VictorJuiz/thesis huggingface dataset:
Roles for hedgehog signaling in zebrafish development [electronic resource]

The zebrafish has emerged as a powerful model organism for the experimental interrogation of the processes that bring about vertebrate development. In this thesis we study functions of Hedgehog (Hh) signaling, a process that is frequently dysregulated in cancer, that occur during the formation of the zebrafish embryo. First, we investigate a possible link between Hh signaling and the directed migration of germ cells to the presumptive gonad in the early embryo and find that Hh-targeting drugs can perturb germ cell migration, but Hh signaling itself does not regulate this process. Second, we study the formation of motoneurons in the developing ventral spinal cord and find that Hh signaling and retinoic acid signaling work together to induce these cells by the same downstream output of Gli transcription factor activity. Third, we generated transgenic zebrafish that reliably report Hh signaling events at multiple levels of the pathway and we apply these tools in initial studies of zebrafish regeneration. In summary, these studies further our knowledge of the roles for Hh signaling in vertebrate development and will lead insight into the pathology of Hh-related disorders.

Keywords: Biochemistry
Advisor: Chen James Kenneth primary advisor. Thesis advisor
Harbury Pehr advisor. Thesis advisor
Krasnow Mark
Straight Aaron
The roles of chromatin modifying enzymes in DNA double-strand break repair [electronic resource]

Efficient DNA double-strand break (DSB) repair is essential for maintaining the stability of the genome. A single long-lived DSB can cause cell lethality (Bennett et al., 1996). Humans with defects in DSB repair are sensitive to DNA damaging agents and are predisposed to developing cancers, as exemplified by such diseases as Nijmegan breakage syndrome, Ataxia telangiectasia, and breast cancer susceptibility in women with mutations in the BRCA1 and BRCA2 genes (Duker, 2002). Repair of DNA damage requires activation of cell cycle checkpoint controls, recruitment of repair proteins to DNA lesions, and transcriptional activation of relevant genes. As shown by our data, deletion of particular histone modification genes produces sensitivity to ionizing radiation in Saccharomyces cerevisiae, suggesting a role for chromatin modification enzymes in the repair process as well. Because damage recognition and repair of lesions are both influenced by chromatin structure, we began by studying the role of histone acetylation in the DNA damage response. Acetylation of the N-terminal tails of histone H4 opens the chromatin to allow repair enzymes to access broken DNA. Through a screen of the yeast deletion pool, we found that deletion of BRE1 and DOT1 genes causes sensitivity to ionizing radiation. Ubiquitination of H2B on lysine 123 (H2B-K123) by ubiquitin ligase Bre1 is necessary for methylation of H3 on lysine 79 (H3-K79) by Dot1. Through the histone modifications they catalyze, these proteins are involved in many aspects of the DNA repair response, as outlined in Sections C, D, and E. Our studies focused on homologous recombination repair defects, genome-wide expression patterns in BRE1 and DOT1 deletion mutants, an analysis of the data regarding proteins purported to bind to methylated H3-K79, and optimization of a protein purification strategy to find Dot1 binding partners. Our yeast deletion pool screen also predicted a role for N-terminal acetyltransferase complex NatB in DNA double-strand break repair. In Section F, we build a case for acetylation of DNA end-binding protein Mre11.

Keywords: Cancer Biology.
Advisor: Brown J. M. (J. Martin) primary advisor. Thesis advisor
Cimprich Karlene advisor. Thesis advisor
Ford James M. (James Matthew) advisor. Thesis advisor
Wysocka Joanna
Rounding by sampling [electronic resource]

