VictorJuiz/thesis huggingface dataset:
Subsequent risk of stillbirth, preterm birth, and small for gestational age: A cross-outcomes analysis of adverse birth outcomes in California from 1997-2011
Keywords:  Department of Health Research & Policy
Birth outcomes
Epidemiology
Reproductive Epidemiology
Pregnancy
Stanford School of Medicine
Department of Epidemiology and Population Health
Thesis

Individuals who experience an adverse birth outcome such as stillbirth, preterm birth, or small for gestational age (SGA) have an increased risk of outcome recurrence in a subsequent pregnancy. There is limited research on cross-outcome risks, i.e., given an adverse outcome in index pregnancy, the risk of a different but related adverse outcome in subsequent pregnancy. Therefore, we assessed cross-outcome risks for subsequent stillbirth, preterm birth, and SGA.
We used birth certificate and fetal death data from 1997-2011 for singleton California births. The study population consisted of sequential birth pairs (index birth and subsequent birth). Stillbirth was defined as delivery at 20 weeks of gestation of a fetus that died in utero; preterm birth as live birth at 20-36 weeks; and SGA as birthweight <10th percentile for infants of the same sex and gestational age. Relative Risks (RR) were computed using modified Poisson regression with robust standard errors; models were adjusted for variables known to be associated with adverse birth outcomes (e.g., maternal age).
Of 1,992,577 birth pairs, 0.6%, 9.2%, and 10.6% of index births were stillborn, preterm, and SGA, respectively. Individuals experiencing a stillbirth at index birth had an adjusted RR 1.98 (95% CI 1.90, 2.07) for the next birth being preterm and 1.39 (95% CI 1.31, 1.47) for subsequent SGA. Among those with preterm birth at index birth, the adjusted RRs were 1.97 (95% CI 1.84, 2.10) and 1.44 (95% CI 1.42, 1.46) for stillbirth and SGA. Among those with SGA at index birth, the adjusted RRs were 1.56 (95% CI 1.46, 1.67) and 1.48 (95% CI 1.46, 1.50) for stillbirth and preterm birth. The adjusted recurrence risk of each adverse outcome was higher than for cross outcomes: 3.50 (95% CI 2.91, 4.21) for stillbirth, 2.80 (95% CI 2.76, 2.83) for preterm birth, and 3.50 (95% CI 3.46, 3.54) for SGA. Similar RRs for cross-outcome risks were reported in the sensitivity cohort restricted to first and second births only, and with adjustment using inverse-probability censoring weights to account for potential selection bias introduced due to differential censorship.
In addition to an increased risk of recurrent adverse outcomes, we found that individuals experiencing an adverse outcome in one pregnancy had an increased risk of a different adverse outcome in a subsequent pregnancy. These findings support the relatedness of the outcomes and could inform mechanistic studies as well as reproductive planning discussions for individuals experiencing an adverse birth outcome, if subsequent pregnancy is desired.
SURVEILLANCE FOR THE MASSES: CHINA’S USE OF DIGITAL SURVEILLANCE TECHNOLOGIES IN RESPONSE TO COVID-19
Keywords: Government
technology
digital surveillance
China
COVID-19
Thesis

China’s usage of digital surveillance technologies proved effective in its COVID-19 containment strategy. What became a driving research question of this thesis was why China had been able to use such technologies with the compliance of individuals’ and businesses’ when other countries that failed to do the same. This paper specifically researches the underlying social, historical, and political frameworks which made such a response by the CCP possible. Using a combination of primary and secondary source documents, literary research, and associated analysis, this paper crafts a holistic theory on China’s usage of digital surveillance technologies during COVID-19 and its related impactions. One revelation from my research is the CCP’s concern for power and control over Chinese society, which has consequently influenced its related interactions with those below it. Another critical discovery is how the CCP and Chinese society have been subject to multiple and at times conflicting ideologies, all of which informed the country’s COVID-19 response. As China’s response to COVID-19 demonstrates, digital surveillance technologies could be used as tools of expanding authoritative rule in the name of national security. It is the hope of this research that awareness of this topic will lead to a better-informed society that can use digital technologies effectively and ethically.
Synthesis and applications of group VI and VIII metal(II) hydrides for homogeneous electrocatalysis
Keywords: Chemistry.

My doctoral work focused on developing and improving electrocatalytic systems for the reduction or oxidation of small molecules, all of which featured transition metal hydrides as key catalytic intermediates. This simple class of reactions has powerful applications, particularly for energy storage and for mild, selective organic transformations. My research interests centered on the capability of detailed mechanistic understanding to improve processes with real-world impacts. Such insight has enabled me and my coworkers to contribute to the understanding of electrocatalyst design principles in the fuel cell and catalysis communities
Synthesis and characterization of BaSnO3 nanomembranes
Keywords: Applied Physics.

