VictorJuiz/thesis huggingface dataset:
Understanding charge transport in semiconducting polymers for applications in organic electronics and bioelectronics [electronic resource]

Organic electrochemical transistors (OECTs), in recent years, have emerged as promis- ing devices for fabricating biosensors using semiconducting polymers. Although in- organic materials have long dominated the semiconductor market, organic semicon- ductors have been found to be much better candidates for interfacing with biological systems due to their high chemical variability, low elastic moduli and ability to per- form both electronic and ionic transport. Because ionic species can penetrate highly porous polymer films leading to large interfacial areas, OECT devices typically ex- hibit extremely large capacitances and display among the highest transconductance values in published literature. Despite great technological advancements in device fabrication and designs over the last decade, there still lacks a thorough understanding of electronic transport, molec- ular doping, and device physics in these systems. My doctoral research focused on developing a more complete picture of these fundamental processes in OECTs. The first few chapters of this thesis will be dedicated to our work in characterizing poly- mer crystal structures, film formation and microstructures, and charge percolation in semiconducting polymer thin films. Subsequently, I will discuss how we can control- lably dope polymer thin films, and the physical and chemical properties that affect the doping process. In the last parts, I will present our electrical model for predicting OECT device responses and how we can extract useful device and biological properties in sensing experiments. Our findings provide important, fundamental insights into physical and electronic processes in semiconducting polymers, and are indispensable for designing better materials and biosensors.

Keywords: Materials Science and Engineering.
Advisor: Salleo Alberto
Bao Zhenan advisor. Thesis advisor
McGehee Michael
Understanding the functional link between adherens junctions and the cytoskeleton [electronic resource]

This thesis focuses on understanding the functional link between the Adherens Junction (AJ) and the cytoskeleton. In order to control tissue integrity, the AJ complex links to the cytoskeleton, including actin and microtubules, and thereby controls intercellular adhesion, cell migration and the orientation of cell division. However, how AJ connection to the cytoskeleton is established and regulated is not well understood. Formation of the AJ is directed by the cadherin-catenin complex (CCC), which in epithelial cells comprises E-cadherin that binds β-catenin, which in turn recruits the F-actin binding and bundling protein αE-catenin. αE-Catenin is essential for cell-cell adhesion, and at cell-cell junctions is thought to link the CCC to F-actin either directly when under force, or indirectly by recruiting additional actin binding proteins (reviewed in Chapter 1). Mammalian αE-catenin also forms a homodimer in the cytosol, which is mutually exclusive with β-catenin binding in the CCC. However, even though the αE-catenin homodimer binds readily to F-actin and has been shown to inhibit Arp2/3 and cofilin activities, its role in cell-cell adhesion remains poorly understood. In Chapter 2 we directly test whether αE-catenin bound to β-catenin in the CCC is sufficient to induce intercellular adhesion, and results from this work show that both junctional monomer and cytosolic homodimer pools of αE-catenin act together to induce strong cell-cell adhesion. However, understanding the specific function of the αE-catenin homodimer and its role in locally controlling actin dynamics at cell-cell junctions has been technically challenging because the N-terminus of αE-catenin mediates both homodimerization and β-catenin binding. Thus, removing the homodimerization domain of αE-catenin also disrupts αE-catenin binding to β-catenin in the CCC. Chapter 3 describes the design of a locked-monomer αE-catenin mutant that uncouples homodimerization from αE-catenin binding to β-catenin. Expression of this mutant in an αE-catenin-/- generated cell line, we show that the αE-catenin homodimer pool is essential for regulation of epithelial intercellular adhesion and cell migration. Finally, in Chapter 4, we identify a link between the AJ complex and the microtubule cytoskeleton in mitosis. Epithelia cells divide parallel to the epithelial plane in order to maintain tissue architecture. Although E-cadherin has been implicated in this, the underlying molecular mechanism remains unclear, and here we identify how E-cadherin is linked to the mitotic spindle in order to instruct the orientation of cell division.

Keywords: Biology.
Advisor: Nelson William primary advisor. Thesis advisor
Kopito Ron Rieger
Theriot Julie advisor. Thesis advisor
Weis William I. advisor. Thesis advisor
Understanding the Relation Between the m6A Methylation and MicroRNA Pathways in Embryonic Stem Cells

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.

Keywords:  Department of Biology
Biology
RNA Epigenetics
Thesis
Advisor: Chang Howard
Fraser Hunter
Understanding the Role of Charge Mobility and Recombination in Organic Photovoltaics

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.

