VictorJuiz/thesis huggingface dataset:
Using multiple high-dimensional feature spaces to model brain activity recorded during naturalistic experiments

The human cerebral cortex comprises many functionally distinct areas that represent different information about the world. It has been challenging to map these areas efficiently. In this dissertation, I present a new approach that addresses this problem. In chapter one, I present a novel voxelwise encoding model based on Tikhonov regression. I discuss the theoretical basis for Tikhonov regression, demonstrate a computationally efficient method for its application, and show several examples of how Tikhonov regression can improve predictive models for fMRI data. I also show that many earlier studies have implicitly used Tikhonov regression by linearly transforming the regressors before performing ridge regression. In chapter two, I present a critique of an alternative method used to study brain representations called representational similarity analysis. I show that this method makes strong assumptions about the relationship between representational models and brain responses. I also show that representational similarity analysis can lead to incorrect conclusions when used to compare representational models. In chapter three, I present a rich paradigm for efficient non-invasive functional brain mapping. In this paradigm, subjects watch interesting short films while their brain activity is measured. Multiple feature spaces are used to model the brain responses to the short films. Each feature space constitutes a hypothesis about the type of representations that might be important for brain regions involved in watching, listening, and understanding the short films. The novel voxelwise encoding model developed in chapter one is then used to find the most predictive feature spaces across the cortical surface and also to recover maps that capture how the individual feature spaces are represented within cortical regions. The results suggest a high degree of homogeneous selectivity for feature spaces across large regions of the cortical surface within individual subjects. These patterns are highly consistent across all subjects. Finally, I explore the functional organization of the middle temporal cortex and show that the visual feature spaces can capture novel functional subdivisions in this region.

Advisor: Gallant, Jack L
Photonics Links -- From Theory to Automated Design

Recent advancements in silicon photonics show great promise in meeting the high bandwidth and low energy demands of emerging applications. However, a key gating factor in ensuring this necessity is met is the utilization of a link design method- ology which transcends the various levels in the hierarchy, ranging from the device and platform level up to the systems level. In this dissertation, a comprehensive methodology for link design will be introduced which takes a two-prong approach to tackling the issue of silicon photonic link efficiency. Namely, a fundamentals-based first principles approach to link optimization will be introduced and validated. In addition, physical design trade-offs connecting levels in the architectural hierarchy will also be studied and explored. This culminates in an intermediate goal of this dissertation, which is the first-ever design and verification of a full silicon photonic interconnect on a 3D integrated electronic-photonic platform. To proceed and further enable the rapid exploration of the link design architectural space, the analog macros for a majority of this dissertation were auto-generated using the Berkeley Analog Generator (BAG). With these key design tools and framework, performance bottlenecks and improvements for silicon photonic links will be analyzed and, from this analysis, the motivation for a new, single comparator-based PAM4 receiver architecture shall emerge. This architecture not only showcases the tight bond in dependency between high-level link specifications and low level device parameters, but also shows the im- portance of physical design constraints alongside fundamental theory in influencing end-to-end link performance.

Advisor: Stojanovic, Vladimir
Neuromodulation IC for System Integration and Self-Interference Cancellation

Recent advances in the brain-machine interfaces (BMI) have demonstrated its clinical efficacy for various applications such as prosthetic controls for motor-disabled patients and neural disease treatments. Among many other signal modalities, electrophysiology is one of the key areas to understand and engineer neural system. While impressive technical breakthroughs on electrodes, signal acquisition, and microstimulation were made, no electrode-based instrumentation reported so far achieved both coverage and resolution required for a closed-loop BMI with a high-degree of freedom and a clinical lifespan./nIn this dissertation, a minimally invasive neural interface system that has a scalability (starting from thousands of neural sites but targeting millions), a fine resolution (<10um, <1ms), a broad coverage (a year, >10cm), an automated electrode insertion, and a low-energy neuromodulation (<500uW for 64-channel recording). This system became feasible by integrating state-of-art sub-components developed across UC Berkeley and UCSF labs. Each subcomponent is reviewed along with discussions on current state-of-arts and challenges. Prototype in vitro and ex vivo results are also shown./nAnother challenge for a bidirectional neural interface is existence of self-interference. While simultaneous stimulation and recording are required for neuromodulation chips to support closed-loop BMI applications, such ICs suffer from large stimulus artifacts. The stimulus artifact is essentially a self-interference that originates from a stimulator pulse and couples into front-end recorders. Because the ICs typically have front-ends with limited input ranges, they saturate and lose desired neural signals./nThis dissertation presents an active cancellation IC that expands the effective dynamic range (uncancelled artifact/noise) of the front-end to 8kHz bandwidth and for up to 200mVpp differential-mode (DM) artifact signals with only a modest (~10%) noise penalty. The analog canceller with its LMS loop handles a majority of the artifact signal at the input of the LNA while the digital canceller with another LMS loop further cancels out residual error. The chip was validated with in vivo cancellation measurement result.