Complex oxide materials exhibit a wide range of exotic magnetic, electronic and optical properties, making them attractive candidates for flexible electronics and nanomechanical devices. In addition, these properties are highly tunable by a number of controls such as applied stress, electric fields and temperature. New advances in thin film growth techniques have led to the synthesis of freestanding complex oxide membranes, allowing them to be integrated in flexible and nanomechanical devices. In this work, I will discuss our efforts to fabricate freestanding La-doped BaSnO3 nanomembranes using the water-soluble sacrificial layer Ba3Al2O6. Doped BaSnO3 is a wide band-gap semiconductor that is known to exhibit high electron mobility at room temperature, showing great prospects as an alternative transparent conducting oxide to the industry standard indium-tin-oxide (ITO). In particular, I will discuss the importance of lattice mismatch and internal strain in the sacrificial layer for producing millimeter-scale perovskite oxide nanomembranes with a high degree of crystallinity. I will also discuss our efforts to measure the mechanical properties of BaSnO3 nanomembranes by probing BaSnO3 drumheads with an atomic force microscope. This technique can be used to extract the Young's Modulus and fracture strength of these nanomembranes. These studies provide important context for future studies on manipulating BaSnO3 nanomembranes and their integration into flexible and nanomechanical devices
Synthesizable mixed-signal building blocks for open source high speed serial links
Keywords: Electrical Engineering.

Generally, design and validation of a high speed serial link require lots of engineering effort, since its performance tightly depends on sophisticated analog and mixed-signal (AMS) circuit blocks. While digital blocks use a set of electrical rules for formal equivalence checking to ensure the Boolean functions of circuits, there are no such universal rules for the AMS blocks -- understanding the rules for dedicated circuits separates novice and experienced AMS designers. Besides, while digital designs are synthesized into standard gates and then laid out using an automatic placement and routing (PnR) tool, AMS blocks rely on a transistor-level custom design flow, which requires a significant amount of non-recurring engineering (NRE) cost. An even bigger problem is that AMS blocks are often the bottleneck for full-chip verification, since they usually require more precision than what is needed for the rest of the system, and hence severely affect the turn-around time (TAT) of product developments. This dissertation proposes a synthesizable and portable architecture of the AMS building blocks of an ADC-based serial link along with an automated design platform. The proposed architecture enables the link to be entirely described by a hardware description language (HDL) using a minimal amount of analog precision. This design is intended to be released to the public with all required design collateral so that its users, even those who do not have deep analog backgrounds, can produce their own PHY easily and efficiently. This platform is called the Open-Source PHY
Synthetic studies of the bis-guanidinium toxin zetekitoxin AB
Keywords: Chemistry.

Zetekitoxin AB (ZTX) is a potent neurotoxin isolated from the endangered Panamanian golden frog, Atelopus zeteki. The tricyclic bis-guanidinium core of ZTX is common to other toxins such as (+)-saxitoxin (STX) and (+)-gonyautoxin II and III (GTX II, GTX III), but ZTX is one of only two known congeners with a C11-alkyl substituent. An unusual guanidinium N, O-acetal and a bridging macrolactam structure composed of a 3,4-cis-disubstituted isoxazolidine render ZTX considerably more complex than all other members of this family of bis-guanidinium natural products. The challenges encountered in efforts to synthesize ZTX from an α-hydroxyketone intermediate resulted in the design and implementation of a new synthetic route towards this complex natural product. The use of a formylpyrrole starting material enables the selective installation of a bromide at the desired C11 position. An in situ derived carbodiimide from glycine allows facile guanidine coupling of the pyrrole moiety. Diastereoselective Mannich cyclization reaction installs the requisite C13 carboxylic acid and generates a key bicyclic intermediate; from this material, the tricyclic guanidinium core is formed through oxidative dearomatization of the pyrrole ring. The tricyclic core accessed in this manner has been shown to be amenable to the synthesis of the bis-guanidinium neurotoxins STX, GTX 2, and GTX 3. The identification of cross-coupling conditions to install a suitable heterocyclic group at C11, followed by macrolactam formation with the C13 carboxylic acid, should ultimately lead to the assembly of ZTX
A tale of two microbes : nanoscale molecular cinematography of bacteria and coronaviruses
Keywords: Chemistry.

