VictorJuiz/thesis huggingface dataset:
Understanding the Relation Between the m6A Methylation and MicroRNA Pathways in Embryonic Stem Cells
Keywords:  Department of Biology
Biology
RNA Epigenetics
Thesis

N6-methyl-adenosine (m6A) is a posttranscriptional modification to RNAs that is critical to the development of many eukaryotic organisms. The identification of both methylases and demethylases suggests that cells can actively control m6A levels to regulate mRNA metabolism. However, the regulatory mechanism of m6A RNA methylation is not well understood. In this study, we aim to understand how the microRNA pathway may regulate RNA methylation. Using qRT-PCR and HPLC, we observe that in knock outs of Dicer and DGCR8, while global mRNA methylation levels remain largely unchanged, methylation in the transcripts of multiple pluripotency genes in mouse embryonic stem cells (mESCs) is reduced. To understand the mechanism by which miRNAs affect mRNA methylation, we determine that the protein and gene expression of methylases, demethylases, and writers remain unchanged following knock out of Dicer, DGCR8, and Argonautes. We have performed m6A-IP seq from Dicer and DGCR8 knockout cells, and we hypothesize that identifying the transcripts that are preferentially methylated or demethylated by DGCR8, Dicer, and Argonautes will allow us to understand how methylation of RNA is regulated by the miRNA pathway. Overall, these results are critical in elucidating the role and regulation of m6A RNA methylation in mammalian embryonic stem cells.
Understanding the Role of Charge Mobility and Recombination in Organic Photovoltaics
Keywords:  Department of Physics
solar cells
photovoltaics
organic solar cells
bulk heterojunctions
simulation
recombination
charge mobility
Thesis

Current organic photovoltaics based on bulk heterojunctions have an active absorbing layer that is typically only 70 to 100 nm thick. While this results in efficient extraction of photogenerated charge carriers, the active layer is too thin for efficient absorption of light. If the active layer were 300 nm thick, close to 100% of the light would be absorbed. However, when devices are made with thicker active layers, recombination of charge carriers reduces the overall efficiency of the device.
In this project, I conduct an in-depth analysis of the effect of charge mobility and recombination in organic photovoltaics. Using a combination of experiments and a 1D simulation software, Seftos, I explain why bulk heterojunction organic photovoltaics suffer from poor performance when made with thick active layers. I experimentally demonstrate charge mobility’s effect on reducing solar cells, then utilize it to extract values of the recombination rate constant for two organic photovoltaic systems. These results provide an overview on the role of charge mobility and recombination in device performance and a road map for designing the next iteration of bulk heterojunction systems.
Unenviable Inevitability: The Negative Outlook of Russia's Eurasian Union
Keywords:  Program in International Relations
Russia
Eurasia
Ukraine
Georgia
Putin
CISAC
geopolitics
Center for International Security and Cooperation
Thesis

Not only those in the West scrambled together a response to Russian action in Ukraine throughout 2014. Russia’s closest allies, Belarus and Kazakhstan, also chafed at an overextension of Russian hegemony in the post-Soviet space. The never before seen indignation that both countries exhibited as a result of Russian action can only signal a downturn in relations between each state and Russia. Consequently, Russia’s primary foreign policy goal, establishment of the Eurasian Economic Union, is in serious jeopardy. Belarusian and Kazakhstani leaders moved their respective states further away from Russian control by aligning closer with other world powers. Distressed by Russian action in Crimea, each government promoted additional policies to ensure that Russian-supported separatism would not undermine either Belarus or Kazakhstan from within. Experts have argued that the best bet for each country has always been to follow Russian initiatives in order to recoup economic or political rewards from the Kremlin. As a result, many analysts expected both states join the Eurasian Union when invited. Indeed, both did. Belarus and Kazakhstan have generally supported Moscow’s positions since the fall of the Soviet Union up until the conflict in Ukraine. They even supported Moscow’s policies during its de-facto annexation of Georgian territory in 2008. However, the Crimean and Eastern Ukrainian episodes are unique even amongst Russian military interventions, and that uniqueness is not lost to the governments of Belarus or Kazakhstan. Both countries appear to be moving away from Russia’s sphere of influence. Therefore, without a change in political realities, the Eurasian Union will inevitably become like other discarded relics of post-Soviet integration: a shell of what could have been.
Unlocking synthetic biomaterials [electronic resource] : manufacture of structural biogenic materials via 3D-printed arrays of bioengineered cells
Keywords: Mechanical Engineering.

