VictorJuiz/thesis huggingface dataset:
Manganese-limitation and TCA cycle regulation of replication via the Sda checkpoint pathway [electronic resource]

Cells of Bacillus subtilis monitor the status of the chromosome to coordinate the initiation of sporulation with DNA replication and repair. When DNA replication is perturbed, transcription of the gene encoding the replication checkpoint protein -- Sda -- is induced, inhibiting sporulation-specific gene expression. Although the regulation of sda by replication stress has previously been studied using transient and chronic blocks to DNA replication factors as well as DNA damaging agents, other kinds of environmental conditions or changes in metabolism might also perturb DNA replication and thus inhibit sporulation. We performed a genetic screen to look for mutations that activate the sda checkpoint and found that many mutations in central metabolism caused a replication stress that activated Sda expression. We have been characterizing two examples in which the Sda checkpoint is active. In the first example, cells lacking the TCA cycle enzyme citB, encoding aconitase, are defective for initiation of sporulation. In the second example, cells grown into stationary phase in the nutrient rich medium LB do not sporulate unless supplemented with additional manganese. As B. subtilis cells enter into stationary phase in the absence of aconitase or when manganese levels are low, the Sda checkpoint prevents cells from initiating sporulation. Since the Sda checkpoint inhibits the initiation of sporulation when the cells are experiencing problems with DNA replication, these data suggest that Sda prevents cells from sporulating when manganese is limited or in aconitase deficient cells because they are encountering difficulties replicating their DNA and hint that the range of situations under which cells are experiencing such stresses is broader than initially anticipated.

Keywords: Biology.
Advisor: Burkholder William
Bergmann Dominique advisor. Thesis advisor
Grossman Arthur (Arthur R.) advisor. Thesis advisor
Markov state models for protein and RNA folding [electronic resource]

Understanding the molecular bases of human health could greatly augment our ability to prevent and treat diseases. For example, a deeper understanding of protein folding would serve as a reference point for understanding, preventing, and reversing protein misfolding in diseases like Alzheimer's. Unfortunately, the small size and tremendous flexibility of proteins and other biomolecules make it difficult to simultaneously monitor their thermodynamics and kinetics with sufficient chemical detail. Atomistic Molecular Dynamics (MD) simulations can provide a solution to this problem in some cases; however, they are often too short to capture biologically relevant timescales with sufficient statistical accuracy. We have developed a number of methods to address these limitations. In particular, our work on Markov State Models (MSMs) now makes it possible to map out the conformational space of biomolecules by combining many short simulations into a single statistical model. Here we describe our use of MSMs to better understand protein and RNA folding. We chose to focus on these folding problems because of their relevance to misfolding diseases and the fact that any method capable of describing such drastic conformational changes should also be applicable to less dramatic but equally important structural rearrangements like allostery. One of the key insights from our folding simulations is that protein native states are kinetic hubs. That is, the unfolded ensemble is not one rapidly mixing set of conformations. Instead, there are many non-native states that can each interconvert more rapidly with the native state than with one another. In addition to these general observations, we also demonstrate how MSMs can be used to make predictions about the structural and kinetic properties of specific systems. Finally, we explain how MSMs and other enhanced sampling algorithms can be used to drive efficient sampling.

Keywords: Biophysics.
Advisor: Pande Vijay primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Herschlag Daniel advisor. Thesis advisor
Matching and unifying records in a distributed system [electronic resource]

Entity resolution (ER) is the process of identifying records in a database that refer to the same real world entity. We consider various aspects of the entity resolution problem: 1) We present multiple methods for efficiently distributing the ER workload across multiple processors and provide guidelines on when to use each method. 2) We explore the use of blocking on multiple criteria at once to reduce the runtime of processing, while minimizing a loss of accuracy. We propose an efficient technique for performing multiple blocking when the full record set is too large to fit in memory at once and must therefore be stored on disk. 3) We present new locality sensitive hashing schemes based on minhash for new data types, including maps, sets with weighted values, and composite data types. These hashing schemes can be used in conjunction with blocking techniques for entity resolution. 4) We describe ER on data with confidences and provide efficient methods of handling the confidences, introducing the concepts of confidence thresholds and domination. 5) We explore how the results of ER algorithms are evaluated against a gold standard result, and propose a new, configurable distance measure that provides an intuitive method of adapting the measure to any given ER application.