Advisor: Alon, Elad
Investigating Genetic Components of the Symbiosis-associated Glycocalyx in Medicago truncatula

Plants form a variety of endosymbiotic relationships with bacteria and fungi that promote plant growth and fitness through reciprocal nutrient exchange. Central to the development and function of endosymbiotic relationships is the synthesis of a specialized host-derived membrane, which compartmentalizes the endosymbiont inside plant cells, and creates a dynamic interface for the exchange of nutrients and information. The development of these interfaces is dependent upon bidirectional signaling between the plant and microorganism, and is highly coordinated with the morphological differentiation of the endosymbiont within plant cells. Previous studies using glycan-directed monoclonal antibodies indicated that glycoproteins, glycolipids, and pectic polysaccharides localize to periarbuscular and symbiosome membranes. Among these epitopes were arabinogalactan proteins (AGPs) and glycosyl inositolphophorylceramides (GIPCs), which have potent signaling properties in plants. These epitopes appeared to be developmentally regulated, which led to the hypothesis that a membrane-associated glycocalyx of glycoproteins and glycolipids might be important for mediating interactions through these membrane interfaces. However, AGPs have not been well documented outside of Arabidosis thaliana and are intrinsically disordered, which make them difficult to identify and study in plants species capable of forming endosymbiosis. Here, we have developed a new bioinformatic search tool that identifies AGP-encoding genes based on the noncontiguous hydroxyproline motifs that direct AGP glycosylation. We used this tool to identify all putative AGP-encoding genes in the Medicago truncatula genome, which were cross-referenced to transcriptomic studies of roots engaged in symbiosis with Sinohizobium meliloti and the arbuscular mycorrhizal (AM) fungus Rhizohagus irregularis. Using this approach we identified a small three-member family of tandemly duplicated SYMBIOSIS-ASSOCIATED ARABINOGALACTAN PEPTIDES (SAPs) that were differentially expressed in root nodules and AM colonized roots. SAPs localized to symbiotic membranes and knockdown of SAP expression using RNAi-mediated gene silencing impaired the growth and differentiation of Sinorhizobium meliloti and Rhizphagus irregularis within these compartments. In parallel we also identified a glycosyltransferase gene highly expressed in root nodules and AM colonized roots as GIPC GLUCOSAMINE TRANSFERASE 1 (GINT1), and showed that the corresponding GINT1 enzyme functions in the synthesis of HexN(Ac) decorated GIPCs in planta. Silencing of GINT1 using RNAi impaired the development of symbiotic membranes, which resulted in the senescence of symbiosomes and arbuscules. Taken together these results provide genetic evidence to support that reprogramming of the membrane-associated glycocalyx with specific AGPs and GIPCs is necessary for endosymbiosis.

Advisor: Scheller, Henrik V
District Central Office Administrators With A Cause: Enhancing the Motivation to Collaborate Among and Between District Central Office Administrators to Better Serve Schools

ABSTRACT/nDistrict Central Office Administrators With A Cause/nEnhancing the Motivation to Collaborate Among and Between District Central Office Administrators to Better Serve Schools/nBy/nMicaela Ochoa/nDoctor of Education/nUniversity of California, Berkeley/nBruce Fuller, Ph.D., Chair/nA new wave of research suggests that strong, coordinated support among offices with central school districts can help to advance deeper learning for all students. However, central offices have traditionally served mainly as administrative or fiscal pass-throughs for federal and state initiatives, managing certain local operations such as facilities, budgets and accounting, purchasing, and personnel. This often fractures work into bureaucratic silos, focuses staff on compliance activities rather than collaborative efforts targeted on gains in teaching and learning. I observed this lack of central office collaboration in a few school districts in Northern California./nMy particular study focuses on a K-12 district in Northern California with central office departments operating in the traditional silos and limited coordination or planning among departments. The study seeks to alter the work at the central office by breaking down the silos and addressing the lack of strategic partnerships and collaboration among Business Services, Educational Services, and Human Resources. The study focuses on shifting work routines and communication structures, redesigning the work roles, providing more opportunities for central office administrators to proactively interact with each other, and increasing the teamwork and partnerships among staff in the three departments. While the study resulted in uneven effects on these relationships, the intervention did help to improve communication among central office departments and better coordinate central office support of local schools.

