VictorJuiz/thesis huggingface dataset:
Active Testing: Predicting and Confirming Concurrency Bugs for Concurrent and Distributed Memory Parallel Systems

Parallel and concurrent software sometimes exhibit incorrect behavior because of/nunintended interference between different threads of execution. Common classes/nof concurrency bugs include data races, deadlocks, and atomicity violations./nThese bugs are often non-deterministic and hard to find without sophisticated/ntools. We present Active Testing, a methodology to effectively find concurrency/nbugs that scales to large distributed memory parallel systems./nActive Testing combines the coverage and predictive power of program analysis/nwith the familiarity of testing. It works in two phases: in the predictive/nanalysis phase, a program is executed and monitored for potential concurrency/nbugs and in the testing phase, Active Testing re-executes the program while/ncontrolling the thread schedules in an attempt to reproduce the bug predicted in/nthe first phase./nWe have implemented Active Testing for multi-threaded Java programs in the/nCalFuzzer framework. We have also developed UPC-Thrille, an Active Testing framework/nfor Unified Parallel C (UPC) programs written in the Single Program Multiple/nData (SPMD) programming model combined with the Partitioned Global Address Space/n(PGAS) memory model. We explain in detail the design decisions and optimizations/nthat were necessary to scale Active Testing to thousands of cores. We present/nextensions to UPC-Thrille that support hybrid memory models as well./nWe evaluate the effectiveness of Active Testing by running our tools on several/nJava and UPC benchmarks, showing that it can predict and confirm real/nconcurrency bugs with low overhead. We demonstrate the scalability of Active/nTesting by running benchmarks with UPC-Thrille on large clusters with thousands/nof cores.

Advisor: Sen, Koushik
Impulse Control and Optimal Stopping

This thesis analyzes a class of impulse control problems for multi-dimensional jump diffusions in a finite time horizon. Following the basic mathematical setup from Stroock and Varadhan, this paper first establishes rigorously an appropriate form of the Dynamic Programming Principle (DPP). It then shows that the value function is a viscosity solution for the associated Hamilton-Jacobi-Belleman (HJB) equation involving integro-differential operators. Finally, it proves the regularity of the viscosity solution for HJB with first-order jump diffusions. Furthermore, it proposes a new regularity framework for second-order jump diffusions in the optimal stopping problem.

Advisor: Evans, Lawrence C
Guo, Xin
Molecular Level Investigations and Mathematical Modeling of Cellulase-catalyzed Hydrolysis of Cellulose

Cellulose-to-glucose conversion costs comprise one of the largest expenses in the production of lignocellulosic biofuels, a renewable alternative to traditional fossil fuels. Efforts to reduce these costs by improving the activity of cellulase enzymes, which act within multi-enzyme mixtures to catalyze the hydrolysis of cellulose, have been hindered by uncertainty surrounding the mechanistic origins of rate-limiting phenomena and by an incomplete understanding of complementary enzyme function. In this work, we employed mechanistic models of enzymatic action alongside experimental studies of enzyme-enzyme synergy to investigate kinetic impediments encountered by cellulase enzymes as they catalyze the hydrolysis of cellulose. Using several mechanistic models of enzymatic hydrolysis, we show how hydrolysis kinetics and optimal cellulolytic mixture compositions are dependent on the nature of the cellulosic substrate (i.e., particle shape, surface area, degree of polymerization) and the conditions under which it is depolymerized (i.e., hydrolysis and fermentation process conditions). By developing a method to estimate catalysis-specific products within multi-enzyme reactions, we show that cellobiohydrolase enzymes, which catalyze processive hydrolysis from cellulose chain ends, encounter rate limitations that result, not from intrinsic kinetics, but from slow rates of chain complexation and from morphological obstacles to processivity. And using photoactivated localization microscopy (PALM) to produce pointillistic maps of carbohydrate-binding modules (CBMs) bound to cotton, we develop an order parameter to quantify the different spatial arrangements of adsorbed CBMs and use that order parameter to explain synergy between cellulase enzymes designed to target different surface structures. The results of this work reveal strategies for using morphological targeting to enhance enzyme-enzyme cooperativity within cellulolytic mixtures, thereby improving their overall activity and lowering the cost of cellulose hydrolysis.