Many complex, biologically-derived materials have extremely useful properties (think wood or silk), but suf- fer from production, manufacturing, and processing limitations. Cells naturally specialize in making complex biomaterials on a micro scale. This work explores a technology concept combining this ability with the re- cently emergent fields of synthetic biology and additive manufacturing in which the end product is a nonliving biomaterial with human-designed shape, structure and composition. A 3D printer capable of printing living cells with near single-cell resolution is used to create 3D-structured arrays of cells bioengineered to secrete different materials. The cells produce the materials in rates and quantities determined by human-controlled stimuli. A proof of concept is described consisting of a two-material array of non-structural proteins. Each step in the end-to-end demonstration has been proven to reach the minimum level of critical functionality. Adding a vast new set of biomaterials, both natural and newly designed, to the traditional metal, plastic and ceramic material toolkit has applications limited by our future imagination; this work is an important first step on that path.
Unraveling the functional significance of regulatory variation across the human genome [electronic resource]
Keywords: Genetics.

Understanding the relationship between genotype and phenotype remains one of the greatest challenges in genetics and medicine today. Recently, a wealth of new genomic and functional data has enabled researchers to catalog human genetic variation, characterize their effects on phenotypic variation, and test hypotheses to uncover their underlying mechanisms. Despite these achievements, basic questions about genetic variants remain unanswered, including their full distribution of effects on heritability, their molecular mechanisms of action, and their interaction with environmental variables. Resolving these questions will improve our resolution of the genetic architecture of phenotypic traits and uncover the molecular basis of human disease. This thesis begins to address these questions by dissecting the role of genetic variants on regulatory variation across tissues and individuals. First, Chapter 1 provides a broad introduction to key biological and technological concepts that form the basis of the work presented in this dissertation. Then, Chapter 2 offers a detailed discussion of the experimental and analytical methods utilized to interrogate regulatory variation. Next, Chapter 3 assesses transcriptomic variation across ten tissues of the human body, with a particular focus on patterns of allele-specific expression for deleterious variation. Lastly, Chapter 4 explores differences in regulatory variation between the sexes with a focus on contributions from the X chromosome and potential mechanisms. Together, these chapters provide insight into the impact and mechanistic basis of regulatory variation across tissues and across the sexes.
Use of bivalves for the improvement of water quality [electronic resource] : removal of trace organic contaminants and microbial pollutants
Keywords: Civil and Environmental Engineering.

Stressed freshwater supplies pose significant risks to society, negatively affecting human health, the environment, and the economy. Because clean freshwater is a limited resource, novel engineering solutions to improve water quality and augment quantity are needed. Use of natural treatment systems to remove various pollutants that lead to degraded water is one potential innovative engineering approach. Unregulated trace organic contaminants, known as contaminants of emerging concern (CECs), and microbial contaminants are two types of pollutants that impair water quality. This dissertation examines how best to harness the ability of bivalves to remove CECs and microbial pollutants. Specifically, the research presented in this dissertation investigates the application of freshwater mussels and clams for removal of a suite of CECs commonly found in aquatic systems and the fecal indicator bacteria E. coli. Laboratory and field experiments were completed to understand the fate and bivalve uptake rates of these two types of pollutants.
Use of Honey in Maya Construction
Keywords:  Department of Anthropology
Maya
Yucatan
Mexico
modern cement
twentieth century
honey-mortar
micorscopy imaging
archaeological
archaeology
mayan
construction
ethnographic
mechanical tests on honey-mortar materials
Stanford University Department of Anthropology.
Thesis

Maya villagers interviewed in Yucatan, Mexico, claim that before the advent of modern cement in the first half of the twentieth century, their elders mixed honey with other substances to make a material described as mortar, glue, or cement. The claims are that the “honey-mortar” was used not only for small patching repairs around the house, but also to build homes, churches, and even ancient monuments. Follow up interviews with local Maya men reveal various ways of mixing honey and lime (calcium oxide) for a variety of construction purposes, including: daub for pole-and-thatch housing, mortar for stone-and-mortar housing, adhesive for sealing cracks, material for roofing, and finish for walls and roofing. The purpose of this research is to investigate the use of honey in Maya construction by analyzing ethnographic and historic data, conducting mechanical tests on honey-mortar materials sourced locally from the Yucatan, and comparing chemical composition and microscopy imaging data with existing literature on archaeological mortars.
The uses of nonsense [electronic resource] : antimodernism in Latin American fiction, 1920-1977
Keywords: Iberian and Latin American Cultures.

