VictorJuiz/thesis huggingface dataset:
Quality control at the ribosome [electronic resource] : insights into the principles of cotranslational ubiquitination

One of the most critical times in the life of a protein is during its biogenesis at the ribosome. A nascent polypeptide cannot achieve its final fold while still bound to the ribosome, and is at risk of being accessed by the cellular quality control machinery. However, the extent to which cotranslational ubiquitination and degradation occur remains under debate. Conflicting reports exist, ranging from 40% of nascent chains being subject to cotranslational degradation to claims that nascent polypeptides are, on the contrary, protected from degradation. Here, we developed a direct and quantitative method to determine the extent of cotranslational ubiquitination using ribosome isolation coupled to ubiquitin-affinity purification. We find that cotranslational ubiquitination occurs at low levels, and that at least a fraction of ubiquitinated nascent chains is targeted to the proteasome for degradation. We determined which proteins are susceptible to cotranslational ubiquitination and find that intrinsic sequence features determine the cotranslational ubiquitination of a specific subset of proteins. These proteins are more aggregation-prone, highly expressed and longer than 400 amino acids. Short proteins seem to be protected from cotranslational ubiquitination. One such mechanism could be the cotranslational formation of folded structures, which lead us to disrupt cotranslational folding by deleting chaperones or through drugs such as azetidine-2-carboxylic acid (AZC). Both lead to an increase of cotranslational ubiquitination as observed by pulse-labeling as well as microarray analysis. Ribosome-associated chaperones and cotranslational folding seem to have evolved to prevent a high degree of nascent chain degradation/ubiquitination. Similarly to ribosome-associated chaperones, the ubiquitin-proteasome-system may also be able to access nascent protein chains, but rather target them for degradation. We therefore determined which parts of the UPS mediate cotranslational ubiquitination. A clear E2-E3 relationship could however not be established, possibly due to redundancy in the cellular ubiquitin ligase network. Finally, we find that disruption of mRNA quality control components also leads to enhanced ubiquitination of nascent chains, suggesting that cotranslational quality control serves to avoid the production of erroneous proteins and protect the cell from resulting toxicity.

Keywords: Biology.
Advisor: Frydman Judith primary advisor. Thesis advisor
Cyert Martha S.
Nelson W. J. (W. James) advisor. Thesis advisor
Quantum imaging of dirac materials [electronic resource]

The realization of massless Dirac fermions in condensed matter systems has led to new opportunities for exploring exotic physics stemming from relativistic quantum mechanics and quantum field theory. "Dirac materials" which embed Dirac fermions, such as graphene and topological insulators, are now distinguished as a new class of materials and have focused large research efforts. Here we use Scanning Tunneling Microscopy/Spectroscopy (STM/STS) to probe the electronic properties of these materials with sub-atomic resolution in real space, along with spectral and momentum-space measurements. We studied two variants of these categories: molecular graphene and antimony. Antimony is a fundamental parent matrix of various topological insulator compounds, which realizes topological surface states that are comprised of Dirac fermions. Molecular graphene is a new Dirac material we built, which is an artificial graphene-like structure assembled by arranging molecules to create a honeycomb lattice of electrons drawn from normal two-dimensional surface states. These experiments provide an unprecedented level of control over Dirac fermions and allow experimental access to a set of phenomena that has previously been considered only theoretically.

Keywords: Applied Physics
Advisor: Beasley Malcolm primary advisor. Thesis advisor
Manoharan Harindran C. (Harindran Chelvasekaran)
Goldhaber-Gordon David
A race forged by hatred [electronic resource] : black identity, racial science, and culture, 1896-1916

This dissertation explores the creation of Afro-American social identity during the Progressive Era by examining black intellectuals use of racial science to define a new racial identity for black Americans. Because historians have been locked into an analytical structure favoring the voices of Booker T. Washington and W. E. B. Du Bois over those of other black leaders in the Progressive Era, we have missed the bulk of black intellectuals' analysis of race during that time. By resurrecting the contributions of black leaders other than Washington and Du Bois, we can get a richer understanding of a time of dramatic change in American race relations. During the Progressive Era, black intellectuals Pauline E. Hopkins, Kelly Miller, Jr., Charles V. Roman, William Hannibal Thomas, Monroe Nathan Work, and R. R. Wright, Jr., used racial science to reassess the nature of race and Afro-Americans' future in America. By engaging in scientific debates, and challenging the validity of doctrines used to justify excluding black Americans from social and civil life, they came to the strikingly modern conclusion that race was nothing more than a social construct. American races could not be distinguished based on biology or physical appearance. Black intellectuals understanding of their racial destiny changed during the first decades of the twentieth century. At first, many Progressive-Era black thinkers expected that the freedmen and their descendants would assimilate into the white race just as Frederick Douglass and other Reconstruction black leaders had desired. They believed that by educating Americans as to the scientifically correct, social nature of race they could cause white race prejudice to abate, thereby permitting black citizens to join with white Americans in a unitary national culture. But, by 1916 they had concluded that white race prejudice would not diminish in the short run. They abandoned hopes for assimilation into a single national culture and began to imbue their race with a distinct set of cultural ideals that would empower Afro-Americans in their long-term struggle to obtain its human rights in America.