In this thesis we introduce a new technique for designing approximation algorithms for a class of discrete optimization problems. The idea, that we call "Rounding by Sampling'', is basically a technique for rounding the optimal fractional solution of the problem (obtained from the relaxation of the original problem into a continuous domain) back to the integral domain. The technique is based on sampling from a maximum entropy distribution over the combinatorial structures hidden in the feasible solutions. The main implication of our technique is that it keeps the combinatorial structures intact, while aiming to preserve the solutions quantitatively. We present our technique on combinatorial structures such as spanning trees and matchings. Our results suggest a new approach to attack discrete optimization problems: the path goes through the well-known idea of relaxation the problem into the continuous domain and then finding a (fractional) optimal solution in the relaxed domain using the known techniques of optimization literature, e.g. interior point method, ellipsoid method, etc. After that, our technique comes to help: it enables us to transform the fractional solution back to an integral feasible solution of the original problem, while ensuring that we do not lose much, quantitatively. Using this approach, we show how to design approximation algorithms for two of the most well-known problems in discrete optimization: the traveling salesman problem and the fair allocation of indivisible goods.

Keywords: Management Science and Engineering
Advisor: Saberi Amin primary advisor. Thesis advisor
Goel Ashish advisor. Thesis advisor
Ye Yinyu advisor. Thesis advisor
Routing to mobile users by exploiting mobility prediction in wireless mesh networks [electronic resource]

With the advent of ubiquitous wireless networks, supporting user mobility has become crucial. Routing algorithms face challenges in supporting mobility while remaining energy efficient. Mobility of human or vehicle makes wireless links in these mobile networks much more volatile than the links in wireless networks of stationary nodes, and the wireless connectivity varies frequently due to moving speeds. Hence reliable data delivery to mobile users is often hard to achieve. In this thesis, we propose a new routing algorithm for wireless mesh networks with mobile users based on the following components: (i) predicting likely next association node of mobile user (short-term mobility prediction), and (ii) predicting a sequence of the future association nodes of mobile user (long-term mobility prediction). Our approach is to understand and characterize the mobility of the mobile users by looking at connectivity patterns over stationary mesh nodes using past history of connectivity information. Our main contribution is the design of techniques that can be used by routing algorithms to leverage the predictive knowledge of user mobility to efficiently deliver data to those users. This work enables a long-term routing plan through a network optimization process, called "data stashing". The data stashing scheme enables reliable data delivery from stationary mesh nodes to mobile users. In this scheme, each mesh node selects a set of possible association nodes on which to stash its data, to be picked up whenever the mobile user passes the stashing node. We show that data stashing significantly decreases routing cost for delivering data from stationary mesh nodes to multiple mobile users compared to immediate routing protocols where mesh nodes immediately deliver data to the last known association nodes of mobile users. We also show that the scheme provides better load balancing, avoiding collisions and consuming energy resources evenly throughout the network, leading to longer overall network lifetime over the immediate routing protocols. More importantly, we demonstrate that given even limited information about the future node associations of mobile users, optimization of routing paths leads to significant improvements in routing performance.

Keywords: Electrical Engineering
Advisor: Guibas Leonidas J. primary advisor. Thesis advisor
Tobagi Fouad A.
Bambos Nicholas advisor. Thesis advisor
Rule-based response assessment framework [electronic resource]

The Rule-Based Response Assessment Framework is a goal-driven, context-driven, and knowledge-based temporal interpretation framework that automates response assessment over clinical data. The goal of this work is to enable consistent application of standardized response criteria for clinical trial data analysis, and to enable research and development of response criteria. The Rule-Based Response Assessment Framework defines the dimensions of response assessment including the knowledge and tasks required to apply response criteria to patient data. The Framework consists of several knowledge models and several sub-methods that make up the Response Assessment Method. The framework is implemented using ontologies and rules with the semantic web formalisms of OWL and SWRL respectively. The framework is applied to two response criteria in the oncology domain and one response criterion for rheumatoid arthritis. I demonstrate that the implementation of the Rule-Based Response Assessment Framework is extensible, reusable and enables consistent application of response criteria to patient data and comparison of response criteria within a clinical domain. Future research directions will incorporate the Rule-Based Response Assessment Framework into a larger informatics infrastructure for application and development of oncology response criteria.