Advisor: Blanch, Harvey W
Clark, Douglas S
Induction of lignocellulose degrading enzymes in Neurospora crassa by cellodextrins

Neurospora crassa colonizes burnt grasslands in the wild and metabolizes both cellulose and hemicellulose from plant cell walls. When switched from a favored carbon source such as sucrose to cellulose, N. crassa dramatically upregulates expression and secretion of a wide variety of genes encoding lignocellulolytic enzymes. However, the means by which N. crassa and other filamentous fungi sense the presence of cellulose in the environment remains unclear. Here, I show that a N. crassa mutant carrying deletions of two genes encoding predicted extracellular β-glucosidase enzymes and one intracellular β-glucosidase enzyme (d3βG) lacks β‐glucosidase activity, but efficiently induces cellulase gene expression and cellulolytic activity in the presence of cellobiose as the sole carbon source. These data indicate that cellobiose, or a modified version of cellobiose, functions as an inducer of lignocellulolytic gene expression and activity in N. crassa. In addition, I have identified two cellodextrin transporters involved in sensing cellulose. A N. crassa mutant carrying deletions for both transporters is unable to induce cellulase gene expression in response to crystalline cellulose. Furthermore, a mutant lacking β- glucosidase enzymes and transporters (d3βGdT) does not induce cellulase gene expression in response to cellobiose.

Advisor: Cate, Jamie HD
Glass, N. Louise
LÃª Thị Huệ: Writing between Exilic Homelessness and Situated Nomadism

Over the past three decades, more than 300 Vietnamese American authors have produced at least 550 novels, 200 collections of short stories and poetry in addition to over 100 volumes of informal reflective and formal commentary essays in their native language. Nonetheless, a majority of this literature remains in utter obscurity, both within and beyond the borders of Vietnamese America. My dissertation focuses on the body of work of the feminist writer LÃª Thị Huệ whose expansive breadth and constantly evolving aesthetics render her an appropriate representative and a singular phenomenon among her contemporaries in the Vietnamese diaspora. I propose the double concept exilic homelessness and situated nomadism as the theoretical framework to read LÃª's body of work and as a means through which to understand LÃª's ethics and aesthetics. I demonstrate that, if multiple historical displacements underlie LÃª's experience as a refugee, woman, and writer, exilic homelessness and situated nomadism reveal the vicissitudes of LÃª's subjectivity as an exile, feminist, and Asian American cyborg and cultural producer. Combining the ethico-critical force of poststructuralist theories (including nomadology, cyborg theory, and ecriture feminine) and politico-aesthetic strength of critical theories (including women-of-color feminism and critical denationalization), I demonstrate how LÃª's work offers a meaningful opportunity to re-imagine Asian American subjectivity and politics of resistance in the contemporary diasporic moment. Ultimately I reveal how reading LÃª's work requires a critical paradigm that incorporates both indigenizing and diasporic modes of Asian American subjectivity and that, not only is such paradigm theoretically and politically productive, it is also desirable.

Advisor: WONG, SAU-LING C
Cobalt-Mediated Vinylic C-H Functionalization of Alkenes

The reaction of cobalt dinitrosyl complexes with alkenes to form cobalt dinitrosoalkane complexes is used to effect the C-H functionalization of alkenes. Deprotonation of cobalt dinitrosoalkane complexes, followed by reaction with neutral electrophiles, yields functionalized cobalt complexes. Thermolysis of such complexes with the parent alkene allows a migration of the cobalt dinitrosyl moiety to the parent alkene, releasing the organic product of C-H functionalization. Progress is presented towards rendering this sequence of reactions catalytic in cobalt. Additionally, the use of reagents derived from Cinchona alkaloids allows for this functionalization to be rendered enantioselective. The enantioselective chemistry has been utilized in the synthesis of chiral diene ligands for rhodium-catalyzed conjugate addition reactions. The use of hydridotris(pyrazolyl)borates, in place of cyclopentadienyls, as spectator ligands for cobalt dinitrosoalkane complexes, is also explored, and the electronic structure of a cobalt mononitrosyl complex studied.