Keywords: History.
Advisor: Campbell James T.
White Richard
Winterer Caroline
Rapid vascular magnetic resonance imaging [electronic resource]

Visualization of the blood vessel anatomy and the measurement of information related to blood flow play a crucial role in the diagnosis of cardiovascular diseases. Magnetic resonance imaging (MRI) is an especially attractive modality for this purpose because of its ability to provide morphological as well as flow-related information in one exam. Despite technological advances, vascular imaging with MRI is still limited by long scan times, which lead to image artifacts, patient discomfort, and high costs. Novel vascular MRI techniques are proposed in this dissertation that greatly reduce scan times compared to conventional methods (scan times on the order of seconds vs. minutes), while achieving similar image information content. First, an ungated Fourier velocity encoding (FVE) method is introduced for quantitating blood velocities in a few seconds. Accurate quantitation of the peak blood flow velocity can play an important role in assessing the severity of cardiovascular diseases. Next, a non-contrast-enhanced (NCE) magnetic resonance angiography (MRA) technique that provides high-contrast renal angiograms in as short as one heartbeat is developed for imaging renal artery stenosis. NCE MRA generates vessel contrast without the aid of external agents, making it the more comfortable, safer and lower cost alternative to traditional contrast-enhanced MRA. Lastly, an abdominal NCE MRA method for imaging the abdominopelvic arteries within a breath-hold is presented. Extending arterial vessel visualization from the renal region to the entire abdominal region enables the diagnosis of peripheral arterial disease in addition to renal artery stenosis.

Keywords: Electrical Engineering
Advisor: Nishimura Dwight George primary advisor. Thesis advisor
Pauly John (John M.) advisor. Thesis advisor
Vasanawala Shreyas advisor. Thesis advisor
Reachability-based control for human and autonomous agents in adversarial games [electronic resource]

Solutions to multi-agent adversarial games are useful in many applications where control actions must be taken in the presence of opposing agents, moving obstacles, or other external disturbances. These applications range from collision avoidance for autonomous cars and air traffic control to team coordination in the military and police. In addition to controlling robotic or autonomous agents, solutions to these games can play an essential role in providing guidance to humans, who may be participating either in supervisory roles or as agents themselves. The critical challenges to obtaining such solutions are the need to robustly account for adversarial actions in scenarios with many agents, and to do so in a computationally tractable fashion. In addition, to be helpful to humans the solutions must be presented so that they fit within the decision-making framework of the humans. This thesis develops solution methods for two types of related multi-agent adversarial games: reach-avoid games, where an attacking agent attempts to reach a target while avoiding other, defending agents, and pursuit-evasion games, where an evading agent attempts to avoid capture by pursuing agents. First, a Hamilton-Jacobi-Isaacs reachability formulation is used to compute guaranteed, optimal solutions to a reach-avoid game involving a single attacker and defender. Then an open-loop reachability formulation is introduced to allow solutions to be found in real time for games involving multiple agents on a side. An efficient method for computing open-loop safe-reachable sets is introduced and used to compute solutions for an attacking agent in reach-avoid games with multiple defenders, and for pursuing agents in pursuit-evasion games involving a single evader and multiple pursuers. These reachability-based game solutions are used to develop intuitive, automated tools to guide human agents in adversarial games as well as to control robotic assets like unmanned aerial vehicles (UAVs). The tools are validated using a novel testbed incorporating smartphones and UAVs in a system with human agents. These experiments demonstrate the use of the tools in realistic scenarios involving varied terrain and noisy communications. In these experiments, the human agents not only directly utilize the computed solutions, but are also able to modify the plans using the associated reachability information when communications failure and other factors render the assumptions made by the automation invalid.

Keywords: Aeronautics and Astronautics
Advisor: Tomlin Claire J.
Klein Daniel
Rock Stephen M. advisor. Thesis advisor
Real-time studies of the mechanisms of nanocrystal structural phase changes [electronic resource]