Advisor: Fuller, Bruce
Mintrop, Rick
The Criminal and the Enemy in Seventeenth Century English Thought

Seventeenth century England saw major theoretical and legal innovations in how political community, sovereignty, and violence were understood—occasioned in significant part by two civil wars in the 1640s and 1680s. In my dissertation, I call attention to an important theme running through many of the major political and legal theoretical treatises, political pamphlets, and popular literature of the period that identifies criminality with the pirate (or his land-based equivalent, the highwayman), and punishment with war. My project begins by drawing a contrast between English natural law thinkers and two of their significant Scholastic predecessors. Whereas for the Scholastics membership had been a precondition of punishment, Hugo Grotius, Thomas Hobbes, and John Locke instead embraced a natural right to punish and a view of the commonwealth as founded upon, rather than giving rise to, the ius gladii or right of blameless violence. Although in some respects these thinkers, along with Alberico Gentili, were engaged in an intellectual project meant to distinguish civil punishment from war outside the commonwealth’s borders, this natural right to punish and a justificatory account of punitive violence tied to an offender’s loss of status ended up reproducing extralegal violence within the commonwealth in Hobbes’s Leviathan and Locke’s Second Treatise of Civil Government. This theoretical tendency has a parallel in the popular identification of the pirate—the hostis humanis generis, or enemy of all mankind—with the highwayman in England during this period. The highwayman, like the pirate, disrupted trade routes by which a nascent English state attempted to project political power and was both an important figure for seventeenth century accounts of crime and punishment, and early efforts at public policing and prosecution. Treason, the subject of most public prosecutions of the period, also underwent a subtle but significant shift between the English Civil War and the Glorious Revolution. Where in the first part of the seventeenth century treason was crime of betrayal against the sovereign, by the 1680s it was increasingly understood as a threat to the status quo and security of the political community. Thus, I argue, the model for the “ordinary” adversarial criminal trial, which has its origins in the Treason Reform Act of 1696, is grounded in a theory of wrongdoing as existential threat. The idea of the “criminal” in English political and legal thought reflects an internalization of concepts associated with war.

Advisor: Lieberman, David
Hoekstra, Kinch
Classical Verification and Blind Delegation of Quantum Computations

In this dissertation, we solve two open questions. First, can the output of a quantum computation be verified classically? We give the first protocol for provable classical verifica- tion of efficient quantum computations, depending only on the assumption that the learning with errors problem is post-quantum secure./nThe second question, which is related to verifiability and is often referred to as blind computation, asks the following: can a classical client delegate a desired quantum compu- tation to a remote quantum server while hiding all data from the server? This is especially relevant to proposals for quantum computing in the cloud. For classical computations, this task is achieved by the celebrated result of fully homomorphic encryption ([21]). We prove an analogous result for quantum computations by showing that certain classical homomorphic encryption schemes, when used in a different manner, are able to homomorphically evaluate quantum circuits./nWhile we use entirely different techniques to construct the verification and homomorphic encryption protocols, they both rely on the same underlying cryptographic primitive of trapdoor claw-free functions.

Advisor: Vazirani, Umesh
‘The Monstrous Gnome’: Confronting Physical Difference in the Art of Toulouse-Lautrec

“Monstrous gnome,” “Quasimodo,” “disgraceful”– The obituaries of Henri de Toulouse-/nLautrec (1864-1901) deployed such pejorative corporeal descriptions, which colored his/nposthumous legacy. Such influential framings suggested that his presumed resentment of Self/nmanifested in the deformation of his graphic subjects. Lautrec scholarship has shifted between/ntwo narrative poles: Lautrec’s appearance as either the bitter root of his art, or as a factor utterly irrelevant to his transcendent creative ‘genius.’/nThe disabled population constitutes the world’s largest minority, yet disability is still/nlargely underrepresented in art history and Lautrec studies. This dissertation works to reclaim the artist’s impairment as a newly productive lens. Rather than focus on his pathology, it expands the scope of Lautrec scholarship by considering the wider reception of his art and his body in a culture obsessed with its presumed degeneracy. Indeed, working in a France recovering from a humiliating defeat in the Franco-Prussian war, Lautrec navigated a society in flux. Faltering industrialization, political volatility under the Third Republic, and the emergence of eugenics all fostered a climate ripe for the stigmatization of difference. Ultimately, I argue that Lautrec and his work were troublesome and thus denigrated as visual manifestations of a France perceived to be in decline. Using an intersectional approach (deploying disability studies’ social model along with conventional art historical methods) reframes Lautrec as more than a debauched aristocrat. It exposes him as a multicultural artist, fashioned equally by his aristocratic birth, the impairment of close friends in addition to his own, his relocation to Montmartre and its socially-marginal population, and the rise of technologies such as electricity and photography.