Advisor: Garcia-Molina Hector primary advisor. Thesis advisor
Ullman Jeffrey D.
Widom Jennifer advisor. Thesis advisor
Matrix completion [electronic resource] : fundamental limits and efficient algorithms

Low-rank models provide low-dimensional representations capturing the important aspects of data naturally described in matrix form. Examples range from users' preferences on movies to similarities between pairs of items. Naturally, the low-rank representations serve as a tool for data compression and efficient computation. But more importantly, they are used in data analysis to learn hidden structures of the data, which is at the heart of machine learning and data mining. Applications include latent semantic analysis, factor analysis, and clustering high-dimensional data. While singular value decomposition provides an efficient way to construct a low-rank model of a fully observed data matrix, finding a low-rank model becomes challenging when we only have a partial knowledge about the matrix. When we observe a subset of the entries, we show that the singular value decomposition is sub-optimal and can be significantly improved upon. In this work, we investigate the possibility of learning a low-rank model from a partial observation of a data matrix. We develop a novel and efficient algorithm that finds a near-optimal solution. Further, we prove that the proposed algorithm achieves performance close to the fundamental limit under a number of noise scenarios. This provides a solution to many practical problems including collaborative filtering and positioning.

Keywords: Electrical Engineering
Advisor: Cover T. M.
Montanari Andrea primary advisor. Thesis advisor
Prabhakar Balaji
MBA Job Placement And Stock Market Performance

Firms that hire MBA graduates from two prominent MBA programs, consistently ranked in the top 10, exhibit abnormally high risk-adjusted stock returns in months leading up to hiring. This paper tests three factors that could explain this phenomenon: self-selection of the MBA graduate, selfselection of hiring firms, and underestimation of risk in firms undergoing expansion. The paper finds the most likely causes of the phenomenon to be the self-selection of hiring firms and the underestimation of firm risk as measured by market beta.

Keywords:  Department of Economics
Stanford Department of Economics
Abnormal Returns
Human Capital
Risk Modeling
Corporate Investment
Job Placement
Thesis
Advisor: Oyer Paul
Measurements and technology for long-term neural prosthetic systems [electronic resource]

Cortical brain-machine interfaces, or BMIs, is a relatively new field with the potential to provide many different clinical treatments, particularly for fully paralyzed patients. In these applications, multichannel electrode arrays are implanted into motor cortical areas in order to extract useful control signals. My research focuses on taking proof-of-concept academic BMI systems, and solving the engineering challenges that currently prevent them from being used in a clinical setting. These challenges include running a BMI for more than a few hours or a single day, and finding ways to minimize the size, cost, and operational complexity of the complete system. This dissertation includes an analysis of neuron stability over long timescales. I will show that the relationship between neurons in motor cortices and behavior remains stationary over time despite substantial noise, which could mitigate some concerns about long-term BMI performance. I will also discuss the development of HermesC, a wireless system for recording multichannel neural data from freely moving primates. This device dramatically reduces the size and cost of current recording technology for real-time neural prosthetic systems, and could be useful for human clinical trials. It may also enable neural prosthetic studies with animals in a less constrained setting. Combining traditional neural recordings with overnight wireless neural recordings, I will also show that there are substantial changes in neural waveforms from single neurons across days. However, the quality of neural decodes (the extraction of useful control signals) is only slightly improved by sorting individual units rather than using simple threshold crossings. This may enable long term BMI operation because multiunit neural "hash" on electrode arrays tends to persist for a long time, perhaps years, after single neuron signals have declined due to various tissue responses. In fact, other recent work from this project has demonstrated high performance neural decodes using only threshold crossings on arrays ~2.5 years after implantation.

