VictorJuiz/thesis huggingface dataset:
The Role of Serial Dependence in Visual Perception

From moment to moment, we perceive objects in the world as continuous despite fluctuations in their image properties due to factors like occlusion, visual noise, and eye movements. The mechanism by which the visual system accomplishes this object continuity remains elusive. Recent results demonstrate that the perception of low-level stimulus features such as orientation and numerosity is systematically biased (i.e. pulled) towards visual input from the recent past. The spatial region over which current orientations are pulled by previous orientations is known as the continuity field, which is temporally tuned for the past 10-15 seconds. This perceptual pull could contribute to the visual stability of low-level features over short time periods, but it does not address how visual stability occurs at the level of complex objects or during visual discontinuities. Here, we examined whether the visual system facilitates stable perception by biasing current perception of objects towards recently seen objects, and whether it operates across disruptions in visibility. First, we used psychophysics to show that the perception of face identity is systematically biased towards identities seen up to several seconds prior, even across changes in viewpoint. This perceptual bias did not depend on subjects’ prior responses or on the method used to measure identity perception. Next, we tested whether this serial dependence, or positive perceptual pull, helps stabilize perceived expression. To test this, observers judged random facial expressions (ranging from happy to sad to angry). We found a pull in perceived expression toward previously seen expressions, but only when the 1-back and current face shared the same identity. Finally, we examined whether the continuity field helps maintain perceived object identity during occlusion. Specifically, we found that the perception of an oriented Gabor that emerged from behind an occluder was significantly pulled towards the random (and unrelated) orientation of the Gabor that was seen entering the occluder. Importantly, this serial dependence was stronger for predictable, continuously moving trajectories, compared to unpredictable ones or static displacements. While this serial dependence in object perception manifests as a misperception, it is adaptive: visual processing echoes the stability of objects in the world to create perceptual continuity. These results provide further evidence for the existence of an object-selective continuity field that helps maintain perceived object stability over time and across visual noise or disruptions.

Advisor: Whitney, David
Synthesis, Reactivity, and Catalysis of Group 3 and Lanthanide Alkyl Complexes

Group 3 and lanthanide alkyl complexes supported by PNP-pincer ligands were prepared to investigate the sigma-bond metathesis reaction. These complexes were found to effectively carry out this reaction. Alkylidene complexes were prepared by sigma-bond metathesis with gamma-hydrogens of neopentyl groups to generate metallacyclobutanes which undergo a retro-[2+2] reaction. These complexes were also competent hydrogenation, semihydrogenation, hydrosilation, semihydosilation, and cross-dehydocoupling (amines and silanes) catalysts. The mechanisms of these catalytic reactions as well as the sigma-bond metathesis reaction in general were thoroughly studied by computational techniques. The sigma-bond metathesis reaction was probed by energy decomposition analysis to reveal that polarizability of the metal complex is key to promoting efficient metathesis. A new energy decomposition analysis was developed to treat these bonds in unbiased ways. Work towards the preparation of 1,3-dilithiopropane, a useful molecule for possible preparation of alkylidene complexes, was reported.

Advisor: Tilley, T. Don
Andersen, Richard A
Mechanical and Opto-mechanical Properties of Branched Semiconductor Nanocrystal Stress Sensors

This dissertation highlights advances in using semiconductor tetrapod quantum dots (tQDs) as stress sensors in structural polymer nanocomposites. Semiconductor nanocrystals have undergone many developments in terms of synthetic control of shape and size since their inception, and one example is the ability to create branched nanocrystals such as tQDs. tQDs are core/shell tetrahedrally symmetric, branched nanocrystals. In this thesis, studies will utilize tQDs consisting of a ~4 nm cadmium selenide (CdSe) core and ~25 nm long cadmium sulfide (CdS) arms. Their type I band alignment and the modulus difference between their core and shell, along with their branching, makes them sensitive to applied mechanical environmental stresses. The CdS arms receive stress from a host matrix in which the tQDs are embedded and transmit it to the CdSe core. The tQD’s photoluminescence emission spectral maximum undergoes a monotonic red-shift, or decrease in energy, with increasing tensile stress, due to widening bond distances in the core. The tQD’s property of nanoscale stress-sensing is of relevance to fields such as polymer dynamics, sensing of premature fracture in service, and biomechanical stress sensing./nWe have fabricated and characterized the structure and opto-mechanical sensing ability of a wide variety of tQD-polymer nanocomposites. We demonstrate tQD sensing of tension and compression as well as more complex stress responses, such as stress relaxation and hysteresis. We perform optical and mechanical tests simultaneously, discovering a new sensing modality, and orders of magnitude of stress amplification in the tQD core. We also discover tQD sensing of dispersion including a switch in optomechanical response characteristic when tQDs are in direct contact./nIn addition to demonstrating and analyzing these new phenomena, we theoretically explore, with micromechanical finite element simulations and atomistic density functional theory, the origins of the tQD stress response. We further examine, experimentally and theoretically, the ability of tQDs to serve as mechanical fillers, finding that they have greater potential to improve the Young’s modulus of structural polymers than linear nanorods and nano-spheres due to their branched shape. The results in this dissertation contribute to the understanding of the structural, mechanical, and optical sensing properties of nanocomposites of polymers and semiconductor tQD nanocrystals.