Advisor: Grimaldo Grigsby, Darcy
The Case of the Leaky Pipeline: Exploring the Experiences of Underrepresented Minority Premed Students in the UC System

The lack of diversity in the physician workforce poses a complex problem for the US healthcare system. Despite numerous efforts over the last 45 years, the lack of representation in the physician workforce persists, with no significant signs of reversing course. There is therefore an urgent need to engage in research to aid in the development of innovative, systemic and sustainable methods of addressing barriers in the educational pipeline leading into medicine for URM students./nMuch of the previous research in this area has focused largely on examining undergraduate program outcomes and impact on physician specialty/service area choice with very few examining the undergraduate premed experience in detail. These experiences can have deleterious effects which serve as barriers to academic achievement and outcomes, thereby preventing matriculation into medical school and the physician workforce. This research seeks to fill this gap in knowledge and employs qualitative methodology to accomplish three overarching goals:/n1. Better understand the experiences of URM premed students as they navigate their undergraduate premed pathway. Focusing on the multi-level factors associated with academic achievement and enrollment in post-bac programs./n2. Explore the role and sustainability of post-baccalaureate premed programs in facilitating entry into medical school for URM graduates of the UC system./n3. Develop empirically based recommendations to ameliorate barriers and challenges reported by URM students in the UC system./nThis dissertation resulted in three papers. The first paper illuminates the barriers and challenges faced by URM premed students and outlines their relation to student achievement and outcomes. The second paper sheds light on URM student perceptions and the specific reasons they apply to post-bac programs in addition to providing data that suggests that post-bacs are not a sustainable strategy to address diversity in the physician workforce. The third paper presents a list of empirically based recommendations aimed at addressing institutional-wide barriers to student achievement such as campus climate, academic/students services and course size and curriculum.

Advisor: Nuru-Jeter, Amani
Control Algorithm Design, Testing, and Use Cases for the INSTAR [INertial STorage And Recovery] System. A Flywheel-Based Dedicated High-Power Energy Storage System for Improved Hybrid Vehicle Fuel Efficiency and Performance with Special Application in Urban Commercial Vehicles

This thesis describes the design of control algorithms, modelling, testing, and analysis of use cases of the INSTAR system, a dedicated high-power, low cost energy storage system designed to increase energy efficiency and performance in hybrid vehicles, with special application in urban commercial vehicles. The system is intended to be combined with an electrochemical battery and small energy generator to provide 3 distinct magnitudes of power delivery and absorption to the traction motors. The advantages of such a system would be decreased generator size, decreased component size, and potentially increased battery service life./nFlywheel control algorithms were developed and tested to absorb excessive electrical energy during regenerative braking, as well as to augment electrochemical battery power during vehicle accelerations. During laboratory testing battery charging currents reaching the battery were controlled through modulation of flywheel throttle signals. These algorithms were applied in road driving conditions to decrease vehicle energy use by 8.9 percent over a predetermined acceleration and deceleration event while decreasing the charging rate of the battery. Laboratory testing showed potential to reduce battery discharge rate during acceleration events by pre-charging the flywheel so that it may be discharged during the acceleration event. Road tests demonstrated that energy use could be reduced by 2.6% over a pre-determined acceleration and deceleration event while simultaneously reducing the magnitude of battery discharge current by around 15%./nSuch a system has use in urban vehicles where much of the vehicle driving is in stop and go type traffic. These vehicles typically have a large internal combustion engine to accelerate the vehicle from a stop. The INSTAR system may be able to reduce the engine output requirement while still providing the same performance. The INSTAR system is particularly applicable in commercial vehicles where fully electric vehicle may not be practical.

Advisor: Lieu, Dennis K
Enzymatic de novo DNA Synthesis Methods

Synthetic DNA is required for nearly all aspects of biological research and bioengineering. Essentially all contemporary de novo DNA synthesis begins with oligonucleotides produced using the nucleoside phosphoramidite method. Despite its remarkable performance for a stepwise synthesis chemistry — often achieving >99% stepwise yields — the phosphoramidite method has certain limitations, including that it is in practice limited to the direct synthesis of ~200mers by side reactions and produces hazardous waste. Synthetic DNA molecules longer than 200 bp must be assembled from oligonucleotides, but the assembly process can introduce errors and is not amenable to all sequences, so new de novo DNA synthesis methods are needed./nHere, I present two novel de novo DNA synthesis methods based on enzymes. Unlike the phosphoramidite method, these enzymatic methods operate in aqueous buffers and need not create hazardous waste. They also both take advantage of the exquisite specificity of enzymes to eliminate side reactions. The first method is based on deoxyribonucleoside triphosphate (dNTP) conjugates of the template-independent polymerase TdT, which extend a single-stranded DNA molecule by one nucleotide. The second method is based on ligation of small duplex DNA “extension units” that extend a growing DNA molecule by a defined sequence. Both methods can be iterated to synthesize a defined sequence./nA single DNA molecule can be amplified more than a million-fold without many errors, so in principle only one “perfect” molecule must be synthesized. Exploiting the unique possibilities offered by this ability, I present a new principle for “real-time error correction” of single-molecule stepwise DNA synthesis that aims to enable direct synthesis of longer DNA molecules than is currently possible with any method.

Advisor: Keasling, Jay D
Savage, David F