The Uses of Nonsense reconsiders four Latin American prose writers as "antiphilosophical" stylists, in the terminology proposed by Alain Badiou and separately, Boris Groys. My thesis argues that Macedonio Fernández, Jorge Luis Borges, João Guimarães Rosa, and Clarice Lispector modeled themselves in the tradition of antiphilosophical thinkers who intervened in Western philosophical thought from across its disciplinary borders, particularly from the realm of fiction. These writers use literary tropes of nonsense to critique what Herbert Marcuse called the "irrational rationality" of both socialist and capitalist modernity. The Uses of Nonsense thus challenges the notion that Latin America produced no original philosophical ideas.
Using motivational cognition and mood management to predict media content pacing and selection over four days of media multitasking [electronic resource]
Keywords: Communication.

This field study applies both state and trait based theories to explore the concept of media multitasking, operationalized as task-switching on a computer. A motivated cognition perspective makes predictions about long-term individual trait differences in content selection and pacing while multitasking. In contrast, mood management predicts that individuals have a tendency to manage short-term situations and maximize positive mood states during media use. This study employs two novel methods. The first accurately and objectively records switching activity in the field by logging screen content every five seconds for four days. The second advances traditional experience sampling methods by contextually surveying emotional state based on switching behavior. Results revealed extremely fast switching between content at the computer: median segment length was just 11 seconds, comparable to 19 seconds found in past research (Yeykelis, Cummings, & Reeves, 2014). Individuals with high baseline levels of appetitive activation (high ASA) switched more, cycled through content faster, had higher arousal at the computer, and preferred more entertainment content than individuals with low appetitive activation (low ASA). Evidence of mood management was found on one day of the experimental period: valence over a day increased for those with high ASA but decreased for those with low ASA. Novel visualizations showed that individual differences in content selection were substantial in the user-selected construction of a media day. Further, the data determined that switching and content predictors of valence and arousal varied greatly across individuals.
Using optogenetics and advanced genetic techniques to study the nervous system
Keywords:  Department of Biology
optogenetics
microtubule polarity
brain
neurons
mice
C. elegans
biology
developmental neurobiology
stroke
neurosurgery
Thesis

Clinical and research efforts have focused on promoting functional recovery after stroke. Brain stimulation strategies are particularly promising because they allow direct manipulation of the target area’s excitability. However, elucidating the cell type and mechanisms mediating recovery has been difficult because existing stimulation techniques non-specifically target all cell types near the stimulated site. To circumvent these barriers, we used optogenetics to selectively activate neurons that express channelrhodopsin (ChR2) and demonstrated that selective neuronal stimulations in the ipsilesional primary motor cortex (iM1) can promote functional recovery. Stroke mice that received repeated neuronal stimulations exhibited significant improvement in cerebral blood flow and the neurovascular coupling response, as well as increased expression of activity-dependent neurotrophins in the contralesional cortex, including brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF) and neurotrophin 3 (NTF3). Western analysis also indicated that stimulated mice exhibited a significant increase in the expression of the plasticity-associated marker GAP43. Moreover, iM1 neuronal stimulations promoted functional recovery, as stimulated stroke mice showed faster weight gain and performed significantly better in sensory-motor behavior tests. Interestingly, stimulation in normal mice did not alter motor behavior or neurotrophin expression, suggesting that the pro-recovery effect of selective neuronal stimulations is dependent on the post-stroke environment. These results demonstrate that stimulation of neurons in the stroke hemisphere is sufficient to promote recovery.
Microtubule polarity plays an instructive role in protein trafficking and is highly conserved across species. The study of microtubule polarity in neurons is particularly interesting because the minus-end is known to be free-floating rather than embedded in a microtubule-organizing center. Previous works indicate that intrinsic cues like microtubule-binding proteins either selectively transport or selectively stabilize microtubules in neuronal processes. However, this study suggests that extrinsic cues like morphogen gradients may also play a critical role. In particular, we show that the UNC-6/Netrin signaling pathway, as well as the WNTs signaling pathway, are important in regulating the microtubule polarity of the sensory neurons in the tail of the worm. We propose that UNC-6 acts via the UNC-40 receptor to regulate UNC-73, while EGL-20 and LIN-44 (members of the WNTs family of proteins) act redundantly to activate UNC-73 via the LIN-17 receptor. UNC-73 then activates downstream genes that function to establish microtubule polarity. Thus, it is the bi-directionality of morphogen gradients that encode information about microtubule polarity.
The vacuum Einstein constraint equations on manifolds with ends of cylindrical type [electronic resource]
Keywords: Mathematics.