Advisor: Alivisatos, Armand Paul
Spatial and temporal linkage of stream-riparian food webs by seasonal migration of mayfly Ephemerella maculata

Stream environments are spatially and temporally heterogeneous. Mainstem rivers are often wide, sunlit, warm and productive, while tributaries are shaded by riparian trees, unproductive, and remain cool in summer. Within mainstem rivers themselves there is substantial spatial heterogeneity in habitat structure and physical conditions, such as water temperature. River environments also change dramatically with season. Organisms that live in the riverine environment respond to and take advantage of such heterogeneous environments by moving between microhabitats or shifting their phenology. I studied the life cycle of a riverine mayfly, Ephemerella maculata (Ephemerellidae), in a northern California river system, its responses to spatial and temporal heterogeneity, and how its movements connect stream and riparian food webs in space and time./nI discovered that E. maculata migrates between the mainstem and tributaries of rivers during its life cycle, thereby linking food webs in these two habitats, and enhancing predator growth in unproductive tributaries. The resource subsidy from productive but warm rivers to cool, unproductive tributaries associated with the mayfly migration increase the growth of stenothermic predators like juvenile salmonids in otherwise food-limited, cool thermal refuges, and increase their resilience to future warming. Furthermore, I examined the resilience of E. maculata to changes in water temperature using field surveys and lab rearing experiments. I discovered that different life stages of E. maculata have different thermal responses, and they shift their phenology depending on the water temperature, allowing each life stage to occur in the most desirable thermal condition. Therefore, as long as the natural seasonal pattern of the water temperature is sustained, E. maculata can resist temperature changes by shifting their phenology. Finally, I have shown that thermal spatial heterogeneity of rivers desynchronizes mayfly emergence timing, prolonging the subsidy period to riparian predators, and changing the predators’ responses to this subsidy.

Advisor: Sousa, Wayne P.
Explaining Racial Disparity in Bipolar Disorder Treatment: How Do Providers Contribute?

Bipolar disorder is a serious mental illness that goes untreated more often among blacks than whites in the U.S. In the current study, I identified and tested a proposed mechanism underlying differential treatment in bipolar disorder, namely how treatment providers’ racial biases contribute to the inadequate care of black patients with bipolar disorder. Findings from research in general and mental healthcare show that providers’ clinical decisions may be related to racial biases based on stereotypes that providers hold. Moreover, general healthcare research has demonstrated the presence of implicit racial biases (defined as unconscious preferences for one race over another) among providers that are linked to the differential treatment of blacks and whites. Unfortunately, much less work has been done to show the presence and effects of implicit racial biases among mental healthcare providers. The hypothesized model in the current study proposes that implicit racial biases held by mental healthcare providers bias diagnostic and prognostic assessments as well as treatment recommendations in bipolar disorder and result in the observed treatment disparities between black and white patients. The Implicit Association Test was used to measure general racial biases in a sample of 82 mental healthcare providers. Clinical decision-making was simulated using clinical vignettes about theoretical black and white patients with psychotic and non-psychotic bipolar disorder. Three-way ANOVAs were used to test for racial disparities in decision-making, and structural equation modeling was used to determine whether providers’ implicit racial biases were associated with decision-making outcomes. Results showed that providers held moderate pro-white/anti-black racial biases and neutral explicit attitudes, also known as an “aversive racism” profile. Racial disparity was observed, but confounded by a mismatch in the severity of symptoms of the hypothetical patients. Composite scores for the vignettes were used to overcome this issue in the SEM analyses. These results revealed that there was no link between racial bias and decision-making. Suggestions for future research are given to improve modeling of the relationship between racial bias and patient care. Despite limitations, findings provide some of the first evidence establishing the presence or implicit racial biases in mental healthcare.