Keywords: Electrical Engineering
Advisor: Meng Teresa H. primary advisor. Thesis advisor
Shenoy Krishna V. (Krishna Vaughn) primary advisor. Thesis advisor
Murmann Boris advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Measurements of B -> V gamma decays [electronic resource]

Observational evidence and theoretical motivation have led us to the conclusion that our current understanding of the universe is incomplete. While new physics is expected to exist above the electroweak scale, its influence can be detected by experiments that operate below this scale. The Babar experiment has recorded approximately 432 fb-1 of data at the center of mass energy of 10.58 GeV, which corresponds to the Y(4S) mass. One of the physics programs is studying radiative decays of the B meson. These decays primarily proceed through loop diagrams, and thus influences of new particles may be detectable. In this thesis, I present results of the measurements of the branching fractions, CP asymmetry, and isospin asymmetry of B -> K* gamma. Results are also presented for the measurements of the branching fractions of B -> rho(omega) gamma. Finally, a search for the decay of B -> phi gamma is given.

Keywords: Physics
Advisor: Leith David W. G. S. primary advisor. Thesis advisor
Burchat P. (Patricia) advisor. Thesis advisor
Hewett JoAnne L. advisor. Thesis advisor
Roodman Aaron J. (Aaron Jay)
Measurements of direct CP violation and constraint on the CKM triangle in B->K*pi decays [electronic resource]

We constrain the apex of the Cabibbo-Kobayashi-Maskawa unitarity triangle with measurements of B-> K*pi amplitudes from analyses of B0-> K+pi-pi0 and B0-> K_Spi+pi- decays. This constraint is consistent with the world average. The B0-> K+pi-pi0 decay mode is reconstructed from a sample of 454 million B0B0bar events collected by the BABAR detector at SLAC. We measure direct CP violation in B0-> K*+pi- decays at the level of 3 sigma when measurements from both B0-> K+pi-pi0 and B0-> K_Spi+pi- decays are combined.

Keywords: Physics
Advisor: Roodman Aaron J. (Aaron Jay)
Burchat P. (Patricia) advisor. Thesis advisor
Macfarlane David
Peskin Michael Edward
Measuring cognitive load during visual tasks by combining pupillometry and eye tracking [electronic resource]

Visualizations and visual interfaces can provide the means to analyze and communicate complex information, but such interfaces often overwhelm or confuse their users. Evaluating an interfaces's propensity to overload users requires the ability to assess cognitive load. Changes in cognitive load cause very small dilations of the pupils. In controlled settings, high-precision pupil measurements can be used to detect small differences in cognitive load at time scales shorter than one second. However, cognitive pupillometry has been generally limited to experiments using auditory stimuli and a blank visual field, because the pupils' responsiveness to changes in brightness and other visual details interferes with load-induced pupil dilations. In this dissertation, I present several improvements in methods for measuring cognitive load using pupillary dilations. First, I extend the set of eye tracking equipment validated for cognitive pupillometry, by determining the pupillometric precision of a remote-camera eye tracker and using remote camera equipment to replicate classic cognitive pupillometry experiments performed originally using head-mounted cameras. Second, I extend the applicability of cognitive pupillometry in visual tasks by developing fixation-aligned averaging methods to to handle the unpredictability of visual attention, and by demonstrating the measurement of cognitive load during visual search and map reading. I describe the methods used to accomplish these results, including experimental protocols and data processing methods to control or correct for various non-cognitive pupillary reflexes and methods for combining pupillometry with eye tracking. I present and discuss a new finding of a cognitive load advantage to visual presentation of simple arithmetic and memorization tasks.

