VictorJuiz/thesis huggingface dataset:
Non-Canonical Protein Isoforms Produce Diversity of Protein Function and Localization in Budding Yeast

Global methods for assaying translation have greatly improved our understanding of the protein-coding capacity of the genome. In particular, it is now possible to perform genome-wide and condition-specific identification of translation initiation sites through modified ribosome profiling methods that selectively capture initiating ribosomes (TIS- profiling). Here we apply this approach to meiotic and mitotic timepoints in budding yeast and show the surprising diversity of protein products that can be revealed by such methods.Chapter 2 describes our use of TIS-profiling to globally annotate translation initiation sites in yeast, with a particular focus on alternative N-terminally extended protein isoforms, which initiate from near-cognate (non-AUG) start codons upstream of annotated AUG start codons. We identified 149 genes with an extended isoform and show that these isoforms are produced in concert with canonical isoforms and are translated with high specificity, resulting from initiation at only a small subset of possible start codons. The non-AUG initiation driving their production is enriched during meiosis and induced by low eIF5A, which is seen in this context. Despite our success in identifying extended protein isoforms, high-confidence identification of new coding regions that entirely overlap annotated coding regions – including those that encode truncated protein isoforms – remained challenging. As described in Chapter 3, we developed a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms. We performed extensive experimental validation of these truncated proteins and defined two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5truncation and Pus1truncation, to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins. Together these findings support the adoption of less static views of gene identity and a broader framework for considering the translational capacity of the genome.

Advisor: Brar, Gloria A
Enumerating small hyperbolic 3-manifolds

This paper documents a computer-assisted procedure for rigorously analyzing small hyper-bolic 3-manifolds. Briefly, we will define a compact six-dimensional space P that parame- terizes pairs of elements of Isom(H3 ), and then construct a regular binary space partition (BSP) tree which subdivides P into subregions Pi and whose leaves are — with a few ex- ceptions — labeled with killerwords. These killerwords will encode miniature proofs that Pi cannot contain any points which correspond to particular choices of pairs of generators of any torsion-free discrete group of Isom(H3 ). This tree of mini-proofs will then be used to ex- haustively isolate all possible manifolds which can have properties related to the dimensions of P. This method has been used as a foundation for tackling multiple long-standing problems at the interface of hyperbolic geometry and low-dimensional topology. In particular: topo- logical rigidity of hyperbolic 3-manifolds; the generalized Smale conjecture for hyperbolic 3-manifolds; finding the closed 3-manifold of least volume; and the Gordon conjecture on exceptional Dehn fillings.

Advisor: Kirby, Robion
Gabai, David
All-Carbon Polyradical Architectures

Scanning probe techniques at the vacuum-solid interface have unlocked new avenues in the synthesis and study of reactive materials. The study of stable radicals has grown as a field since the onset of the twentieth century. Polyaromatic hydrocarbons (PAHs) have represented a significant portion of these studies. Though as the degree of radical or radicaloid nature of target structures increases, their solution synthesis and study become more challenging. Diradical(oid)s have been studied more regularly since the end of the twentieth century, with the achievement of tetraradical(oid)s and hexaradical(oid)s occurring only in the last few years. The solid-vacuum interfaces and scanning probe microscopy (SPM) have permitted an enormous leap in the accessibility of target structures and the robustness of characterization. For example, zigzag-edged graphene nanoribbons, unsubstituted triangulene molecules, and magnetic porphyrins have been studied using these methods. These methods have allowed a more detailed inspection of the magnetic properties of open-shell carbon materials. The work described in this dissertation targets all-carbon polyradical nanomaterials for the study of fundamental phenomena in carbon magnetism. This work has implications for next-generation spintronics and quantum computing. Chapter 2 focuses on the synthesis of a modular spin supergraphene of S = ½ phenalenyl and its 1-dimensional superpolyacetylene analogues. Chapter 3 focuses on the analogous study of S = 1 triangulene modular periodic materials. Chapter 4 focuses on 1-dimensional polyradical graphene nanoribbons (GNRs) in solution and at the vacuum-gold interface. These materials hold promise for achieving fully integrated molecular circuits. And finally, Chapter 5 focuses on 0-dimensional magnetic structures, biphenalenyl and bottom-up synthesis of a nitrogen-vacancy (NV) center.

