VictorJuiz/thesis huggingface dataset:
Resource constrained scheduling problems in next-generation computing and networking [electronic resource]
Keywords: Management Science and Engineering.

With the explosion of traffic on computer networks along with the proliferation of applications that grow increasingly demanding of device and network resources, it has become imperative to find efficient algorithms for scheduling the delivery of this traffic. Starting with a focus on wireless communications, and continuing with a discussion of related issues in sensor networking and failure management in computing, we offer both a methodology for modeling these issues as well as algorithms for optimizing performance under the resource constraints at hand. We first investigate a key issue of scheduling the transmission of data frames across lossy channels when there is simultaneously a constraint on channel usage as well as a deadline by which all transmissions must be made. A tradeoff between throughput and power usage is profiled, and concepts from dynamic programming and control are applied to solve the real-time scheduling decision problem in question. This general type of resource limited scheduling problem appears in a number of areas in addition to wireless communications, including remote sensing and failure management in computing systems, which we also discuss at length. This work also addresses decision problems in which rather than a limitation on power, the key issue is a limitation on the routes that can be taken through a switch controlling the passage of packets to their respective destinations. A hard deadline by when packets must be delivered is once again considered. Routing constraints of this type are profiled in both a wireline as well as wireless communications framework, and we offer powerful yet intuitive solutions for these problems.
Response spectrum compatibilization and its impact on structural response assessment [electronic resource]
Keywords: Civil and Environmental Engineering.

Quantification of the seismic performance of structures is a critical step in the design and analysis of our built environment. This is sometimes accomplished using response history analysis, which requires ground motions resulting from (or attempting to simulate) real earthquakes. This thesis describes statistical studies of structural analysis results obtained from ground motions developed using response spectrum compatibilization (a.k.a. ``spectrum matching''), in order to evaluate whether the compatibilization approach produces ground motions that induce lower levels of demand on structures relative to those developed using other methods. Ground motions strong enough to cause significant damage are rare yet inevitable, motivating research on how to select, modify, or synthesize appropriate records for analysis. The spectrum matching process is a modification procedure used to provide such ground motions through nonlinear modification of spectral shape, and may be useful either to reduce spectral variability among a suite of records, or to change unsuitable spectral shapes to make them suitable. Response history analysis can be quite time-consuming, and a reduction in spectral variability generally leads to a reduction in nonlinear structural response variability, implying fewer ground motions (and fewer hours) are required to obtain an estimate of mean response. A drawback of using matched ground motions is that there is not yet consensus as to whether they will produce biased structural response results relative to results obtained from ground motions that were not matched. This thesis demonstrates the existence of a statistically significant and unconservative response bias for a variety of structural models and response parameters when ground motions are matched to reduce spectral dispersion. The cause for this bias is fully attributed to the impact of spectral shape variability, as characterized within a suite of ground motions by conditional spectral dispersion. A modified variable-target matching methodology is then proposed to provide rare, intense ground motions that produce unbiased response estimates by maintaining appropriate spectral shape variability. Finally, general recommendations are provided on the use of spectrum matching for design and analysis, and both the limitations of this study and future opportunities are discussed.
Retino-hypothalamic regulation of light-induced sleep in mice [electronic resource]
Keywords: Biology.

The daily organization of sleep is regulated by a complex interaction between circadian and homeostatic processes. Light indirectly modulates sleep through its ability to phase shift and entrain the circadian system. However, light can also exert a direct, circadian-independent effect on sleep. In diurnal animals, an acute exposure to light promotes arousal whereas the same exposure induces sleep in nocturnal animals. The mechanisms whereby light directly influences sleep are not well understood. Chapter 1 reviews both the neurobiology and current hypotheses of how light acutely modulates sleep at the level of the retina and hypothalamus. Chapter 2 highlights the selective effects of light on murine sleep. By using single light pulses of different intensities and durations, the data demonstrate that (1) mice are highly responsive to the sleep inducing properties of light during the dark phase, (2) the transition to sleep is characterized by a rapid induction, period of maintenance, and a rapid compensatory recovery, and (3) the melanopsin photoreceptors in the eye are primarily important for maintenance of light-induced sleep. Chapter 3 focuses on the modulation of light-induced sleep by the melanopsin photoreceptors and histamine H3-receptors. We found that (1) millisecond light flashes are able to induce sleep in mice over a fairly large range of intervals, and similar to studies using continuous light, the response is melanopsin dependent. (2) We further show that the acute administration of ciproxifan, a selective histamine H3 receptor antagonist, attenuated the increase in sleep by continuous light early in the dark period. Chapter 4 contains a summary of the main findings of this dissertation and a discussion of new avenues for research on this topic which is still in its early stages. Overall, the work here highlights fundamental characteristics of light-induced sleep in mice. Such knowledge will be important for future studies assessing the mechanisms involved in the acute modulation of sleep by light in mammals.
Retroviral impact on mammalian placenta evolution [electronic resource]
Keywords: Genetics.