Advisor: Hanrahan P. M. (Patrick Matthew) primary advisor. Thesis advisor
Klemmer Scott advisor. Thesis advisor
Tversky Barbara advisor. Thesis advisor
Measuring Japan's nursery quality within the UNCRC framework [electronic resource] : international standards for young children's social services and their implications for Japan

In response to mounting concerns regarding the decline in birthrate in Japan and the increasing aged population, center-based daycare has assumed an important role in Japanese society. In order to tackle the issues of low birthrate and longevity, demand for policies that encourage women to both participate in the workforce and have children is greater than ever. Since 1997, this perceived need has brought about a policy transformation in Japan's postwar system of approved nursery centers (i.e., nursery facilities that meet the national daycare quality standards), which had—until then—operated measures entirely under the control of the municipalities, as part of the child welfare policy of the Japanese government. In order to respond to the urgent need for daycare services and facilities, the government has instigated a policy of privatization throughout its nursery centers system and has relaxed many of the regulations in the field of daycare services provision. However, in the course of the privatization of public nursery centers, the government has been widely regarded as prioritizing "capacity (quantity)" concerns over "quality" concerns when constructing its policies. Because the nursery centers system has undergone legal reform and because quality concerns are on the rise, both researchers and administrative officers have come to recognize how important it is to define and measure quality nursery daycare. With this issue in mind, this study proposes an approach to assess the quality of Japan's nursery daycare against international standards, particularly from the standpoint of a state party's obligations under the 1989 United Nations Convention on the Rights of the Child (UNCRC). The following research questions are central to this study: To what extent does Japan comply with international standards on daycare quality? Are there international standards that Japan should be permitted exemptions from, and if exemptions are appropriate, what is the rationale for such exemptions? This study is the first detailed examination of Japan's nursery daycare policies under the framework of the UNCRC written in English. The introduction of a daycare quality assessment method to Japan—one that is based on international standards—serves as a useful basis both for the smooth formulation and implementation of nursery policies that ensure daycare provisions (in terms of quantity and quality) and to provide a benchmark against which reasonable judicial rulings can be made on the basis of the "the best interests of the child, " one of the core principles in the UNCRC. Furthermore, it will also help provide some insights into how stakeholders of nursery daycare in OECD countries are able to ensure that daycare quality takes children's best interests into account while also considering the historic, cultural, and social contexts of respective countries.

Keywords: Law.
Advisor: Hensler Deborah R.
Friedman Lawrence M. (Lawrence Meir)
Stacy Helen advisor. Thesis advisor
Mechanisms for delivering hydrogen from ammonia-borane via protons, hydrides, and a dative bond [electronic resource]

The hydrogen economy is a hypothetical replacement for the world's reliance on fossil fuels. Concerns over carbon dioxide and global warming have driven research into creating reliable systems to utilize hydrogen as a vehicular fuel. Because molecular hydrogen is a gas, storage at practical densities is a major problem for its utilization. One highly promising material for hydrogen storage is ammonia-borane (AB), or NH3BH3. AB has a high weight percent hydrogen (~20%) and its protic (N-H) and hydridic (B-H) hydrogens appear ripe for dehydrogenation. However, reversible release of H2 from AB requires fine control over dehydrogenation mechanisms. Using ab initio simulations, we elucidate the fundamental mechanisms involved in removing hydrogen from AB. Herein, we investigate mechanisms for the dehydrogenation of AB by homogeneous catalysis and thermolysis. We show that unexpected active catalysts and experimentally unobservable intermediates are key aspects of this chemistry. Furthermore, the effects of solvent and dynamics are vital to understanding product distributions. Finally, two-hydrogen transfer is highlighted as a fascinating chemistry involving the simultaneous transfer of protic and hydridic hydrogen.