Advisor: Fischer, Felix R
Intervention Acceptability of a Digitized Self-Monitoring Procedure for ADHD

Evidence-based ADHD interventions such as self-monitoring are scarcely used by educators,especially those teaching in secondary schools (Sibley et al., 2016). Common barriers to intervention use include restricted time, poor knowledge of ADHD, and feelings of frustration and stress associated with teaching students with ADHD (Szép, 2021). Because barriers are often related to stimuli and events that result in increased mental effort, one theoretical lens through which such barriers can be understood is cognitive load. Therefore, in the present research, I used cognitive load theory as a framework to guide the design of a novel, computerbased, self-monitoring intervention intended to reduce barriers to teachers’ intervention use. The purpose was (a) to evaluate the cognitive load experienced by teachers when implementing a self-monitoring intervention, and (b) to explore teachers’ acceptability of the novel, computer-based self-monitoring intervention. To this end, secondary school teachers from the United States read a vignette description of an adolescent with ADHD and were subsequently randomly presented with one of two self-monitoring intervention modalities— computer-based or paper-and-pencil based—to support the student. Then, participants completed rating scales that assessed their likelihood of intervention use and perceived cognitive load associated with the intervention procedures. 336 participants met eligibility criteria to participate, but only 89 were included in the final analysis after listwise deletion of cases that failed to pass the validity check for adequate engagement with the intervention and vignette. Participants’ acceptability ratings for both the computer-based intervention and analog intervention were favorable, and ratings for the computer-based intervention were somewhat higher than their ratings for the analog intervention. However, the difference was not practically significant. Limitations and future directions are discussed.

Advisor: Worrell, Frank C
Reconstitution of kinetochore motility and microtubule dynamics reveals an interdependence of a microtubule polymerase and a motor protein in establishment of kinetochore end-on attachments

During mitosis, individual microtubules make attachments to chromosomes via a specialized protein complex called the kinetochore to faithfully segregate the chromosomes to daughter cells. Translocation of kinetochores on the lateral surface of the microtubule has been proposed to contribute to high fidelity chromosome capture and alignment at the mitotic midzone, but has been difficult to observe in vivo because of spatial and temporal constraints. To overcome these barriers, we used total internal reflection fluorescence (TIRF) microscopy to track the interactions between microtubules, kinetochore proteins, and other microtubule-associated proteins in lysates from metaphase-arrestedSaccharomyces cerevisiae. TIRF microscopy and cryo- correlative light microscopy and electron tomography indicated that we successfully reconstituted interactions between intact kinetochores and microtubules. These kinetochores translocate on the lateral microtubule surface toward the microtubule plus end and transition to end-on attachment, whereupon microtubule depolymerization commences.These kinetochore dynamics we were able to reconstitute in vitro resembled the process of chromosome congression seen in cells. Chromosome alignment on the mitotic spindle, also referred to as congression, is facilitated by translocation of side- bound chromosomes along the microtubule surface, which allows the establishment of end-on attachment of kinetochores to microtubule plus ends. This is exactly what we observed in our reconstitution assay. We observed kinetochore translocation on the lateral microtubule surface toward the microtubule plus end, which we found that the directional kinetochore movement is dependent on the highly processive kinesin-8, Kip3. We propose that Kip3 facilitates stable kinetochore attachment to microtubule plus ends through its abilities to move the kinetochore laterally on the surface of the microtubule and to regulate microtubule plus end dynamics. Additionally, we also observed kinetochore motility was dependent on Stu2. However, we showed that these proteins display distinct dynamics on the microtubule. Kip3 is highly processive and moves faster than the kinetochore. Stu2 tracks both growing and shrinking microtubule ends but also colocalizes with moving lattice-bound kinetochores. In cells, we observed that both Kip3 and Stu2 are important for establishing chromosome biorientation, Moreover, when both proteins are absent, biorientation is completely defective. All cells lacking both Kip3 and Stu2 had declustered kinetochores and about half also had at least one unattached kinetochore. Our evidence argues that despite differences in their dynamics, Kip3 and Stu2 share roles in chromosome congression to facilitate proper kinetochore- microtubule attachment.

