VictorJuiz/thesis huggingface dataset:
Plasticity of neural circuits in the auditory system

An understanding of plasticity, the ability of the brain to reorganize based on experience, is fundamental to understanding how the brain functions. Previous research has uncovered the molecular and cellular mechanisms by which neural activity leads to specific neural circuit modifications, but in order to appreciate their role in learning and memory, studies of large- scale neural systems are required. In this dissertation, I describe several studies that take advantage of mouse lines possessing mutations in genes known to be important for distinct types of plasticity./nA mouse line lacking the Fmr1 gene replicates many of the disease phenotypes of Fragile X Syndrome (FXS), the most common single-gene determinant of mental disability in humans. Fmr1 knock-out (KO) mice do not undergo the critical period for auditory map plasticity, by which auditory cortex adapts to the sound milieu experienced immediately after hearing onset. Pharmacological blockade of group I metabolic glutamate receptors (mGluR) with 2-Methyl-6-(phenylethynyl)pyridine (MPEP) rescues this critical period, in agreement with the mGluR Theory of FXS./nI also present work in a mouse that lacks tumor necrosis factor-alpha (TNF-alpha), which is critical for the expression of homeostatic regulation of synaptic strength. Auditory cortical development is disrupted in the TNF-alpha KO mouse, however auditory map expansion occurs normally. TNF-alpha is also required for in vivo homeostatic regulation using a multi-frequency tone exposure paradigm. Early-life acoustic stimulation with multiple frequencies leads to a homeostatic decrease of spontaneous activity and narrowing of receptive field frequency bandwidths in wild-type animals, contrasted with KO animals, which experience an anti- homeostatic increase in spontaneous activity and broadening of receptive field bandwidths./nFinally, I describe a mouse model study of the role of homeostatic plasticity in tinnitus, a phantom sound percept that commonly accompanies partial hearing loss. The development of salicylate-induced and unilateral hearing loss-induced tinnitus-related behavior/nrequires the presence of TNF-alpha. Direct application of recombinant TNF-alpha is sufficient to cause tinnitus-related behavior. In addition, reallocation of the deprived auditory cortex to ipsilateral ear inputs requires TNF-alpha expression. Single-gene knockout animals are valuable tools to extend our understanding of plasticity mechanisms from the molecular and cellular scale to the level of circuits and the intact brain.

Advisor: Bao, Shaowen
Operating System Support for Parallel Processes

High-performance, parallel programs want uninterrupted access to physical resources. This characterization is true not only for traditional scientific computing, but also for high-priority data center applications that run on parallel processors. These applications require high, predictable performance and low latency, and they are important enough to warrant engineering effort at all levels of the software stack. Given the recent resurgence of interest in parallel computing as well as the increasing importance of data center applications, what changes can we make to operating system abstractions to support parallel programs?/nAkaros is a research operating system designed for single-node, large-scale SMP and many-core architectures. The primary feature of Akaros is a new process abstraction called the "Many-Core Process" (MCP) that embodies transparency, application control of physical resources, and performance isolation. The MCP is built on the idea of separating cores from threads: the operating system grants spatially partitioned cores to the MCP, and the application schedules its threads on those cores. Data centers typically have a mix of high-priority applications and background batch jobs, where the demands of the high-priority application can change over time. For this reason, an important part of Akaros is the provisioning, allocation, and preemption of resources, and the MCP must be able to handle having a resource revoked at any moment./nIn this work, I describe the MCP abstraction and the salient details of Akaros. I discuss how the kernel and user-level libraries work together to give an application control over its physical resources and to adapt to the revocation of cores at any time - even when the code is holding locks. I show an order of magnitude less interference for the MCP compared to Linux, more resilience to the loss of cores for an HPC application, and how a customized user-level scheduler can increase the performance of a simple webserver.