Keywords: Biomedical Informatics.
Advisor: Das Amar K. (Amar Kumar) primary advisor. Thesis advisor
Rubin Daniel (Daniel L.) primary advisor. Thesis advisor
Fagan Lawrence Marvin
Ruthenium-catalyzed redox- and cycloisomerizations [electronic resource] : atom economic syntheses of carbo- and heterocycles

A facile and 100% regioselective cycloisomerization--6-pi-cyclization method for obtaining pyridines is described. The unsaturated ketones and aldehydes derived from the cycloisomerization of primary and secondary propargyl diynols in the presence of CpRu(MeCN)3PF6 are converted to 1-azatrienes which in turn undergo a subsequent electrocyclization--dehydration to provide pyridines with excellent regiocontrol. The ruthenium-catalyzed cycloisomerization is a mild, atom-economical method for obtaining the requisite dienone and dienal substrates. The cycloisomerization--6-pi-cyclization sequence may be carried out in one pot or in two independent steps. Additionally, the azatriene cyclization may be carried out in 1-3 hours under microwave irradiation or, for more sensitive substrates, at lower temperatures for longer periods of time (6--24 hours at 90 °C). An atom-economical method for the convenient synthesis of tetrahydropyrans and tetrahydrofurans is also described. Enones and enals derived from the [IndRu(PPh3)2Cl]-catalyzed redox-isomerization of primary and secondary propargyl alcohols undergo a subsequent intramolecular conjugate addition to provide cyclic ethers in excellent yields. Lastly, we have developed complementary methods for the transition metal-catalyzed enyne cycloisomerizations of cyclic olefins. By using distinct ruthenium and palladium catalysts, decalins and 7,6-bicycles can be obtained with dichotomous stereochemical outcomes. The change in mechanism that accompanies the change in metal affords trans-fused 1,4-dienes with ruthenium and their cis-fused diastereomers under palladium catalysis. In the reactions under ruthenium catalysis, a coordinating group is required, and acts to direct the metal to the same side of the carbocycle, resulting in the observed trans diastereoselectivity. Subtle changes in the carbocyclic substrate led to the discovery of a heretofore-unobserved mechanistic pathway, providing bicyclic cycloisomerization products under palladium catalysis, tricyclic products under ruthenium catalysis in DMA, and a 1:1 mixture of the two under ruthenium catalysis in acetone. The different coordination requirements of the two paths allow for the reaction to be shuttled through the metallacycle pathway (generating tricyclic products) when DMA is used as a solvent. This method of obtaining these cyclobutene products complements the existing methods for catalyzing the [2+2] cycloaddition of alkynes. While other methods have been demonstrated for larger ring sizes with palladium, and for specific alkyne termini with platinum and gold, this method is unique in its substrate scope. To the best of our knowledge, this is the first example of a [2+2] cycloaddition catalyzed by CpRu(MeCN)3PF6.

Keywords: Chemistry
Advisor: Trost Barry M. primary advisor. Thesis advisor
Waymouth Robert M. advisor. Thesis advisor
Wender Paul A. advisor. Thesis advisor
Scaled planar floating-gate NAND flash memory technology [electronic resource] : challenges and novel solutions