Advisor: Johnson, Sheri
Viral Politics: Sex Worker Activism and HIV/AIDS Programs from Bangalore to Nairobi

This dissertation studies the international success story of India’s HIV/AIDS response and the activism of sex workers and sexual minorities that produced it. A number of recent ethnographies have turned their attention to the workings of state programs in middle-income countries (e.g. Baiocchi 2005; Sharma 2008; A. Gupta 2012; Auyero 2012), demonstrating both the micro-effects of state strategies for managing poverty on poor people and the ways in which state programs are produced outside the visible boundaries of “the state”—through NGOs and social movement organizations as well as transnational donors and research institutes. Yet, even as state programs are constituted through struggles over resources and representations within and outside the official agencies of the state, states also derive legitimacy from projecting themselves as cohesive rather than disaggregated, and as autonomous from society rather than anchored within it (Abrams 1988; Mitchell 1991b; Mitchell 1999; A. Gupta 2012). The representation of state programs as cohesive, pre-constituted, exportable “models” serves as a new way of consolidating state legitimacy within a global, hierarchical order of development “success.” However, this dissertation argues that the traveling policies disseminated through transnational expert communities are a selective codification of hard-fought struggles among institutions within the state, between the state and organizations, among organizations, and among groups within organizations over the aims and strategies of social policies and programs. These struggles shape what travels in traveling policies and what is left out. Drawing on over 150 in-depth interviews and a year of participant observation with sex workers involved in implementing policy in community-based organizations, NGOs, and activist groups, I show how the material and social conditions of men, women, and transgender women in sex work, mediated through community-based organizations, constituted the successful approaches to HIV prevention that were later, sometimes selectively, translated around the world.

Advisor: Ray, Raka
Scalable High-Quality 3D Scanning

Over the past decade, vendors across fields ranging from entertainment to retail to architecture have increasingly been shifting everyday consumable media from the 2D plane to the 3D world. Applications in these fields such as augmented/virtual reality, online shopping, and indoor scene reconstruction all have one crucial problem that needs to be addressed: the task of acquiring high-quality 3D models. Currently, designing novel 3D content involves a substantial human component; indeed, most 3D models were created via modeling software, e.g., 3DS Max, Maya, by a human with vast expertise. Although several research communities have explored automated 3D scanning over the course of several decades, the lack of an out-of-the-box solution has precluded this field from permeating the industry. Prior approaches to 3D scanning can largely be divided into image-based reconstruction (IBR) and active reconstruction (AR). While IBR methods produce reconstructions by taking in as input a collection of calibrated RGB images, AR methods actively project patterns onto observed scenes during reconstruction. IBR and AR techniques each have advantages and pitfalls. State of the art methods in 3D scanning typically fall purely within IBR or AR./nIn this thesis, we outline a novel scanning approach which merges IBR and AR methods. First, we discuss how to physically construct and calibrate a 3D scanner using commodity hardware. We use this 3D scanner in the collection and release of the BigBIRD dataset, which serves as a key benchmark for the algorithms in this thesis and comprises of 600 12 MP images, 600 registered RGB-D point clouds, and several other processed data for each of 125 objects. Next, illustrating that the advantages and pitfalls within IBR and AR complement each other, we present a novel shape re- construction algorithm that capitalizes on the strengths of each approach, yielding less than 2 mm of RMS error during reconstruction. We then present a color reconstruction algorithm, with which we produce high quality 3D color meshes of scanned objects; we demonstrate that this color reconstruction algorithm outperforms the state of the art. Finally, with any growing dataset, large-scale data visualization becomes increasingly important. Although the 3D scanning world is not yet at the large scale level, it is only a matter of time before it is. In addition, there already exists an eclectic array of fields, including computer vision, particle physics, and botany, where large-scale visualization techniques can benefit research. We present a novel and highly flexible GPU-based nonlinear dimensionality reduction technique capable of visualizing datasets with tens of millions instances and millions of features. Our algorithm’s flexibility and speed yield an implementation that is an order of magnitude faster than state of the art implementations of stochastic neighbor embedding algorithms.

Advisor: Abbeel, Pieter
Malik, Jitendra
Local Capacity for Implementing a State Climate Planning Mandate: The Politics of Cooperation and Regional Governance in California

This dissertation examines the local and regional politics of state-mandated sustainability planning using a survey and case studies of regions in California post-SB 375. Data collection included interviews with local and regional actors in the Bay Area and the Los Angeles region on multiscalar cooperation and a survey of local planning directors in four regions (Sacramento, Bay Area, Los Angeles, and San Diego) on local political and capacity constraints on implementation. It finds unevenness in the local implementation of the law’s Sustainable Communities Strategies within and across regions, but that greater than anticipated levels of cooperation occurred between cities and county level agencies. A variety of interpretations of sustainability and a broad range of incentives are at work in local planning that contributes to regional emission reductions. Suburban and rural areas face different challenges but potentially large opportunities for reducing vehicle emissions, yet their work during the first round of SCSs occurred largely under the radar of regional incentives. Regional sustainability planning is having some impact at the local level, but that state incentives and mandates are a primary factor in local smart growth planning. This dissertation contributes to understandings of plan implementation, regional governance, and the politics of sustainability planning.