Advisor: Bergman, Robert G.
Toste, Dean
Dancing Africa, Making Diaspora

Dancing Africa, Making Diaspora concerns the industry of West African dance in the United States. Considering the relationship between dance, diaspora, and belonging, Dancing Africa works to reveal the power of dance in shaping participants' individual and collective identities through the premise of African connectedness. In other words, this dissertation considers West African dance as a meaning-making practice. Through the study of multiple West African dance and drum contexts - a Broadway show, dance classes in one Californian community center, a dance "homecoming" workshop in Guinea - it interrogates the ways everyday people (those typically excluded by the field's privileging of textual archives) conceptualize, embody, and make use of the African diaspora. Ultimately, this dissertation shows how dance links the symbolic and physical dimensions of diaspora: the imaginative work that fosters diasporic connectedness and the physical movement through and across space that has, and continues to, yield variegated African diasporic communities./nThis dissertation examines U.S. evocations of Africanness through West African dance in an effort to raise and answer questions about the performative capabilities of West African dance and to investigate the processes by which African diasporic communities are shaped because of and through this dance form. Based largely on ethnographic observations and interviews with West African dance participants, Dancing Africa, Making Diaspora shows how West African dance influences how participants understand what the African diaspora is, and how they see their own raced and gendered bodies in relation to it. This project reveals the bearing that West African dance has on participants' lives by asking the following questions: In what ways did diaspora play a role in the career of West African dance as a formal practice in the US? Why do people take part in West African dance and what "work" does it do for them? How does gender and nationality affect one's positioning in these various communities? And finally, how has the commodification of the form impacted meanings of diaspora, blackness, and Africanness? Dancing Africa reveals the operations through which this dance economy both widens the circle of African diasporic "we" and continues to police its ever-shifting boundaries of belonging.

Advisor: Catanese, Brandi
Molecular Mechanisms of Anthrax Toxin Assembly and Transport

Because proteins carry out their cellular functions in specific locations, protein transport represents a crucial step in the central dogma of biochemistry. Transport across a membrane barrier requires energy; therefore, nature has provided a class of molecular machines known as translocases that catalyze protein translocation. Often, these machines contain channels that are too narrow to transport a folded protein; thus, substrate unfolding adds another layer of complexity to the poorly understood transport mechanism. The anthrax toxin system represents a useful model for elucidating the mechanisms of translocation-coupled protein unfolding, both in terms of structure and function./nIn order to understand the mechanism by which an unfolding machine interacts with its substrate, the X-ray structure of an anthrax protective antigen (PA) oligomer prechannel was solved in complex with the amino-terminal PA-binding domain of the substrate lethal factor (LFN). The structure revealed how PA interacts with unfolded polypeptide via a hydrophobic cleft we call the &alpha clamp. Working with my colleague, Katie Thoren, we show how the &alpha clamp is critical for toxin assembly, substrate binding, unfolding, and translocation through a nonspecific binding mechanism./nThe recent discovery that PA can form two oligomeric states exemplifies the complexity of multimeric protein nanomachine assembly. In order to better understand the molecular mechanism of heterogenous assembly, a series of PA constructs with varying length crosslinks was produced, their structures were solved to high resolution, and their assembly products were analyzed by electron microscopy. The flexibility of PA's receptor-binding domain (D4) relative to the main body of the protein provides a mechanism for controlling oligomeric stoichiometry, whereby D4 can adopt a pro-heptamer or pro-octamer conformation./nFinally, an overall model for protein translocation is presented, based on data discussed herein and other recent studies involving anthrax toxin transport.