Advisor: Brewer, Eric
Martin-Löf Randomness and Brownian Motion

We investigate the Martin-L�of random sample paths of Brownian motion, applying techniques from algorithmic randomness to Brownian motion, an active area of research in probability theory./nIn Chapter 2, we investigate many classical results about one dimensional Brownian motion in the context of Martin-L�of randomness. We show that many results which are known to hold almost surely for the Brownian motion process - including results concerning the modulus of continuity, points of increase, time inversion, and law of large numbers - hold for every Martin-L�of random sample path. We also show that scaling invariance and the strong Markov property hold for every Martin-L�of random path, with suitable effectivization./nIn Chapter 3, we investigate the zero set of one-dimensional Brownian motion. We prove that the set of zeroes is characterized by having high effective dimension. We also demonstrate that, although the zeroes are highly noncomputable in the sense of effective dimension, many of them are layerwise computable from a Brownian path./nIn Chapter 4, we give a new proof that the solution to the Dirichlet problem in the plane is computable. It is a well-known result of Kakutani that the solution to the Dirichlet problem can be found using expected hitting times of Brownian paths to the boundary. We show that the hitting times of Martin-L�of random Brownian paths on a computable boundary are layerwise computable in the path, and thus the expected value of the hitting times is computable, and so the solution to the Dirichlet problem is computable./nIn Chapter 5, we further investigate planar Martin-L�of random Brownian motion. We demonstrate that a Martin-L�of random planar Brownian path only hits points such that the path is not random relative to those points (except the origin), which implies that a Martin-L�of random planar path has area zero and that every point except the origin is hit by only measure 0 many paths. We also show that every Martin-L�of random planar Brownian path has points of uncountable multiplicity.

Advisor: Slaman, Theodore
Human Mechatronics Considerations of Sensing and Actuation Systems for Rehabilitation Application

With the predicted increase in worldwide elderly population in the future and already significant populations of disabled people, assistive technologies and rehabilitation devices are demanded significantly. Utilizing a human mechatronic approach results in several advantages, including capability of measuring insightful information for patient's condition and providing proper assistive torque for abnormal movement correction. This dissertation investigates several domains, including (1) human dynamics model, (2) monitoring systems, and (3) design and control of active lower extremity exoskeleton./nThe dissertation begins with a study of a human dynamic model and sensing system for diagnosis and evaluation of patient's gait condition as first step of rehabilitation. A 7-DOF exoskeleton equipped with multiple position sensors and smart shoes is developed, so that this system can deliver patient's joint motion and estimated joint torque information. A human walking dynamic model is derived as it consists of multiple sub-dynamic models corresponding to each gait phase. In addition, a 3D human motion capture system is proposed as it utilizes an inertial measurement unit (IMU) sensor for 3D attitude estimation with embedded time varying complementary filter. This sensing system can deliver 3D orientations of upper extremities, and a forward kinematics animation. For the development of a rehabilitation device, an active lower extremity exoskeleton is proposed. A rotary series elastic actuator (RSEA) is utilized as a main actuator of the exoskeleton. The RSEA uses a torsion spring yielding elastic joint characteristics, which is safe for human robot interaction applications. A RSEA controller design is implemented, including a PID controller, a feedforward controller for friction compensation, and a disturbance observer for disturbance rejection. All sensing and actuation systems developed in this dissertation are verified by simulation studies and experiments.

Advisor: Tomizuka, Masayoshi
Semiparametric Prediction, Variable Importance, and Effect Estimation in Critical Care

Trauma injury is one of the leading causes of death in the United States, accounting for over 120,000 deaths in 2010 according to the CDC. Understanding the underlying mechanisms and improving the treatment of trauma is of great clinical and public health interest. The systematic collection and study of critical care data originated in combat conflicts and wars and more recently to civilian centers. Improving patient outcomes, the quality of care received, and identifying high-risk patients are unmet needs in this field./nClinicians rely on their intuition, training, and heuristic scoring systems to identify patients who are likely to die or experience other outcomes such as the need for a massive transfusion, which resuscitates the patient via the infusion of blood products such as plasma, platelets, and red blood cells. We assessed the ability of measured covariates to predict various clinical outcomes, demonstrate the utility of machine-learning prediction algorithms, and examined the predictive performance of a commonly-used score to predict massive transfusion. This highlights the need for a principled approach to predicting outcomes that does not rely only on ad hoc procedures./nIn addition to the prediction of clinical outcomes, we defined a measure of variable importance for ranking predictors based on their relationship with the outcome of interest. This parameter was motivated by causal inference and requires a systematic approach to the question of interest that helps translate it into a parameter with a clinically meaningful interpretation rather and maintains transparency about the assumptions required to deem the parameter a causal effect. We apply this procedure to gene expression data from critically injured patients to illuminate how the coagulation and inflammation pathways react to trauma injury./nFinally, we compare the quality of care received at different trauma center types around the United States using another parameter motivated by causal inference. This allowed us to simulate what would have happened to a patient if they had been treated at a different trauma center and obtain an objective comparison that identified sites where severely injured patients would benefit most from being treated./nThis research highlights the utility of causal inference for framing problems, motivating clinically meaningful statistical parameters, and interpreting the results. We also advocate for the use of semiparametric prediction algorithms to allow for greater flexibility in modeling assumptions and demonstrate their performance in practice.