Advisor: Chapple, Karen
Deakin, Elizabeth
The Regulation of Smoothened Activity in the Hedgehog Response Pathway

Sonic Hedgehog (Shh) is a vertebrate signaling molecule that is indispensable for patterning during embryogenesis and for the maintenance of adult stem cell populations. Impaired regulation of the Hedgehog (Hh) pathway can lead to birth defects and disease, thus insight into the regulation of signal transduction is critical for understanding developmental mechanisms and for generating new therapeutic strategies./nThe function of the ligand, the receptor, and the signal transducer are separated into distinct molecules and the state of pathway activity depends on their interaction. In the absence of the Shh ligand, the canonical receptors, Patched1/2 (Ptch1/2), are potent inhibitors of Smoothened (Smo), the GPCR-like signal transducer of the Hh pathway. The mechanism by which Shh acts through Ptch1/2 to activate Smo and thereby the Hh response remains unclear./nHere we find that Ptch1LacZ/LacZ;Ptch2-/- cells have a low level of Hh pathway activity and are unresponsive to exogenously supplied ShhN, unless transfected with Ptch1, including forms of Ptch1 lacking antiporter activity required for the inhibition of Smo. However, this Ptch1 requirement can be circumvented by ShhN transfection; Ptch1LacZ/LacZ;Ptch2-/- cells expressing ShhN have an activated Hh response that requires Smo. Mutant forms of Shh that cannot bind Ptch1/2 or the Shh co-receptors, and thus unable to induce the Hh response when applied to Ptch1/2 proficient cells, are nevertheless potent inducers of the Hh response after transfection into Ptch1LacZ/LacZ;Ptch2-/- cells and in vivo. Forms of Smo lacking the N-terminal extracellular Cysteine Rich Domain (CRD) retain their sensitivity to Ptch1-mediated inhibition, but can no longer be activated cell-autonomously by Shh. Our findings support a model in which the role of Ptch1/2 as an allosteric inhibitor of Smo is complemented by a role as a facilitator of a Shh-mediated Smo activation event that is independent of Shh (co-) receptors.

Advisor: Roelink, Henk
Rule of Law against the Odds: Legal Knowledge, Poverty & Compliance along the India-Nepal Border

This dissertation seeks to understand whether and how regulatory compliance can be achieved in areas of state weakness. The existing literature suggests that, absent a strong and capable state, compliance with law should be irregular, particularly when legal norms differ from social norms. It also generally assumes that the law is widely known and understood and that all parties are similarly situated to comply with it, assumptions that are untenable in areas of state weakness and where poverty is widespread. Utilizing a natural experiment along the open India-Nepal border, I examine compliance with three different regulations—those related to conservation, education and child labor. My large-N survey and qualitative data indicate that in areas of state weakness inaccurate legal knowledge and widespread poverty are significant barriers to widespread regulatory compliance, but that states that design and implement their regulations pragmatically can work around these obstacles and achieve widespread compliance at relatively little cost. In the cases I examined, regulatory pragmatism involves avoiding bureaucratic principal-agent problems and designing for legal knowledge dissemination via delegated enforcement or through local leaders. It also involves taking steps to reduce the cost of compliance for the poor so that they can afford to both comply and meet their own basic needs. The implications of these findings are potentially far-reaching. They suggest that regulatory pragmatism can guide weak or under-funded states to effective legal design and implementation choices in a variety of contexts. As a result, these states should be able to generate large-scale compliance in the absence of significant state capacity.

Advisor: Chhibber, Pradeep
Kagan, Robert
Principles of Metalevel Control

Intelligent agents perform computations to help them decide how to act. But which computations will best inform these decisions? How long should an agent think before acting? Given the impracticality of performing all possible relevant computations, AI systems need effective strategies for metalevel control—that is, for choosing computations that contribute most to the (object-level) action selection problem./nThis thesis presents a theoretical basis for metalevel control problems, situating it within the frameworks of Bayesian selection problems and Markov decision processes. We present some fundamental results concerning the structure of these problems and the nature of their solutions. These results establish bounds on the number of computations performed by optimal policies and clarify how the context of multiple actions affects the choice of computation./nFor a more empirical investigation of metalevel control, we apply reinforcement learning techniques to the problem of controlling Monte Carlo tree search. This requires learning a metalevel policy to choose which computation to perform as a function of the internal state of the tree search. To represent an learnable class of efficient policies, we describe how Monte Carlo tree search can be implemented using pointed trees, a recursive data structure that allows efficient evaluation of recursive functions and their derivatives. We propose a concrete class of policies that includes UCT and AlphaGo as special cases, along with a method for providing metalevel shaping rewards. We show that by initializing the metalevel policy to UCT, reinforcement learning can find metalevel policies that outperform UCT for smaller numbers of computations in the domain of computer Hex./nThese results demonstrate the benefits of a solid theoretical understanding of metalevel control, as well as the potential for using metalevel reinforcement learning to replace hand- crafted algorithm design.

Advisor: Russell, Stuart