laser oscillation in as-grown nanopillars. To prove the CMOS compatibility, these nanolasers are monolithically grown onto silicon-based transistor chips, without compromising the electronic performance of chips. In addition, horizontal nanopillar growth is developed to integrate nanolasers with silicon waveguides in an end-fire manner. The coupling between laser and waveguide is prominently observed under photoluminescence experiment, serving as a proof-of-concept for integration with more complicated photonic circuits. To avoid laser emission absorbed by silicon, long wavelength lasers are obtained with InP/InGaAs/InP quantum well nanpillars and three novel optical cavities. Detailed laser modeling is also performed to provide guidance for further laser optimization. For electrical pumping, we also explores methods to make perfect nanopillar diodes. Furthermore, an optical link with nanopillar devices and polymer waveguide is shown to be functional to transmit signals on silicon substrate. With these experimental demonstrations, this III-V nanolaser strategy presents a great potential to achieve on-chip laser source.

Advisor: Chang-Hasnain, Constance J
The Importance of Zeroth-Order Approximations in Molecular Quantum Mechanics

The work herein is concerned with developing computational models to understand molecules. The underlying theme of this research is the reassessment of zeroth-order approximations for higher-level methods. For second-order Moller-Plesset theory (MP2), qualitative failures of the Hartree-Fock orbitals in the form of spin contamination can lead to catastrophic errors in the second order energies. By working with orbitals optimized in the presence of correlations, orbital-optimized MP2 can fix the spin contamination problem that plague radicals, aromatics, and transition metal complexes. In path integral Monte Carlo for vibrational energies, the zeroth-order propagator is typically chosen to be the most general possible, the free particle propagator; we chose to be informed by the molecular structure we have already attained and apply a propagator based on the harmonic modes of the molecule, improving sampling efficiency and our Trotter approximation.

Advisor: Head-Gordon, Martin
The Statistics of Disparity in Natural Viewing

Humans and many animals have forward-facing eyes providing different views of the environment. Precise depth estimates can be derived from the resulting binocular disparities, but determining which parts of the two retinal images correspond to one another is computationally challenging. To aid the computation, the visual system focuses the search on a small range of disparities. Analysis of the statistics of natural scenes has revealed evidence that the brain exploits regularities to efficiently encode the visual world. We asked whether the brain similarly exploits the disparities encountered during binocular viewing of the natural environment. We did this by simultaneously measuring binocular eye position and 3D scene geometry during natural tasks using a novel device that can reconstruct a participant’s retinal image while they perform natural tasks such as socializing, navigating, and making a sandwich. We find that the natural distribution of disparities is indeed matched to the statistics of natural disparity, allowing for a smaller range of correspondence search. Furthermore, the distribution of disparity explains the perception of some ambiguous stereograms. Finally, disparity preferences of macaque cortical neurons are consistent with the natural distribution. Analysis of the disparities resulting from simulated eye positions yields notably different distributions, suggesting that models of disparity processing should carefully consider how assumptions about eye position could influence the results. We conclude that binocular neural processes are well-matched to the regularities of the 3D environment.

Advisor: Banks, Martin S
Anti-malarial Antibody Responses & Applications for Assessing Malaria Exposure

This dissertation describes the discovery of highly informative serologic biomarkers of recent exposure to Plasmodium falciparum, the most deadly species causing malaria. An innovative approach that combined detailed individual-level exposure data, high-throughput screening of hundreds of antibody responses, and robust statistical methods was used to identify the most informative signatures of exposure. The novel antigens described here and, more importantly, the outlined approach for biomarker discovery will allow for the development of public health and research tools that are imperative for the control and elimination of malaria. Additionally, the methodologies outlined here are highly applicable to the discovery of biomarkers of exposure for other infectious diseases./nSerology has been used for decades to measure exposure to Plasmodium species and other infectious diseases. While useful, most existing assays for measuring P. falciparum exposure have been based on population-level responses to a few target antigens chosen by convenience rather than utility, resulting in relatively coarse exposure estimates. Here, detailed assessments of malaria exposure in Malian and Ugandan children were used to identify novel serologic biomarkers of malaria exposure and calibrate responses to quantitative estimates of individual exposure. The power of obtaining these individual-level estimates was illustrated by their ability to accurately identify individuals with infection in the recent past; to obtain precise estimates of malaria incidence in a population from cross-sectional samples of as few as 20 individuals; and to accurately estimate heterogeneity in recent exposure within a community using data from a single time point./nInterest in the development of improved serologic assays has increased in recent years as more investment is made in malaria control and elimination. There is need for widely available, accurate estimates of malaria exposure that will allow for targeting and evaluation of public health interventions. This dissertation initiates a response to the call to develop accurate field-based assays for rapid and cost-effective assessment of malaria exposure, with the ultimate goal of putting cohort-quality data into the hands of malaria control programs.