Advisor: Hubbard, Alan E
Non-Gaussian Component Analysis

Extracting relevant low-dimensional information from high-dimensional data is a common pre-processing task with an extensive history in Statistics. Dimensionality reduction can facilitate data visualization and other exploratory techniques, in an estimation setting can reduce the number of parameters to be estimated, or in hypothesis testing can reduce the number of comparisons being made. In general, dimension reduction, done in a suitable manner, can alleviate or even bypass the poor statistical outcomes associated with the so-called ``curse of dimensionality.''/nStatistical models may be specified to guide the search for relevant low-dimensional information or ``signal'' while eliminating extraneous high-dimensional ``noise.'' A plausible choice is to assume the data are a mixture of two sources: a low-dimensional signal which has a non-Gaussian distribution, and independent high-dimensional Gaussian noise. This is the Non-Gaussian Components Analysis (NGCA) model. The goal of an NGCA method, accordingly, is to project the data onto a space which contains the signal but not the noise./nWe conduct a comprehensive review of NGCA. We analyze the probabilistic features of the NGCA model and elucidate connections to similar well-known models and methods in the literature, including a hitherto-unseen and surprising connection to a set of models proposed by Cook in the context of dimension-reduction in regression. We review the literature on NGCA, catalogue existing NGCA methods, and compare them to the method proposed in Chapter 2./nWe also propose and analyze a new NGCA method based on characteristic functions called CHFNGCA. We show CHFNGCA is, under mild moment conditions on the non-Gaussian sources, consistent and asymptotically normal; the latter property has not been demonstrated for any other NGCA method in the literature. We conclude by highlighting areas for future work./nThe proof of all stated propositions, lemmas and theorems are contained in Appendices A and B.

Advisor: Bickel, Peter J.
El Karoui, Noureddine
Insights into the Physiology, Evolution, and Design of Bacterial Chlorate Reduction

Bacterial chlorate respiration is an important part of the biogeochemical cycling of chlorine in the environment, but very little is known about the metabolism at the molecular level. This work extends our current understanding of microbial chlorate reduction by genome sequencing isolates and uncovering the novel architecture of chlorate reduction composite transposons (Chapter 2); by characterizing the physiology of an environmental isolate Shewanella algae ACDC using proteomics, RNA-seq, and genetics (Chapter 3); by engineering the ability to reduce chlorate de novo in the non-chlorate reducer Shewanella oneidensis MR-1 (Chapter 4); and by applying genetic tools (Bar-seq, allelic exchange) to dissect the metabolism in Pseudomonas stutzeri PDA (Chapter 5).

Advisor: Hermanowicz, Slawomir W
Plotting Sex: Pornography's Performatistic Screen

The early 1970s witnessed the mainstreaming of feature-length, hard core pornography. Though derided by critics, this newly minted genre had two notable features: broader narratives within which sex occurred, and an insistent focus on the visual display of male pleasure. Plotting Sex claims that, by embedding sex within a story, sex itself takes on narrative qualities./nTo support this claim, it teases out small shifts in the twentieth century's episteme that collectively contributed to the early 1970s emergence of what it terms pornography's performatistic screen, or the base, plotted structure of bodily performance and engagement underpinning sexual displays as enacted over time in orgasmically-oriented hard core film. This project starts with the twin Foucaultian poles of law and "human/nsciences" as represented by the metonyms of American obscenity jurisprudence and sexology, finding in both a late 1960s pivot to issues of social construction and utility as tethered to narrative. Following this, it narrows focus to look at increasing rates of oral sex in American sexual practice and the changing production and exhibition of filmed/npornography. After analyzing then-contemporary concepts of desire in readerly narrative, it finishes by proposing a model for how plotted sex works both within and alongside broader narrative./nIn all of these analyses, this project pays particular attention to the shifting role narrative occupies in matrices of power, knowledge, and pleasure. It argues that narrative plotting, when applied to sex, increasingly functions as a tool for both policing and reduplicating social and cultural norms.