Nanocrystals provide ideal systems with which to study structural phase changes. By making use of the ultra-short pulsed nature of synchrotrons and free-electron lasers, one may visualize with atomic-resolution and in real time how nanosized systems rearrange and potentially resolve the transition state itself. Such information could lead to new material design opportunities in which the phase-change behavior is optimal for a given application. Here are presented ultrafast studies of both temperature and pressure-driven phase changes in nanocrystalline materials, utilizing x-ray diffraction and x-ray spectroscopy to monitor the atomic rearrangement on femtosecond time-scales. For a thermally-driven phase change, the onset of superionicity is considered, a unique superposition of liquid-like cationic conductivity within a solid-phase anionic lattice. Using near-edge spectroscopy, the superionic structural transformation is observed to occur faster than twenty picoseconds in laser-excited copper (I) sulfide nanocrystals, and it is shown that it is the ionic hopping time which determines this time-scale. For pressure-induced studies, the dynamics of the well-known change of cadmium selenide nanocrystals from a wurtzite to rock-salt unit cell under increasing pressure are investigated. Laser-induced shock compression is used to initiate the phase transformation and hard x-ray scattering acts as as the probe. Finally, the efforts to introduce time-resolved capabilities at SSRL are presented. In particular, measurements of the x-ray pulse duration under different synchrotron operating conditions show the ability to perform experiments with single-picosecond resolution at SSRL. These single-photon sensitive measurements allowed the optimization of the pulse compression for future x-ray experiments at SSRL.

Keywords: Materials Science and Engineering
Advisor: Lindenberg Aaron Michael primary advisor. Thesis advisor
Reis David A.
Toney Michael Folsom advisor. Thesis advisor
Reasoning over combinatorial spaces for multi-object inference [electronic resource]

In this thesis, we study a set of tools and methodology for reasoning over combinatorial spaces, i.e., permutations and homogeneous spaces, with applications to multi-object tracking. Recently, the Fourier machinery for representing distributions over permutations has been introduced. Due to the uncertainty principle, the Fourier representation suffers from high complexity for representing sparse distributions. We present an algorithm that can adaptively decompose the large tracking problem into independent components under the Fourier representation framework. Such an adaptive algorithm helps greatly to improve the scalability of the non-adaptive Fourier approach. Another line of research of representing distributions over permutations uses the information form representation for the problem. We identify an interesting duality relationship between Fourier representations and the information form representations. The pros and cons of the two representations compensate for each other, which motivates us to develop a hybrid algorithm that can switch between two representation forms. It turns out that using a hybrid approach can yield better balance between inference accuracy and scalability. In many cases, it suffices to tell the class of a moving object, say if it is a friend or foe, rather than exactly tell who it is. In such a case, one can collapse the space of permutations to a smaller combinatorial space, e.g., a homogeneous space. It turns out that the Fourier bases for permutations are then collapsed into Radon bases. The binary structure of the Radon bases allows us to do several computations in a very fast way. With the Radon machinery, we study the property management problem using a novel over-complete bases representation framework. We also consider an inverse problem based on Radon base representations, which can help us to discover high level community structures about the objects of interest. An optimization problem that can identify the community structures among the objects is formulated. Such an optimization problem has theoretical guarantees about the existence, correctness, uniqueness, and stability of the solution. We also develop a column generation based approximation algorithm, which achieves polynomial time complexity for this problem. We justify our results with experiments on real-world data.

Advisor: Guibas Leonidas J. primary advisor. Thesis advisor
Carlsson Gunnar
Ye Yinyu advisor. Thesis advisor
Recognition of hapten molecules by gamma delta T cells [electronic resource]

The adaptive immune system is composed of [alpha beta] T cells, [gamma delta] T cells, and B cells, all of which express diverse rearranged antigen receptors and have been conserved together through evolution. [gamma delta] T cells make up the minority of circulating T cells and perform many of the same effector functions as [alpha beta] T cells, including cytotoxic functions and the production of cytokines like IL-17, IFN-[gamma], and IL-4. However, the conservation of [gamma delta] T cells suggests that they fill a non-redundant role in the adaptive immune system. Because their functions overlap, it is likely that [gamma delta] T cells are distinctive from [alpha beta] T cells in the way they are triggered by antigen. These antigenic triggers of [gamma delta] T cells remain poorly defined, but a more thorough knowledge of this repertoire will enhance understanding of the role of [gamma delta] T cells in the immune response. The identification of new [gamma delta] T cell antigens was undertaken, resulting in the discovery of hapten small molecule [gamma delta] T cell ligands and the identification of a diverse group of additional candidate [gamma delta] T cell ligands. With the discovery that [gamma delta] T cell receptors can recognize small molecules in addition to their known large protein ligands, it is clear that [gamma delta] T cells fill a unique role in the adaptive immune system is solidified with a broad capacity for antigen recognition along with all the functionality of T cells, and are uniquely situated to function together with [alpha beta] T cells and B cells in a concerted antigen-specific response.