Advisor: Barnes, Georjana
Drubin, David G
Feedforward MLSE Equalization for High Speed Serial Links

An ever-increasing demand for high data rate wireline links must be met to support the continual scaling of computing and communication systems. Typical serial link architectures use feedback-based channel equalization schemes, which can be challenging and even infeasible to realize for data rates beyond 100 GBaud/s. To alleviate this feedback-induced latency bottleneck, this thesis explores feedforward equalizers inspired by the maximum likelihood sequence estimation (MLSE) algorithm. Targeting short-reach, die-to-die links, a 1-tap fully feedforward MLSE architecture is shown to achieve comparable error statistics with the conventional 1-tap decision feedback equalizer (DFE)./nA 160 Gb/s NRZ receiver implementing the 1-tap MLSE equalizer is taped out in a 16 nm FinFET process to evaluate the future promise of the proposed approach. The feedforward MLSE is time-interleaved to achieve the desired throughput. Current integration techniques provide energy-efficient analog latches used in the MLSE datapath. The datapath is designed using the Berkeley Analog Generator (BAG) framework. Both the top level datapath and its subblocks are created using parameterizable circuit schematic and layout generators. Measurement and design scripts identify the impact of inter-subblock routing parasitics, facilitating agile subblock design iteration with top level floorplanning in mind./nAs the channel characteristics are unknown a priori, the coefficient settings of the MLSE must be adapted in real time. An adaptation scheme for the feedforward MLSE equalizer is proposed with separate loops for each interleaved MLSE slice to account for process variation. The receiver is taped out along with a corresponding 160 Gb/s NRZ transmitter and tested over an on-package loopback channel of 8.5 mm, which incurs 3 dB of loss at the Nyquist frequency. The receiver is simulated to operate at an energy efficiency of 2.08 pJ/bit, with the datapath itself consuming 0.72 pJ/bit.

Advisor: Stojanovic, Vladimir
Alon, Elad
Three Studies of U.S. Mortality

We are far from a complete understanding of the social determinants of mortality in theUnited States. Despite the longstanding interest in racial and class-based inequalities in health and mortality in the United States, research is often hampered by data limitations. However, new advances in data linkage have allowed mortality researchers to construct ad- ministrative datasets with millions of mortality records and demographic covariates. The unprecedented scale and richness of these administrative datasets allow social scientists to make new discoveries into the contours of mortality disparities in the United States./nThis dissertation is comprised of three studies of mortality using large-scale, linked U.S.Census and administrative death records. In my second chapter, I investigate the relationship between owning a home in early adulthood and life expectancy, demonstrating that owning a home in early adulthood has a causal effect on life expectancy. My second study assesses the predictability of individual-level longevity, demonstrating the challenges of predicting individual-level mortality. The final study of the dissertation examines the Black-White crossover, finding evidence that the crossover is not a data artifact and cannot be uncrossed using sociodemographic variables alone.

Advisor: Goldstein, Joshua R.
Self Consistent Excited State Mean Field Theory: Development and Applications

In the wide spectrum of excited state quantum chemistry methods, there is no direct analogue to Hartree-Fock theory. This dissertation presents the theory and initial applications for a self consistent framework for Excited State Mean Field (ESMF) theory. This method presents a self consistent equation analogous to the Roothaan-Hall equation, that is constructed with mean-field one-electron operators. The convergence criteria is described by a commutator condition between Fock-type operators and density operators, just like in Hartree-Fock theory. Finally, this method is accelerated via direct inversion of the iterative subspace (DIIS), akin to acceleration in the ground state theory. Futhermore, this work discusses applications of ESMF to larger solvated systems, afforded by ESMF's scaling -- the method costs roughly twice the cost of a Hartree-Fock calculation. Getting an accurate physical picture of excited states in solvated systems is challenging, and the second half of this dissertation focuses on a comparative analysis of various methods, their degree of correlation, and their ability to qualitatively describe donor and acceptor regions for a charge transfer excitation. This comparison shows that ESMF can accurately describe the degree of participation of solvent water molecules in the excitation, unlike Density Functional Theory (DFT) based methods. However, when there is minimal participation from the solvent, Restricted Open-shell Kohn Sham methods fare better, indicating that the lack of correlation in ESMF prevents the method from providing a more quantitatively accurate picture. Using ESMF as a stepping rung for developing a hierarchy of excited state specific methods is a promising platform to achieve affordable excited state specific calculations.