Advisor: Greenhouse, Bryan
Harris, Eva
Childhood ADHD and Perceived Relationship Quality in Young Women: Core Findings and Adolescent Mediators

Attention-Deficit/Hyperactivity Disorder (ADHD) in females is associated with notable interpersonal difficulties during childhood and adolescence, yet little is known about the relationship quality of young women with histories of childhood ADHD. The purpose of this study was to examine the association between childhood ADHD and self-reported peer and parent relationship quality in young women, and to examine potential adolescent pathways of this association. Data were drawn from the Berkeley Girls with ADHD Longitudinal Study (BGALS, N = 228), composed of females with childhood ADHD (n = 140) and healthy comparisons (n = 88). Participants were followed prospectively from childhood (Wave 1; M age = 9.6 years) and assessed during adolescence (Wave 2; M age = 14.2 years) and young adulthood (Wave 3; M age = 19.6 years). A principal component analysis (PCA) on items from the Interview of Parent and Peer Relationships (Armsden & Greenberg, 1987), yielded a single peer and a single parent factor, with higher scores reflecting better perceived relationship quality (e.g., more trusting, accessible, and reliable) and lower scores reflecting poorer perceived relationship quality (e.g., less trusting, accessible, and reliable). Participants were compared with respect to Wave 1 ADHD status and symptom severity to their Wave 3 relationship quality. Parallel bivariate analyses were conducted according to ADHD diagnostic subtype at Wave 1 and diagnostic persistence over time. Potential pathways linking Wave 1 ADHD and Wave 3 relationship quality were explored via mediational analyses using four candidate variables assessed during adolescence (Wave 2 social skills, response inhibition, internalizing symptoms, and externalizing symptoms). Analyses were conducted with inclusion of psychiatric, cognitive, and demographic covariates. After covariate adjustment, ADHD diagnostic status was associated with significantly poorer peer and parent relationship quality, with small and medium effect sizes, respectively. There were no differences in relationship quality with respect to diagnostic subtype at Wave 1. Relative to having a lifetime non-diagnosis or transient diagnosis of ADHD, persistent ADHD was associated with significantly lower quality peer and parent relationship quality. Finally, social skills and response inhibition partially mediated the Wave 1 ADHD – Wave 3 relationship quality associations, although only the social skills variable was in the expected direction. In females, childhood ADHD, regardless of diagnostic subtype, is a specific risk factor for diminished quality of relationships with peers and parents during young adulthood. Persistent ADHD appears to be detrimental to parent relationship quality in particular. Interventions targeting adolescent social skills in girls with ADHD may help to improve the quality of their peer and parent relationships as they transition to adulthood.

Advisor: Hinshaw, Stephen P.
Developmental Genetic Basis of Tooth Number Evolution in Stickleback Fish

Teeth are a classic model for studying vertebrate organogenesis and evolution. Despite the incredible phenotypic diversification of dentition in vertebrates, our understanding of the molecular and developmental basis behind this variation is limited. A derived benthic freshwater stickleback population has evolved a nearly two-fold increase in ventral pharyngeal tooth number compared to their ancestral marine counterparts. This evolved tooth gain provides an excellent system to study the developmental and molecular genetic basis of evolved dental variation. To ask when during development evolved tooth gain appears, we generated lab-reared developmental time courses of a low-toothed marine population and this high-toothed freshwater population. Early in development, no differences in dental patterning are observed. However, at late larval stages, an increase in tooth number, an increase in tooth plate area, and a decrease in tooth spacing arise. We identified genomic regions controlling these evolved patterning changes by mapping quantitative trait loci (QTL) controlling tooth number, area, and spacing in a marine by freshwater F2 cross. One large effect QTL controlling tooth number fine-maps to a genomic region containing an excellent candidate gene, Bone morphogenetic protein 6 (Bmp6). Stickleback Bmp6 is expressed in developing teeth, but no coding changes are found between the two populations. However, by quantitatively comparing allele specific expression of Bmp6, we find cis-regulatory changes have down-regulated the relative expression level of the freshwater Bmp6 allele at late, but not early, stages of development. To functionally test the role of Bmp6 in controlling tooth patterning, we generated predicted loss-of-function alleles of Bmp6 in freshwater sticklebacks. We found that Bmp6 is required for tooth formation and tooth plate area mirroring aspects of the evolved changes. Next, to discover enhancers that contain marine/freshwater sequence differences, we compared the chromosome 21 genomic sequences from fish with the tooth QTL to fish without the QTL. We identified a partially conserved region of the fourth intron of Bmp6 containing QTL-associated variants. This region is a tooth and fin enhancer that drives partially distinct expression patterns during tooth development compared to a 5’ Bmp6 tooth and fin enhancer we previously discovered that lacks consistent sequence differences associated with the tooth QTL. Future genetic and transgenic approaches will functionally test this intron 4 enhancer of Bmp6 as a candidate for underlying evolved tooth gain in sticklebacks.

Advisor: Miller, Craig T