Advisor: Chien Yueh-Hsiu
Davis Mark M. advisor. Thesis advisor
Garcia K. Christopher advisor. Thesis advisor
Monack Denise M. advisor. Thesis advisor
Reconsidering the Roots of Crude Coercion: a Policymaking Analysis of 'the Oil Weapon'

In 1973-1974, several Arab oil-producing countries embargoed oil shipments to the United States while cutting oil production, in order to pressure the US to diminish its support of Israel. Despite expectations at the time, such large-scale use of the "oil weapon"; has not become a commonplace policy. This thesis explores potential explanations for these changing patterns of use of "the oil weapon", drawing on policymaking, neo-realist, and offensive realist frameworks, then employing various case studies to evaluate the explanatory power of such frameworks. This thesis finds that whereas a punctuated equilibrium model best explains the buildup to "the oil weapon" in 1973-1974, Kingdon's multiple policy streams model best explains the deployment patterns for this policy from 1973‐2003. In case studies of Venezuela, Iran, and Russia’s “oil weapon” use and rhetoric during the 2003‐2008 period of heightened oil prices, Kingdon’s model best explains Venezuela case, an offensive realist framework best explains Russia’s, and a hybrid of the two models, Iran’s. The conclusion addresses the current EU‐Iran oil embargo to gauge how “the oil weapon” might develop in the future. This thesis’ findings will help inform oil‐importing countries’ calibrations of their policies for addressing oil‐producing countries’ potentially hostile export policies.

Keywords: CISAC
Center for International Security and Cooperation
Stanford University
OPEC
Organization of Petroleum Exporting Countries
oil embargo
international relations
foreign policy
Thesis
Advisor: Blacker Coit D.
Reconstructing Ximing Monastery [electronic resource] : history, imagination and scholarship in medieval Chinese Buddhism

Presented in the cultural context of medieval Chang'an and the broader network of Buddhist Asia, this dissertation provides an interdisciplinary study on a range of topics concerning the celebrated Ximing Monastery (Ximingsi) in Tang China (618-907). As a premier center of Buddhist learning, Ximingsi not only served as a prominent national monastery active in state-protection movement, but also attracted a steady stream of Chinese pundits, Indian missionaries, Korean scholars and Japanese pilgrims, seeking to spread the Buddhist dharma across Asia. Drawing from a large body of literature including Buddhist texts, secular archives, epigraphy, illustrated manuscripts, annals, royal charters, archeological reports, as well as numerous marginal notes, the present thesis offers a study of Ximingsi that seeks to shed light onto its legend, history, art, and scholarship. Situated near the palace city in Chang'an, Ximingsi proved to be a powerful representative of a state Buddhism in support of the nation. The first part of this study offers a consideration of the monastery's dark prehistory, a sketch of its image in the literary imagination, and a reconstruction of its complex religio-political history, with special attention to the interaction between state politics and monastic Buddhism. At the same time, the monastery stood at the center of a broader story in the architectural history of East Asian Buddhism. The second part of the dissertation takes up that story and attempts to reconstruct the religious space of Ximingsi in relation to the Indian Jetavana Vihāra and the Daianji Monastery in Japan. This part focuses on two texts —— the Illustrated Scripture of Jetavana (Guanhzong chuangli jietan tujing) and the Illustration of Ximingsi (Saimyōjizu) preserved in Japan —— and combines art historical studies with archaeological discoveries at the present monastery site. Lastly, the final chapters explore the celebrated library of Ximingsi, which was built around rich collections of Buddhist scriptures and secular texts. Digging into the two major catalogues at the monastery —— the Da Tang neidian lu and Zhenyuan shijiao lu —— the dissertation highlights the Buddhist bibliographical tradition at Ximingsi and its role in cultural exchange between China and Japan.

Keywords: Religious Studies
Advisor: Bielefeldt Carl primary advisor. Thesis advisor
Shao Dongfang advisor. Thesis advisor
Harrison Paul advisor. Thesis advisor
Reconstruction of galaxy star formation histories from redshift eight to the present day [electronic resource]

In this dissertation, I present a comprehensive analysis of the gravitational influence of dark matter on the formation of stars in the universe from the epoch of reionization to the present day. This analysis is the first to self-consistently link observations of galaxy stellar mass and star formation rates to dark matter halos in simulations to redshift 8, along with full estimates of uncertainties inherent to the method. This allows direct constraints on the average rate of star formation in galaxies as a function of halo mass and redshift. Derived quantities are also presented, including average star formation histories, stellar ages, the relationship between star formation and baryon accretion rates, the buildup of the intracluster light, and limits on current observational inconsistencies. As they are required for this process, new calibrations of halo mass functions, satellite halo fractions, halo mass accretion histories, halo merger rates, and the expected disruption rate of merging galaxies into the ICL are presented. Finally, this dissertation discusses future work made possible by this analysis, including the potential to constrain individual galaxies' variations from the average star formation rates presented.

Keywords: Physics
Advisor: Wechsler Risa H. (Risa Heyrman) primary advisor. Thesis advisor
Abel Tom G.
Blandford Roger D. advisor. Thesis advisor