The placenta plays a fundamental role supporting pregnancy in all mammals, but exhibits unexpected and striking morphological and physiological variation across species. The rapid evolutionary diversification of the mammalian placenta is hypothesized to be a product of recurrent genetic conflict between parent and offspring. In this work, I investigate the genetic basis of rapid placenta evolution by using high-throughput genomic approaches, and address three major issues in placental biology. First, given that highly conserved genes govern placental development, the molecular mechanisms underlying the rapid diversification of placental morphology have remained unresolved. Our study reveals that the genome-wide regulatory landscape of placental development is highly divergent between closely related species, strongly implicating non-coding regulatory evolution as the major force driving placental morphological diversity. Second, endogenous retroviruses (ERVs) that are normally repressed throughout the embryo are rampantly expressed in the placenta, but the biological rationale—if any— behind this apparent paradox has been unclear. We demonstrate that species-specific ERVs serve as a major source of functional enhancers during placental development, which provides a clear mechanism where placental ERV activity may facilitate the evolutionary diversification of placental morphology. Finally, our findings suggest a novel evolutionary model where placental ERVs provide an adaptive benefit under parent-offspring conflict. Given that genetic conflict predicts rapid diversifying evolution to maintain maximal fitness, we propose that placental ERVs act to dramatically increase the developmental evolvability of the placenta by serving as a rapidly evolving, epigenetically restricted source of polymorphic regulatory elements.
Revenue‐Maximizing Mechanism Choice in Divisible Good Auctions: An Empirical Analysis of the Thai Treasury Auction Market
Keywords:  Department of Economics
Stanford Department of Economics
Multi-unit auctions
Treasury auctions
Collusion
Thesis

An important question that prevails in the theory of divisible-good auctions is to determine whether a discriminatory auction yields higher revenues to the auctioneer than a uniform price auction or Vickrey auction. One way to answer this question empirically is to use estimates of the bidders’ true marginal valuations on the auctioned goods. This Honors Thesis conducts empirical studies of revenue comparisons under discriminatory and uniform price auction mechanisms and the studies of collusion on winning bid data from Thai Treasury bill auctions in 2008 and 2010. This Honors Thesis is one of the first to perform an empirical analysis using a structural econometric approach suggested by the recently developed approximate Linear Bayesian demand function equilibria (LBDFE) by [Ollikka(2011)] to estimate the model primitives and bidder valuations and simulate counterfactual auction outcomes from estimated structural parameters, then make analysis similar to methods in [Horta¸csu and Mcadams(2010)] and [Kastl(2011)]. Bank of Thailand currently employs discriminatory auctions in distributing Treasury bills. But results are generally in favor of uniform price mechanism except for those auctions with longer maturities where both auction mechanisms perform equivalently. However, practical auction experiments are necessary since the analysis modified from [Athey et al.(2011)Athey, Levin, and Seira] suggest the existence of collusion opportunities, which would not allow the uniform price mechanism to outperform the discriminatory one. Moreover, this Honors Thesis provides an indicative regression-based test for valuation implied by the data. The approaches suggested in this Honors Thesis can be extended to analyze divisible-good auctions.
Reversing the brain drain? Skilled return migration and the global movement of expert knowledge [electronic resource]
Keywords: Sociology.