Keywords:  Department of Physics
solar cells
photovoltaics
organic solar cells
bulk heterojunctions
simulation
recombination
charge mobility
Thesis
Advisor: McGehee Michael D.
Burchat Patricia R.
Unenviable Inevitability: The Negative Outlook of Russia's Eurasian Union

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.

Keywords:  Program in International Relations
Russia
Eurasia
Ukraine
Georgia
Putin
CISAC
geopolitics
Center for International Security and Cooperation
Thesis
Advisor: Blacker Coit D.
Naimark Norman
Unlocking synthetic biomaterials [electronic resource] : manufacture of structural biogenic materials via 3D-printed arrays of bioengineered cells

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.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Rothschild Lynn J.
Sheppard S. (Sheri) advisor. Thesis advisor
Unraveling the functional significance of regulatory variation across the human genome [electronic resource]

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.

Keywords: Genetics.
Advisor: Montgomery Stephen
Snyder Michael
Fraser Hunter B. advisor. Thesis advisor
Pritchard Jonathan (Jonathan K.) advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Unsupervised learning across multiple datasets [electronic resource]

Subtypes define distinctive subgroups of objects found within a larger cohort; these subtypes can help domain experts define actionable recommendations for each subgroup to improve outcomes. With the relatively recent explosion of large datasets accompanied by large numbers of features, a popular way to define subtypes is unsupervised learning, or clustering, algorithms. Unfortunately, unsupervised learning algorithms have a serious drawback: there is no ground truth. While a set of clusters may correlate strongly with an outcomes variable, an outcomes, or response, variable, is not used in an unsupervised learning algorithm; this means that the accuracy of clusters derived from such algorithms, by nature, cannot be quantified. One way to ensure subtypes represent true signal is to conduct the clustering analysis on multiple datasets. However, there is a lack of methods for unsupervised learning across multiple datasets. In this dissertation, I propose novel methods for unsupervised clustering across multiple datasets, by finding a consensus across clusters derived from each individual dataset. I propose an algorithm, COINCIDE, that encompasses these novel methods; COINCIDE interprets each cluster as a node in a network. I apply COINCIDE to cancer gene expression and pathology datasets, and finally sepsis gene expression datasets, to illustrate the ability of COINCIDE to conduct unsupervised learning across multiple datasets to discover robust subtypes.

Advisor: Gevaert Olivier Michel Simonne
Musen Mark A. advisor. Thesis advisor
Salzman Julia
Use of bivalves for the improvement of water quality [electronic resource] : removal of trace organic contaminants and microbial pollutants

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.

Keywords: Civil and Environmental Engineering.
Advisor: Luthy Richard G. primary advisor. Thesis advisor
Boehm Alexandria advisor. Thesis advisor
Mitch William A. advisor. Thesis advisor
Use of Honey in Maya Construction

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.

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
Advisor: Fox Jim
Durham William
Uses of adult and pluripotent stem cells for treatment of heart disease [electronic resource]

Heart disease is the leading cause of morbidity and mortality in the developed world. Adult and pluripotent stem cells offer the potential to revolutionize medical treatment of cardiovascular disease through generation of patient and disease-specific cadiomyocytes heart tissue and blood vessels for the first time. However, translation of stem cell-based technologies to the patient bedside face a number of challenges including acute donor cell death, poor differentiation into therapeutic cell populations, and tumorigenicity. Here, we outline several of the major hurdles limiting cell therapy efficacy in patients suffering from heart disease as well as several applications of molecular imaging modalities to address these challenges. We furthermore describe several novel applications of stem cell platforms for modeling patient-specific heart disease and personalized drug screening. Finally, we describe the identification of a novel vessel forming adult stem cell population, which may have future applications in cell therapy for treatment of ischemic injury.

Advisor: Wu Joseph Ching-Ming
Calos Michele P. advisor. Thesis advisor
Chen James Kenneth advisor. Thesis advisor
Longaker Michael T.
Wysocka Joanna
The uses of nonsense [electronic resource] : antimodernism in Latin American fiction, 1920-1977

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.

Keywords: Iberian and Latin American Cultures.
Advisor: Hoyos Ayala Héctor primary advisor. Thesis advisor
Rocha Marília Librandi primary advisor. Thesis advisor
Predmore Michael P. advisor. Thesis advisor
Ruffinelli Jorge advisor. Thesis advisor
Using motivational cognition and mood management to predict media content pacing and selection over four days of media multitasking [electronic resource]

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.

Keywords: Communication.
Advisor: Reeves Byron
Bailenson Jeremy advisor. Thesis advisor
Hamilton James
Monin Benoît