Advisor: Neuscamman, Eric
Towards Robust and Scalable Supercooling for Sub-Zero Ice-Free Biopreservation

Organ transplantation represents one of the greatest medical advancements of the past century and is often the final option for patients suffering from end-stage organ disease. Despite our ability to perform these lifesaving operations, our simple inability to preserve organs for extended periods during ex vivo handling has caused immense logistical constraints that result in a majority of otherwise healthy donor organs not being transplanted. The current clinical standard for organ preservation, static cold storage, takes advantage of the Arrhenius temperature dependence of metabolism by placing organs on ice in order to slow expiration but enables just a few hours of viable preservation. Lower temperatures could further suppress metabolism and extend preservation, however ice crystallization results in irreversible damage. Being an activated process, freezing does not occur immediately at the equilibrium phase transition temperature, allowing water to remain metastably supercooled below 0°C. By preserving an organ in a supercooled state, the metabolism suppressing benefits of lower temperature can be attained while entirely avoiding ice formation. Ice crystallization is initiated by heterogeneous nucleation however, which is an inherently random process whose rate scales unfavorably with temperature, volume, and supercooled duration. This unpredictability poses significant challenges to the advancement and ultimate clinical translation of supercooled preservation techniques. This thesis has two primary objectives. The first is to identify methods, such as aspects of device and preservation solution design, that increase stability of supercooled systems. This involves both the development of new experimental tools necessary for probing supercooling stability and accompanying mathematical models for contextualizing key observations, such as the effect of rigid confinement. The second objective is to develop models to characterize the inherent stochastic nature of heterogeneous nucleation. These models enable prediction of freezing probability as a function of temperature, supercooled duration, volume, and solution composition. Ultimately, by applying engineering methods to understand the underlying molecular processes and model stochastic nucleation processes, these efforts establish a framework that enables the rational design of robust supercooled preservation protocols.

Advisor: Rubinsky, Boris
Essays in Behavioral and Development Economics

This dissertation applies behavioral economics concepts to understand key issues in firms’ and individuals’ decision making. In particular, this dissertation investigates the presence of behavioral biases on firms’ managerial decisions and on individuals’ annuitization decisions through the use of field and incentivized experiments, respectively./nIn the first chapter, we run a field experiment with micro-entrepreneurs in Brazil (N = 742) to shed light on the constraints that lead to the under-adoption of improved business practices. We randomly offer entrepreneurs micro-incentives, which include reminders, deadlines and small monetary payments, to implement record keeping or marketing for three consecutive months, following a business training program. Our intervention is designed to have a significant impact on firms’ decisions only in the presence of behavioral biases. Compared to traditional business training, micro-incentives significantly increase adoption of marketing (13.2 p.p.) and record keeping (19.2 p.p.), with positive effects on firm survivaland investment over four months. Additional survey evidence is consistent with biases, such as inattention, time inconsistency and information avoidance, inhibiting the adoption of improved practices. Taken together, our results show that behavioral biases have a significant impact on firms’ managerial decisions./nIn the second chapter, we study psychological biases in take-up of annuities, using an incentivized experiment with a probability-based sample (N = 3,038). Choosing an annuity was payoff-maximizing in the experiment at all prices, but take-up was incomplete and price elastic. Reformulating decisions as insurance against a “bad” outcome rather than insuranceagainst “longevity risk” did not increase take-up. Instead, we find substantial failures of contingent reasoning: participants underappreciated how annuitization mitigated the need for less-efficient means of saving for retirement. Increasing the salience of the interaction with savings decisions, or eliminating the need to think through this interaction altogether, substantially increased annuity take-up.

Advisor: DellaVigna, Stefano
Simulation-Based Testing, Validation, and Training with Probabilistic Programming

Cyber-physical systems (CPS) are increasingly becoming autonomous. Self-driving cars, for example, need to navigate through bustling streets of San Francisco. To avoid the risk of injuries, simulation provides a safe setting to extensively test these systems prior to their deployment. However, as these autonomous systems operate in more complex environments, this poses a challenge as to how to formally model and generate these environments in simulation. In this dissertation, we argue that a domain-specific probabilistic programming language (PPL) can be an adequate formalism to naturally capture the stochasticity and the constraints deriving from physical interactions of these systems with their environments./nThe contribution of this thesis is to show how a domain-specific PPL can be effectively used as an environment modeling formalism to test, validate, and train autonomous systems. First, we formalize a machinery to scalably test a system of multi-objectives in parallel simulations with distributions of environments, and summarize the likely causes of those failures in an interpretable manner. Second, we validate whether the identified system failures in simulation transfer to reality, with probabilistic programs as consistent environment models across both simulation and reality. Informed by the validated system failures, we develop algorithms to train components of autonomous systems to be robust against those failures. Furthermore, we devise a personalized algorithm to also train human-CPS (h-CPS), cyber-physical systems that operate in concert with human operators, via simulations in augmented and virtual reality.

Advisor: Seshia, Sanjit
Sangiovanni-Vincentelli, Alberto