NAND flash memories are ubiquitous in their use as portable storage media in cellphones, cameras, music players, and other portable electronic devices. The NAND flash memory device, consisting of a floating-gate transistor cell, is the most aggressively scaled electronic device, as evidenced by ever-increasing memory capacities. In this work, we will examine possible problems arising from continued scaling of these structures, and discuss novel solutions to overcome them. Firstly, we investigate scaling of the conventional poly-silicon floating-gate, aimed at reducing cell-to-cell interference. We experimentally delineate a new reliability concern for the first time, with programming current through ultra-thin poly-silicon floating-gates becoming increasingly ballistic. We also experimentally demonstrate doping-related issues in the poly-silicon floating-gate. We then apply a novel metal-based floating-gate cell for the first time, designed to overcome the problems discussed above. We explore factors that influence the choice of metal, and demonstrate excellent functionality in ultra-thin metal floating-gate cells scaled down to 3 nm TiN floating-gate thickness, thus greatly reducing cell-to-cell interference. Finally, in order to facilitate continued scaling of the control dielectric, we explore replacement of the conventional silicon oxide-nitride dielectric with high-k dielectric materials. We integrate poly-silicon and metal floating-gate cells with Al2O3 high-k control dielectric. Further, we establish that a deeper work-function control gate is helpful in reducing gate-injection. Combining ultra-thin metal floating-gate, high-k control dielectric and deep work-function control gate, we enable the planar floating-gate cell as a scalable candidate.

Keywords: Electrical Engineering
Advisor: Nishi Yoshio
Saraswat Krishna primary advisor. Thesis advisor
Krishnamohan Tejas
The search for dark matter [electronic resource] : from colliders to direct detection experiments

This thesis is devoted to searches for dark matter at colliders and direct detection experiments. The first half of the work focuses on the Tevatron and LHC. Jets and missing energy searches at these colliders are sensitive to a broad class of models and dark matter candidates. I show that current jets plus missing energy analyses can miss signals for new physics, and suggest an alternative model-independent search strategy that broadens the reach of these experiments I also discuss searches for Higgs bosons that decay to light pseudoscalars. Information about the Higgs sector obtained through such searches may hint at the nature of the dark matter. The second half of the thesis turns to direct detection experiments, with a focus on inelastic dark matter. I discuss the prospects for discovering inelastic dark matter at upcoming experiments, and present two models with inelastically scattering dark matter. One of these models posits composite dark matter and has unique phenomenology that can be studied with directional detection experiments.

Keywords: Physics
Advisor: Wacker Jay primary advisor. Thesis advisor
Dimopoulos Savas
Peskin Michael Edward
Seismic design and behavior of self-centering braced frame with controlled rocking and energy-dissipating fuses [electronic resource]

This research aims to develop a self-centering controlled rocking structural system for earthquake resistant buildings that provides significantly improved performance through reduction in structural damage, repair costs, and downtime of buildings subjected to severe earthquakes. The controlled rocking system primarily consists of a post-tensioned steel braced frame that is designed to rock upon its foundation during an earthquake, elastic post-tensioning strands to provide overturning resistance and self-centering action, and replaceable structural fuses to dissipate earthquake energy. The system can minimize earthquake-induced damage and facilitate quick and economical post-earthquake repairs through its self-centering capability and concentration of inelastic deformation in the replaceable fuses. Steel shear plates with butterfly-shaped links are employed as structural fuses, and their ductile performance was verified by quasi-static cyclic tests. A two-thirds scale shaking table test of a three-story rocking system was conducted at the E-Defense facility in Japan. Test results demonstrated that the system responds predictably to earthquake excitation with column uplifting and frame rigid-body rotation. Under input motions scaled to the level of the Maximum Considered Earthquake, the resulting roof drift ratio stayed below the implied building code limit of 3%, and the braced frame completely self-centered without any damage. Effectiveness of key design details and behavior of the major structural components are examined, and a numerical model is validated through comparison with the test results. Analytical case studies are conducted and a general design procedure is proposed, which is compatible with current building code approaches. Simple methods are formulated to predict the earthquake-induced rocking frame drifts and member force demands. The proposed methods are validated through nonlinear dynamic analyses of various case buildings subjected to a set of 22 earthquake ground motions.