Advisor: Krantz, Bryan A
Understanding the Mechanism of Stimulatory NK-cell Ligand Expression

Natural killer (NK) cells are lymphocytes that play a major role in the elimination of virally-infected cells and tumor cells. NK cells recognize and target abnormal cells through activation of stimulatory receptors such as NKG2D. NKG2D ligands are self-proteins, which are absent or expressed at low levels on healthy cells but are induced upon cellular stress, transformation, or viral infection. The exact molecular mechanisms driving expression of these ligands remain poorly understood./nUsing mouse cytomegalovirus (MCMV) as a model, the present dissertation describes three distinct factors that contribute to the induction of the RAE-1 family of NKG2D ligands during MCMV infection. First, we show that activation of the phosphatidylinositol-3-kinase (PI3K) pathway, which is often dysregulated during infection and tumorigenesis, is required for RAE-1 expression in MCMV-infected cells as well as in transformed cell lines. Second, genetic manipulation of the MCMV genome has revealed a novel viral protein encoded by the m18 gene that is both necessary and sufficient to induce RAE-1 expression. Finally, studies using mouse strains that are deficient in various innate signaling molecules demonstrate that innate signaling through the MyD88 adaptor protein and the IRF3 transcription factor are involved in RAE-1 induction./nCollectively, we have shown that RAE-1 expression during MCMV infection involves a combination of signals to ensure that its expression is limited to truly diseased cells.

Advisor: Coscoy, Laurent
Matrix Factorization and Matrix Concentration

Motivated by the constrained factorization problems of sparse principal components analysis (PCA) for gene expression modeling, low-rank matrix completion for recommender systems, and robust matrix factorization for video surveillance, this dissertation explores the modeling, methodology, and theory of matrix factorization./nWe begin by exposing the theoretical and empirical shortcomings of standard deflation techniques for sparse PCA and developing alternative methodology more suitable for deflation with sparse "pseudo-eigenvectors." We then explicitly reformulate the sparse PCA optimization problem and derive a generalized deflation procedure that typically outperforms more standard techniques on real-world datasets./nWe next develop a fully Bayesian matrix completion framework for integrating the complementary approaches of discrete mixed membership modeling and continuous matrix factorization. We introduce two Mixed Membership Matrix Factorization (M3F) models, develop highly parallelizable Gibbs sampling inference procedures, and find that M3F is both more parsimonious and more accurate than state-of-the-art baselines on real-world collaborative filtering datasets./nOur third contribution is Divide-Factor-Combine (DFC), a parallel divide-and-conquer framework for boosting the scalability of a matrix completion or robust matrix factorization algorithm while retaining its theoretical guarantees. Our experiments demonstrate the near-linear to super-linear speed-ups attainable with this approach, and our analysis shows that DFC enjoys high-probability recovery guarantees comparable to those of its base algorithm./nFinally, inspired by the analyses of matrix completion and randomized factorization procedures, we show how Stein's method of exchangeable pairs can be used to derive concentration inequalities for matrix-valued random elements. As an immediate consequence, we obtain analogues of classical moment inequalities and exponential tail inequalities for independent and dependent sums of random matrices. We moreover derive comparable concentration inequalities for self-bounding matrix functions of dependent random elements.

Advisor: Jordan, Michael I
The aggregate effect of turns on urban traffic networks

This dissertation furthers the understanding of macroscopic traffic behavior on urban networks. In particular, it focuses on the aggregate effect of turning maneuvers in networks with multiple routes. The presence of turning between different routes on a network is found to have two effects: 1) it causes chaotic and inefficient behavior, especially when the network is congested; and, 2) it may reduce maximum vehicle flows across the network. Fortunately, this work finds that designing networks that are redundant (i.e., have multiple unique routes between all origin-destination pairs), helping drivers avoid locally congested regions and limiting the rate at which vehicles are allowed to enter the network can help mitigate the first effect, and this allows the network to operate more efficiently. It is also found that the second effect may not always be harmful---lower network flows do not necessarily result in decreased network efficiency if the lower flows are accompanied by more direct routing between origins and destinations. In fact, two-way networks, which accommodate conflicting left-turns and result in lower maximum vehicle flows than one-way networks, are found to serve trips at a higher rate because drivers travel shorter distances on average. Thus, in many cities, maximum network efficiency can be improved by converting one-way streets to two-way operation.