Since the first optical detection of a single molecule 32 years ago, single-molecule microscopy has revolutionized our understanding of complex chemical and biological systems. Precise localization combined with switchable or blinking fluorescent labels allows super-resolution microscopy to view biological systems down to the ~10 nm scale. In this thesis, I will discuss the hidden secrets of two tiny creatures revealed by single molecule nanoscopic imaging: 1) The bacterium Caulobacter crescentus programs bifunctionality into a regulatory protein to drive asymmetric cell division. 2) Imaging the spatial organization of human coronavirus HCoV-229E genomic RNA and double stranded RNA during infection of lung epithelial cells gives insight into the viral replication process. This thesis will begin with a short introduction on the basic scientific concepts critical to my work and I will go into the theoretical and experimental framework are foundational for research in this dissertation in Chapter 2. Asymmetric cell division yields two distinct daughter cells by mechanisms that underlie cellular diversity in all kingdoms of life. The bacterium Caulobacter crescentus orchestrates this complex process with less than 4000 genes. In Chapter 3, I will describe a strategy deployed by Caulobacter where a regulatory protein, PopA, is programmed to perform distinct roles based on its subcellular address. Combining biochemistry and single-molecule tracking, I will show that depending on the availability of the second messenger molecule, cyclic di-GMP, the PopA protein adopts either a monomer or dimer form. The two oligomeric forms interact with different partners at the two cell poles and mediate the function of two distinct molecular machineries. In addition, I discovered a novel binding partner of PopA at the swarmer pole, which uncovered its additional function. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen causing the ongoing COVID-19 pandemic. In Chapter 4, I will review the development, in collaboration with Stanley Qi lab, of a super-resolution imaging framework that allows us to study coronavirus infection at the nanoscale in a mammalian host cell, using a less infectious model, human coronavirus HCoV-229E. Using this approach, we revealed a striking spatial separation of genomic RNA and double-stranded RNA, which is the intermediate in viral amplification, and showed their distinct structures at different stages of the infection
Tamagawa numbers of smooth connected groups
Keywords: Mathematics.

In this thesis, I define and investigate some questions about Tamagawa measures and Tamagawa numbers of smooth connected group schemes over global fields beyond the traditional affine and projective cases. In particular, over number fields, for every (smooth) connected group scheme I construct certain extensions by a split torus and prove a formula for the Tamagawa number of such extensions when either the initial group scheme is commutative or the map from each pure inner twist to the maximal abelian variety quotient is surjective on local points at each real place
Target-oriented elastic full-waveform inversion
Keywords: Geophysics.

Wave-equation-based parameter estimation techniques can retrieve accurate and high-resolution subsurface physical properties from seismic data acquired close to the surface of the Earth. In fact, multiple acoustic full-waveform inversion methods have been proposed over the years to retrieve the P-wave velocity of the subsurface. Moreover, researchers have extended full-waveform inversion approaches to estimate anisotropic and absorption parameters as well. Nowadays, some applications of elastic full-waveform inversion can also be found. However, given its prohibitive computational cost compared to the acoustic counterpart, elastic wave-equation inversion workflows still have limited applicability within seismic exploration datasets. To tackle this challenge, I propose a novel wave-equation-based elastic parameter estimation workflow based on wave-equation operators. I refer to the entire approach as target-oriented elastic full-waveform inversion. The method is composed of two steps. In the first one, I apply an extended linearized waveform inversion to the surface data. The obtained subsurface image is then employed to synthesize data as if they were acquired close to a target area. Finally, this dataset is inverted using an elastic full-waveform inversion workflow to estimate the subsurface elastic parameters. I demonstrate its efficacy on a 2D synthetic test and an ocean-bottom-node dataset acquired in the Gulf of Mexico, showing its ability to retrieve the elastic parameters of potential subsurface prospects. Compared to the elastic inversion of the surface dataset, the proposed method has a computational cost lower by two orders of magnitude
Task-driven Modeling of the Drosophila Head Direction Circuits
Keywords:  Symbolic Systems Program
Task-driven Modeling
Symbolic Systems Program
Thesis

Animals rely on internal representations of their head direction to stay oriented while navigating their environments. In the Drosophila brain, these representations are instantiated by head direction cells in a brain region called the central complex. Like the head direction circuits of other animals, the central complex exhibits dynamics that can be modeled by a class of recurrent neural networks called ring attractors. Earlier work has shown that artificial neural networks trained to perform angular velocity integration, the tracking of an agent’s heading angle from its angular velocity over time, naturally recapitulate ring attractor dynamics and other features of biological head direction circuits. In this paper, I build upon this earlier task-driven modeling work, further characterizing the dynamics and connectivity of RNNs trained to perform a modified form of angular velocity integration. Like the preceding study, I find that these trained models develop single unit response properties that mirror those of biological head direction cells, display low-dimensional ring attractor-like dynamics, and develop a connectivity pattern of short-range excitation and long-range inhibition characteristic of ring attractor networks. In addition, I also explore how these networks behave in the absence of inputs and respond to the stimulation of subsets of their units.
Teaching and talking with baby : antecedents and consequences of enriching input from caregivers
Keywords: Psychology.