My dissertation explores how skilled return migrants adapt the expertise they gained working abroad to workplaces in their home countries. To study this, I conducted a survey of 4,183 skilled returnees from 81 countries, who had worked abroad in the U.S., as well as 161 interviews with skilled returnees from 25 countries. The respondent pool came from U.S.'s largest organizational sponsor of J1 Visas for professionals. As the largest survey of skilled return migrants ever compiled, the dataset includes information on the respondents' career histories, attitudes, and work activity. My data analysis generated three main findings. One, less than half of the respondents report implementing some aspect of their professional knowledge gained overseas in the workplaces of their home countries. Whether returnees are successful channels of cross-border knowledge depends less on their ability to demonstrate or articulate novel ideas and more on the normative conditions of the professional environments in their home countries. Two, returnees who are effective brokers of knowledge bring back ideas about organizational and management practices, such as new methods of training, more than they do technical knowledge. Three, returnees are more likely to venture into self-employment if they have strong local ties to their home countries; moreover, the effect of these local ties on entrepreneurial transitions is stronger for returnees in home countries with high rates of self-employment. Finally, I show that the very returnees who are most successful as knowledge brokers are also most likely to venture abroad again. Thus, the returnees who could benefit their home countries the most are also the least like to stay. These findings challenge the conventional notion of return migrants as agents of economic transformation, suggesting that many institutional and cultural challenges stand in the way of their ability to broker knowledge and resources across country borders. This work also ties contributes to theoretical perspectives on international migration, organizational learning, social networks, and the sociology of knowledge.
Robot telemanipulation in unstructured environments [electronic resource] : sensors, algorithms, interfaces
Keywords: Mechanical Engineering.

This dissertation presents methods for robot teleoperation, or equivalently, human-in-the- loop robotics. Human-in-the loop systems have the potential to handle complex tasks by combining the cognitive skills of a human operator with autonomous tools and behaviors. Along these lines, we present novel methods in grasp planning, haptic (force-feedback) rendering, and robot control which allow synergy in interaction between a human operator and a robot. We describe the interfaces that employ these algorithms, and validate them through user experiments. Our goal is to see robot technologies make a bigger impact in peoples' everyday lives, getting robots out of the laboratory and factory, and into homes, offices, and other unstructured human spaces. Our algorithms focus on three distinct areas of telerobotic manipulation but are unified by their common reliance on 3D point cloud data obtained from emerging sensor technol- ogy; we do not depend on environment or object models known a priori since it difficult to anticipate the things a robot will encounter in unstructured settings. First, since grasp- ing is a prerequisite for many manipulation tasks, we present two algorithms for planning grasps on clusters of 3D points. Next, we explore how to perform force-feedback haptic rendering of 3D point cloud data. This enables an operator to use the sense of touch to learn about environment geometry and potential collisions. Finally, we present a controller that uses a sequence of convex optimization steps to produce constrained arm motions that follow time-varying goal poses commanded by an operator. Using 3D sensor data to form motion constraints in real-time, the robot is responsive to changing goals from the user yet also avoids collisions and unfavorable arm configurations. We demonstrate the integration of our algorithms into a telerobotic system that enables an operator to perform varied and unscripted manipulation tasks in arbitrary settings. We describe tools for navigation, perception, and manipulation, ranging from direct control of a gripper or mobile base to autonomous sub-modules that perform collision-free base navigation or arm motion planning. Most importantly, we share results from testing these interfaces in a variety of settings, including user studies with non-expert operators and a case study with a motor-impaired operator using the robot in his own home.
The rogue transcriptome [electronic resource] : using sequencing to track RNA regulation and identify unusual RNAs
Keywords: Genetics.

First, we take a look at the function of a specific type of RNA editing mediated by ADAR (adenosine deaminase that acts on RNAs). We test our hypotheses on ADAR activity and target specificity through transcriptome analysis in the context of exogenous RNAi response pathway in C. elegans. By examining of small RNA and mRNA populations in adar mutants and additional RNAi defective mutants, we show that the activity and specificity of the ADAR enzyme likely precludes the detection of its targets through conventional methods of sequence capture and analysis. Based on this understanding, we develop novel computational approaches for analysis of small RNA and mRNA populations and identify a broader set of ADAR targets, leading to a deeper understanding of the ADAR pathway, the conserved functionalities of the ADAR enzyme, and its relationship with the exogenous RNAi pathway in C. elegans. Second, we examine the dynamics of the transcriptome upon and after exposure to extreme heat. We hypothesize that the recovery response after removal from heat exposure might involve alternations in transcription regulation that are more complex than a reversal of the heat-shock induced effects, and that one such form of long-term regulation might involve the endogenous RNAi pathway and regulation via synthesis of endogenous siRNAs. By examining the dynamics of the C. elegans transcriptome during time-course of heat exposure and recovery, we reach a deeper understanding of heat shock biology and explore the relationship between endogenous siRNAs and their sequence complementary mRNA targets in the context of environmentally induced perturbance.
The role of body mechanics in touch sensation in the nematode Caenorhabditis elegans [electronic resource]
Keywords: Mechanical Engineering