Advisor: Daganzo, Carlos F
Automatic Calibration of Freeway Models with Model-Based Fault Detection

This dissertation presents system identification, fault detection and fault handling methodologies for automatically building calibrated models of freeway traffic flow. Using these methodologies, data driven algorithms were developed as part of a larger scheme of a suite of software tools designed to provide traffic engineers with a simulation platform where various traffic planning strategies can be analyzed. The algorithms that are presented work with loop detector data that are gathered from California freeways./nThe system identification deploys a constrained linear regression analysis that estimates the so-called fundamental diagram relationship between flow and density at the location of a given sensor. A triangular fundamental diagram is assumed that establishes a bi-modally linear relationship between flow and density, the two modes being free flow and congestion. An approximate quantile regression method is used for the estimation of the congested regime due to this mode's high susceptibility to various external factors./nThe fault detection algorithm has been developed to facilitate the automatic model building procedure. The macroscopic cell transmission model, which is the model assumed in this study, requires consistent observations along the modeled freeway section for an accurate calibration to be possible. When detectors are down or missing, the model has to be modified to a less accurate representation to conform with a configuration where a sensor is assigned to each cell of the model. In addition, on most California freeways the ramp flows in and out of the mainline are not observed. Since the estimation of these unknown inputs to the system also hinge on healthy mainline data, the identification of faulty mainline sensors becomes crucial to the automatic model building process. The model-based fault detection algorithm presented herein analyzes the parity between simulated and measured state, along with estimated unknown input profiles. Subsequently, it makes use of a look-up table logic and a threshold scheme to flag erroneous detectors along the freeway mainline./nFinally, the fault handling algorithm that accompanies the fault detection aims to revert the model to its original configuration after the aforementioned modifications are made to the model due to missing or bad sensors. Using a relaxed model-constrained linear optimization, this algorithm seeks to fill in the gaps in the observations along the freeway that are a result of poor detection. This method provides a reconstruction of the unobserved state that conforms with the rest of the measurements and does not produce a state estimate in a control theoretical sense.

Advisor: Horowitz, Roberto
Photodissociaion Dynamics of Neutral Free Radicals

Photofragment translational spectroscopy was used to study the photodissociation dynamics of the phenyl and tert-butyl radicals. These radicals were produced in a collisionless environment from the flash pyrolysis of the appropriate precursor, nitrosobenzene for phenyl and azo-tert-butane for the tert-butyl radical. The photodissociation dynamics of the phenyl radical (C6H5) were investigated at 248 and 193 nm. At 248 nm, the only dissociation products observed were from hydrogen atom loss, attributed primarily to H + o-C6H4 (ortho-benzyne). The observed translational energy distribution was consistent with statistical decay on the ground state surface. At 193 nm, dissociation to H + C6H4 and C4H3 + C2H2 was observed. The C6H4 fragment can be either o-C6H4 or l-C6H4 resulting from opening of the phenyl ring. The C4H3 + C2H2 products dominate over the two H loss channels. Attempts to reproduce the observed branching ratio by assuming ground state dynamics were unsuccessful. This discord, between the experimentally observed branching ratio and the theoretically predicted branching ratio led us to reinvestigate the dissociation dynamics of the phenyl radical at 193 nm, while producing the radical under different source conditions./nThe photodissociation dynamics of the tert-butyl radical (t-C4H9) were investigated at 248 nm. Two distinct channels of approximately equal importance were identified: dissociation to H + 2-methylpropene (C4H8), and CH3 + dimethylcarbene (C3H6). Neither the translational energy distributions that describe these two channels nor the product branching ratio are consistent with statistical dissociation on the ground state, and instead favor a mechanism taking place on excited state surfaces. The studies presented in this dissertation show that although hydrogen atom loss is sometimes expected to be the only major dissociation pathway in the photodissociation of hydrocarbon radicals this is not always a justified assumption.

Advisor: Neumark, Daniel M