The nature of the early environment affects children's outcomes across socioemotional and cognitive domains of functioning. In infancy, caregivers' behaviors largely determine the nature of the early environment. Specifically, through interactions with their caregivers, infants receive the psychosocial stimulation they need for healthy development. In this dissertation, I use a multi-dimensional, multi-modal approach to characterize the psychosocial stimulation that 6-month-old infants receive from their caregivers. I design, implement, and assess three studies that expand understanding of the effects of the quantity and consistency of stimulation, operationalized through language input, on infant risk for psychopathology (chapter 2) and brain function (chapter 3), and the mechanisms that drive variation in the quantity and quality of the stimulation that caregivers provide (chapter 4). Findings from these studies demonstrate that: 1) the consistency of language input that infants receive from adults predicts their subsequent symptoms of psychopathology in toddlerhood, 2) the quantity of vocal exchanges that infants engage in with adults in their everyday environments is associated with their brain function in language networks at rest, and 3) caregivers' explicit goals about providing stimulation influence the degree to which they engage in behavior that may counter infant autonomy and disrupt infant exploration. Together, findings from these studies suggest that different aspects of the stimulation infants receive from their caregivers differentially influence aspects of infant psychobiology. Moreover, the quality of the stimulation infants receive from their caregivers can be modified by shifting caregivers' goals. I discuss the implications of these findings for future research of the impact of the early environment on children's psychobiological development and for the design of interventions to improve the early environment
Techniques for Collecting Shadow-Free Imagery with Unmanned Aerial Vehicles in Precision Agriculture
Keywords:  Department of Electrical Engineering
Electrical Engineering
NIFA
UAV
unmanned aerial vehicles
precision agriculture
drone
shadow
cloud
aerial imagery
removing shadows
Thesis

Rising populations and anthropogenic climate change continue to augment pressures on the agricultural industry to produce more with less land. Imagery from unmanned aerial vehicles (UAVs) has shown promise in meeting this demand, allowing farms to precisely monitor the status of their crops and target areas for intervention. Variations in cloud cover represent a serious challenge when aerial imagery is processed to generate agricultural insights, as even small variations in lighting may result in inaccurate prescriptions of crop inputs. This work introduces a method for processing wide angle imagery to automatically determine the location of shadows cast by clouds. A communication protocol is also developed for directing UAVs to avoid flying over shadowed regions and retrieving UAV imagery for monitoring both crops and cloud cover. This work comprises a critical foundation of core functionality necessary for end-to-end development of multi-vehicle UAV systems to collect shadowless imagery.
Testing the limits : non-minimal extensions of popular beyond the standard model frameworks
Keywords: Physics.

While the Standard Model (SM) represents perhaps the most successful scientific theory ever constructed by humans, it is hardly complete. In the five decades since its inception, a number of intriguing extensions to the SM have been put forward by the physics community which might address questions that the SM leaves unanswered. In this thesis, we consider non-minimal extensions to several of the most popular frameworks for physics beyond the Standard Model (BSM): The Randall-Sundrum model of a warped extra dimension, the introduction of gauged flavor symmetries, and the vector portal/kinetic mixing paradigm for dark matter. Each of these models attempts to address a different unresolved problem within the SM: The Randall-Sundrum model naturally explains the enormous hierarchy between the gravitational and electroweak energy scales (the gauge hierarchy problem), while gauged flavor symmetries attempt to impose a structure on the intricate pattern of fermion masses and mixings present in the Standard Model, and vector portal/kinetic mixing models of dark matter represent a well-motivated subset of models of particle dark matter. In this thesis, we explore directions in which each of these BSM frameworks may be extended beyond their minimal constructions. In Chapter 2, we perform a detailed exploration of brane-localized kinetic terms, which may be added as additional parameters in Randall-Sundrum constructions, analytically identifying the values of these parameters which avoid spacetime instabilities or ghost-like (negative probability) states in the theory. In Chapter 3, we present a model in which a gauged flavor symmetry is incorporated into a Randall-Sundrum framework, and perform a detailed exploration of the resulting distinctive flavor phenomenology. In Chapter 4, we discuss a realization of the vector portal/kinetic mixing dark matter paradigm with a compactified extra dimension, in which the scalar which break the Standard Model electroweak gauge group and the scalar ``dark Higgs'' which breaks the additional dark-sector gauge symmetry proposed by this class of models are localized on opposite 3-branes, naturally eliminating phenomenologically concerning mixing between the dark and SM Higgs fields. In Chapter 5, we present a model which unifies the dark gauge group of vector portal/kinetic mixing models with an SU(3) gauged flavor symmetry, in which an additional fourth generation of matter particles serves as ``portal matter'', facilitating the kinetic mixing required by the dark matter paradigm. We then explore the phenomenology of this construction, noting that some behavior (such as portal matter fields decaying into conventional vector-like fermions) does not emerge in models that include portal matter or a gauged flavor symmetry alone, and will yield unique collider signatures