Keywords: Chemical Engineering
Advisor: Jaramillo Thomas Francisco primary advisor. Thesis advisor
Musgrave Charles primary advisor. Thesis advisor
Waymouth Robert M. advisor. Thesis advisor
Mechanisms of deep brain stimulation revealed by optogenetic deconstruction of diseased brain circuitry [electronic resource]

Deep brain stimulation (DBS) is a powerful therapeutic option for intractable movement and affective disorders (Parkinson's disease or PD, tremor, dystonia, Tourette syndrome, chronic pain, obsessive compulsive disorder, depression, bipolar). The benefits of DBS are immediate and dramatic, manifested as instantaneous improvements in motor function in the case of PD patients. However, due to the nonspecificity of electrical stimulation, DBS has variable efficacy and can lead to serious side effects. The mechanisms behind the effects of DBS are still highly controversial and there is tremendous interest from both neuroscience and clinical communities to understand and improve DBS. We have developed a novel technology based on two microbial opsins, Channelrhodopsin (ChR2) and Halorhodopsin (NpHR), that allows to directly and specifically control the activity of distinct cell-types with high temporal precision in well defined brain regions, therefore allowing us to overcome the lack of specificity of electrical DBS. This study provides the first investigation of the role of specific cell types in ameliorating PD symptoms addressed by effective DBS treatment. The focus of the thesis was twofold: (1) to develop and optimize optogenetic technologies (molecular and hardware) for safe and effective use in behaving mammals; and (2) to employ the above developed optogenetic toolkit to deconstructing diseased brain circuitry, with focus on Parkinson's disease. The framework and technological toolbox presented here can be employed across many brain circuits to selectively control individual components and therefore systematically deconstruct intact and disordered brain processes.

Keywords: Neurosciences.
Advisor: Deisseroth Karl primary advisor. Thesis advisor
Bronte-Stewart Helen advisor. Thesis advisor
Buckmaster Paul S. advisor. Thesis advisor
Shatz Carla J. advisor. Thesis advisor
Mechanistic insights towards new reactions and materials [electronic resource]

Catalysis is the enabling science of polymer synthesis, and new catalytic mechanisms yield new materials. The developement of organocatalysts for polymer synthesis has, particularly in the last decade, spawned an impressive array of new catalysts, processes and mechanistic insights. While the focus of most recent research in organocatalysis has concentrated on enantioselective synthesis of small molecules, organocatalysis offers a number of opportunities in polymer synthesis and was among the earliest methods of catalyzing the synthesis of polyesters. The enthalpy of ring opening of cyclic esters or carbonates drives the majority of organocatalyic polymerization reactions catalyzed by a still-evolving array of organocatalysts. Organocatalysts are thought to effect polymerization of cyclic esters by several mechanisms. Some proceed via a monomer activated mechanism whereby the catalyst activates the cyclic ester towards transesterification to the polymer chain. Others operate by an alcohol activation mechanism where the alcoholic end group of the growing polymer chain is activated to induce transesterification. Some are thought to be operative by a combination of these mechanisms. The unique reactivity offered by organocatalysts has provided access to precisely controlled macromolecular architectures and well-defined (co)polymers including a wide array of functionality. The notion that rate must be sacrificed to implement organocatalysts is fading with the discovery of transesterification organocatalysts that rival in reaction rate even the most active metal-containing catalysts. Cyclopentadienyl ruthenium complexes with quinaldic acid-type ligands are robust allylation catalysts in alcoholic solvents, but they are sensitive to dissolved oxygen, requiring reactions to be conducted in an inert atmosphere. Moving from alcoholic to neat aqueous solvents decreases the rate of deallylation but allows the reaction to be conducted in air without loss of catalyst activity over the course of the reaction. These complexes are also effective for the formation of allyl ethers, allowing the synthesis of poly(2,5-dihydrofuran) from the condensation polymerization of 2-cis-butene-1,4-diol. This material was previously deemed inaccessible via traditional polycondensation catalysts.

Keywords: Chemistry
Advisor: Waymouth Robert M. primary advisor. Thesis advisor
Kool Eric T. advisor. Thesis advisor
Trost Barry M. advisor. Thesis advisor