The mechanics of our skin determine how our skin and specialized mechanically-sensitive neurons within it are stressed and strained when touched. Understanding the interplay between skin mechanics and touch sensitivity is paramount in uncovering the fundamental molecular mechanisms underlying touch sensation and in understanding and treating touch insensitivity due to diseases like peripheral neuropathy. Despite this importance, the interplay between skin mechanics and sensitivity is poorly understood. The organism Caenorhabiditis elegans is an excellent model system in which to test the hypothesis that skin mechanics affect touch sensitivity. C. elegans detects body touch with just six mechanically-sensitive neurons. These neurons are embedded in the outer shell (consisting of the cuticle, hypodermis and body wall muscles) of the body plan, which dominates the overall body mechanics. If skin mechanics are important in touch sensitivity in C. elegans, stiffening or softening the outer shell should alter the ability of the animal to detect applied mechanical stimuli. I demonstrate that a piezoresistive cantilever force clamp system and methods that alter C. elegans body mechanics can be combined to directly test the hypothesis that mechanics modulate touch sensitivity. In particular, I build on prior work demonstrating that genetic mutation of cuticle proteins alters body stiffness, and use optogenetic modulation of body wall muscle tone to demonstrate that the body wall muscles modulate C. elegans body mechanics. Combining piezoresistive cantilevers capable of applying minute forces with these techniques to alter the mechanics of the body allows us to directly quantify the affect of body stiffening or softening on force or indentation depth sensitivity in C. elegans. I find that even small shifts in body stiffness have a significant effect on force sensitivity, with body stiffening leading to a reduction in force sensitivity and vice versa. Further, I demonstrate that indentation depth sensitivity is less affected by changes in body mechanics, suggesting that the mechanically-sensitive neurons involved in body touch in C. elegans respond more directly to applied indentation than to applied force. These findings emphasize the importance of considering skin mechanics in understanding the sense of touch and insensitivity due to diseases like peripheral neuropathy.
Saxitoxin-derived probes for the study of voltage-gated sodium channels in living cells and animals [electronic resource]
Keywords: Chemistry.

Voltage-gated sodium channels (NaV) serve an essential role in physiology. Accordingly, their dysfunction is associated with a number of human diseases and disorders, including epilepsy, cardiac arrhythmias, and chronic pain conditions. Designed by Nature as a chemical weapon, the naturally occurring channel blocker (+)-saxitoxin (STX) can be repurposed as a tool for studying these large integral membrane proteins. Access to new toxin derivatives through de novo synthesis offers a unique strategy to probe NaV structure and function, circumventing key limitations associated with existing methods for studying these proteins. The preparation and electrophysiological evaluation of an expanded library of N21-modified STX analogues is described herein. Characterization of the binding properties of these nanomolar NaV inhibitors has contributed to the development of an enhanced model for the structure of the inner pore of the channel. A select set of STX-fluorophore conjugates that bind reversibly to NaV with submicromolar potency serve as fluorescent markers of channels in living cells to study channel motility in the cell membrane. By contrast, maleimide-conjugated STX derivatives can be engineered to act as irreversible inhibitors of ion conductance when applied to wild-type NaV isoforms. The unique binding behavior of these derivatives has been leveraged to develop a new class of NaV probes for use in live cell imaging experiments and protein profiling studies. Maleimide-toxin conjugates with bioorthogonal reactive groups have been synthesized and can be employed for ligation of visualization and isolation tags to covalently modified channels. Appendage of fluorine-18 to a modified STX affords a probe for studying NaV expression in living subjects. An efficient synthetic route yields a derivative that binds with nanomolar affinity to several NaV isoforms. Biodistribution, autoradiography, and PET-MRI imaging studies demonstrate accumulation of the radiotracer at the site of injury in a rat model of neuropathic pain. This uptake correlates with the previously reported upregulation of NaV isoforms at this site, validating the utility of this probe as a NaV imaging agent. Collectively, these STX derivatives, uniquely available through chemical synthesis, represent a novel set of molecular probes for studying NaV function in vitro and in vivo.