This dissertation concerns the vacuum Einstein constraint equations on manifolds possessing end regions which are asymptotically periodic, including the special case where the ends are conformally asymptotically cylindrical. We will first apply the conformal method to construct a large class of vacuum initial data on any such manifold with positive Yamabe invariant, and then extend these existence results to manifolds which may also have asymptotically Euclidean ends. We will also show that, in the conformally asymptotically cylindrical case, any solution to the constraints one obtains via the conformal method which preserves the end geometry must have a unique asymptotic limit. Finally, we describe two different approaches to gluing generic asymptotically periodic initial data sets end-to-end, thereby allowing us to construct a large family of initial data sets with ``long neck'' regions.
Valid inference after data snooping [electronic resource]
Keywords: Statistics.

This dissertation consists of three unrelated parts: - Only Part I is related to the title of this thesis, Valid inference after data snooping. It provides a unified framework for understanding the flurry of recent work in post-selection inference, unifying the three goals of estimation, testing, and confidence intervals. I have attempted to provide a clean exposition of the motivation, theoretical results, and algorithms. - Part II is a collection of two published IEEE conference papers relating to statistics and audio signal processing. Both papers study low-rank models of audio spectrograms. - Part III describes the design of OHMS, an online homework system I designed and developed with Naftali Harris. This will hopefully be useful to people wishing to use and improve upon our open-source system. Details on how to obtain our code can be found in the Appendix.
The visible college [electronic resource] : how social network analysis informs our understanding of knowledge production and exchange in the university
Keywords: Education.

This dissertation uses social network analytical techniques to illuminate questions of central interest to higher education scholars. In it, I investigate the role that the university, as a formal organization, plays in knowledge creation, with particular focus on interdisciplinary research, asking how interdisciplinary research centers shape the lives of faculty and the organizational form of the university. The first chapter reviews the existing literature applying social network analysis in higher education, and then maps the network of co-citations among papers in this domain, providing a picture of where links are strongest and where gaps remain. Chapters 2 and 3 examine the interplay between the network of collaborative relations among faculty members and the organizational form of the university, touching on questions of university governance, faculty productivity, and knowledge creation. These chapters examine how interdisciplinary centers bring colleagues together in new collaborations, how they position faculty members within the social structure of the university, and whether they influence the content of the work scholars produce. Social network analysis (SNA), I argue, provides unique traction on these issues. Through this dissertation, I explore the potential of SNA methods to deepen our understanding of higher education, of knowledge production and exchange, and of the university as a formal organization.
Visual word recognition with large-scale image retrieval [electronic resource]
Keywords: Electrical Engineering.

OCR techniques that were developed for scanned high-resolution images suffer from poor text recognition accuracy on camera images. In this dissertation, we cast text recognition as a word patch retrieval problem. By comparing visual text queries against a database of labeled word images, we demonstrate a text recognition system that achieves significantly improved performance on camera images. Robust visual text features are the foundation for optimal word patch retrieval. We introduce Text Aggregated Gradients (TAG), a visual text descriptor discriminatively learned using easily obtainable training data. At the query stage, query words can be accurately recognized via Approximate Nearest Neighbor search. In the interest of system scalability to a large number of fonts, a font recognition method is developed to facilitate fast query retrieval. We show that by employing a Bayesian network, surprisingly good font recognition accuracy can be achieved via probabilistic inference. A compact database is highly desirable for our large-scale word patch retrieval. To eliminate inter-font redundancies from the database, we perform feature aggregation within groups of similar fonts. Using Canonical Correlation Analysis, our database can be compressed by a factor of 5x without any loss of word retrieval accuracy.
A wall of many heights [electronic resource] : the uneven enforcement of the Canadian-United States border
Keywords: History.

This dissertation examines the creation, demarcation, and enforcement of the Canadian-United States border from the American Revolution until 1924. Although diplomats often viewed the division between national spaces as a clean and uniform line, the Canadian-United States border is better understood as a series of interlocking, uneven, and inconsistent walls. Federal administrators created national border policy, but local agents dictated the practical impacts this policy could have. Inconsistent policy decisions ensured that the border closed at different times in different regions and created an uneven set of impositions on borderland communities. As a result, federal border policy cannot be understood by looking at a single racial, ethnic, or tribal group. Europeans, Chinese, African Americans, Cree, Sioux, Nez Perce, Métis, Stó:lō, Haida, Ojibwe, and Iroquois all experienced the impacts of border closure in different ways and to different extents.