Advisor: Williams, Linda
Millimeter-Wave/Sub-Terahertz CMOS Transceivers for High-Speed Wireless Communications

Millimeter-wave and sub-terahertz frequency bands are available for wideband applications such as high data-rate communication systems. As the respective wavelength is on the order of a millimeter, a compact on-chip antenna can be designed, thereby reducing the overall form factor and obviating expensive off-chip packaging. However, the channel propagation loss increases significantly with the frequency. Although CMOS technology is prevalent in digital processing and data communication, CMOS devices are lossy and inefficient at such high frequencies. Thus, it is challenging to implement an efficient and wideband transceiver at sub-terahertz frequencies using CMOS technology./nThe aim of this dissertation is to demonstrate sub-terahertz wireless links for high-speed chip-to-chip communication in CMOS. First, transceiver architectures and building blocks are discussed to address the challenges and limitations of the CMOS process. Two fully integrated CMOS transceivers, a 260 GHz OOK transceiver and a 240 GHz QPSK/BPSK transceiver, are then demonstrated using on-chip antennas. Frequency multiplication and mixer-first design are employed to operate beyond the cut-off frequency. In the QPSK modulation, a maximum data rate of 16 Gbps is realized with an energy efficiency of 30 pJ/bit./nThese demonstrations show that millimeter-wave/sub-terahertz wireless communication can be a promising solution for high-speed chip-to-chip communication. Improvements in the energy efficiency and silicon area of these wireless links can result in replacing or complementing existing wired links.

Advisor: Niknejad, Ali M
Development and Applications of Well-Defined Antibody and Antibody Fragment Bioconjugates

Antibodies have been widely used in many biological applications, including reseach tools, imaging, and therapeutics, due to their excellent binding specificity and affinity. As therapeutics, the ability to elicit immune effector functions and plasma half-life extension through the function of the constant domain (Fc) render antibodies superior to small molecules in these aspects. This work describes the use of chemical-based bioconjugation techniques to develop novel bioconjugates from antibody fragments and full-sized antibodies for therapeutic and imaging purposes. The complex structures of this class of biomolecules -- with the presence of multiple polypeptide chains, extensive disulfide networks, and critically important glycosylation patterns -- make it difficult to manipulate these biomolecules in a controlled manner. Thus, protein modification techniques play important roles in enabling the development of these constructs. In this work, we discuss the generation of Fc-synthetic molecule hybrids as antibody mimics, full-sized antibody-synthetic molecule conjugates as bispecific antibodies, and MS2-antibody conjugates as targeted delivery vehicles. The ability to conjugate different moieties into one molecule provides the ability to shuffle and combine synergistic advantages of the component molecules.

Advisor: Francis, Matthew B.
The Effect of Cognitive Biases and Visceral Factors on Economics Decisions

This work presents new evidence of effects that cognitive biases and visceral factors, particularly hunger, have on economic decisions. In Chapter 1, I test whether individuals display inattention to the decimal digits of a price (i.e. left-digit bias). Using data from a unique experiment conducted by Chetty et al. (2009), who find that tax-salience decreases demand, I find that if tax-salience shifts the price left-most digit upwards the decrease in demand is larger. This study presents new evidence on left-digit bias and also suggests that this is the main channel through which tax salience affects consumers' decisions. In Chapter 2, I motivate a new research agenda by drawing parallel evidence from psychology, economics, and neuroscience, and posing the question: does cognitive-fatigue and hunger affect time preferences? Using data from a novel laboratory experiment, I find that hunger and cognitive-fatigue exacerbate impatience. On one hand, cognitive-fatigue appears to decrease attention and increase the use of heuristics, resulting on a higher degree of utility curvature. On the other hand, hunger has a larger effect on impatience when monetary rewards are immediate, resulting in present-biased preferences. These results show that present bias is a visceral response activated when sooner rewards are immediate, and can help explain why the poor tend to make more shortsighted economic decisions.

Advisor: Villas-Boas, Sofia
Discrete Sliding Control for the Dynamics of Engine Cold Start

The increasing complexity in automotive systems has prompted the use of the Verification & Validation procedure in the industry. In particular, powertrain control design follows the validation of achieving the control targets and the verification that the correct controllers were selected. Within this process, there is an area of significance residing in the early stages of Verification & Validation that addresses issues arising when digital controllers are implemented on continuous time physical systems. The work in this thesis explores that realm via the design of control algorithms that mitigate errors and uncertainties in the software-hardware interface. In particular, control algorithms that mitigate sampling time, quantization, fixed-point processing, and model uncertainty are presented. The formulations include discrete time sliding control, discrete time sliding control with uncertainty bounds, and decoupled as well as multiple-input, multiple-output discrete time sliding control with adaptation. The algorithms are demonstrated on engine cold start dynamics, with a secondary objective of addressing the issue of hydrocarbon emission reduction, with simulation and experimental results.

Advisor: Hedrick, J. Karl