Advisor: Deierlein Gregory G. (Gregory Gerard)
Billington Sarah L. (Sarah Longstreth)
Krawinkler Helmut advisor. Thesis advisor
Selective growth of type II methanotrophic bacteria in a biological fluidized bed reactor [electronic resource]

Type II methanotrophic bacteria are superior to Type I methanotrophs in accumulating polyhydroxybutyrate (PHB), a biodegradable alternative to polypropylene and other petro-chemical plastics, under nutrient limiting conditions. We evaluated the growth of Type I and Type II methanotrophs in a 15.2-liter bench-scale fluidized bed reactor (FBR) over a 270-day period. The aim was to identify operational characteristics and selection pressures that would favor Type II over Type I methanotrophs. The results indicate that Type II methanotrophs can be grown in an FBR under the appropriate conditions and that such a method may be a viable means of producing large quantities of biomass for PHB production.

Advisor: Criddle Craig advisor. Thesis advisor
Self extension into robots [electronic resource] : an examination of variables that promote overlap in the concepts of self and robot

Current research on the psychological aspects of human-robot interaction tends to focus on social encounters between humans and autonomous robots. However, many robots today are controlled by human operators. Numerous features of robot teleoperation are predictors of self extension, whereby an object comes to represent and maintain the self. Understanding the causes of self extension into robots is increasingly important, as some tasks benefit from minimizing self extension, and others from maximizing self extension. This dissertation presents an evaluation of five variables predicated to affect self extension. Study 1 examined the effects of robot form and operator robot-building experience on self extension in a 2 (robot form: humanoid vs. car) x 2 (assembler: self vs. other) between-participants experiment design (N = 56). Significant main effects demonstrated that anthropomorphic form inhibits self extension, while functional form promotes self extension and elicits positive evaluations of robot personality. Results also revealed that an operator's experience interacting with a robot before controlling it can affect self extension, as participants who operated a robot they assembled demonstrated greater self extension and more positive affect than participants who operated an identical but different robot than the one they assembled. Study 2 examined the effects of robot autonomy, mediation, and artificiality on self extension in a 2(autonomy: autonomous v. teleoperated) x 2(mediation: direct view v. mediated view) x 2(artificiality: artificial v. actual) between-participants design (N=96). Results indicated that autonomy and actuality promote self extension and positive evaluations of robots. Mediation had little direct effect on participants, suggesting that artificiality has a more powerful impact on attitudes and self extension. A number of significant interactions are presented, and theoretical and design implications are discussed.

Keywords: Communication
Advisor: Nass Clifford Ivar primary advisor. Thesis advisor
Bailenson Jeremy advisor. Thesis advisor
Hinds Pamela advisor. Thesis advisor
Reeves Byron
The self-protective function of the model minority myth for white Americans [electronic resource]

I investigated the hypothesis that endorsing the model minority stereotype--the belief that Asian Americans are intelligent, hard-working, and successful--increases Whites Americans' self-esteem. I argue that this occurs because Whites' self-esteem is threatened by the possibility that they do not deserve their position in society. The model minority stereotype provides evidence for Whites that minority groups can succeeded based on merit, bolstering the belief that society is fair and Whites deserve what they have. In four studies, I demonstrate the link between the model minority stereotype and self-esteem as well as for the idea that the model minority stereotype impacts self-esteem because of Whites' concerns over system legitimacy.

Advisor: Lowery Brian
Flynn Francis J. advisor. Thesis advisor
Mullen Elizabeth advisor. Thesis advisor
The self-protective function of the model minority myth for white Americans [electronic resource]

I investigated the hypothesis that endorsing the model minority stereotype—the belief that Asian Americans are intelligent, hard-working, and successful--increases Whites Americans' self-esteem. I argue that this occurs because Whites' self-esteem is threatened by the possibility that they do not deserve their position in society. The model minority stereotype provides evidence for Whites that minority groups can succeeded based on merit, bolstering the belief that society is fair and Whites deserve what they have. In four studies, I demonstrate the link between the model minority stereotype and self-esteem as well as for the idea that the model minority stereotype impacts self-esteem because of Whites' concerns over system legitimacy.

Keywords: Business.
Advisor: Lowery Brian
Flynn Francis J. advisor. Thesis advisor
Mullen Elizabeth advisor. Thesis advisor