VictorJuiz/thesis huggingface dataset:
DIRECTED DIFFERENTIATION of Female Induced Pluripotent Stem Cells Using BMPs and Retinoic Acid

Development of the human cell lineages has been the subject of much study since the first derivation of human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs). These cell types can be directed to form early endoderm, mesoderm, ectoderm, trophectoderm, as well as germ cells. Factors such as bone morphogenetic proteins (BMPs) 4 and 8 can differentiate iPSCs to primordial germ cells (PGCs) as well as other lineages such as mesoderm and trophoblast. To address the effect of BMPs and Retinoic Acid (RA) on directed differentiation of female iPSCs, we conducted a 14-day directed differentiation experiment using four treatments and examined the formation of ectoderm, endoderm, pluripotency, germ cell, and trophoblast/mesoderm cell types through analysis of gene expression. Based on previous data from the laboratory, it was hypothesized that the presence of RA during directed differentiation of female iPSCs, in particular, would lead to differentiation of trophoblast or mesoderm tissues, preferentially over other fates including primordial germ cells (PGCs), while BMPs would function to maintain pluripotency and germ cell fates.
Following directed differentiation, pluripotency, mesoderm, germ cell, and ectoderm associated genes experienced a gradual decrease in expression while trophectoderm and endoderm genes exhibited an increase in expression throughout the 14 days across all treatments. The hypothesis that the addition of RA would induce trophoblast was supported by increased expression of associated markers. However, addition of +RA did not upregulate mesoderm as hypothesized, with +BMP resulting in negative regulation. Similarly, the hypothesis that +BMP treatment would upregulate germ cell fates was not supported, with all treatments resulting in significant downregulation of germ cell related genes. Variations from the hypothesis may be due to timing of exposure and an unknown pathway mechanism, which merit further investigation. It was further determined that 1) neuroectoderm may be the default differentiation pathway; 2) +BMP upregulates endoderm cell markers and downregulates PGC and mesoderm markers; 3) +BMP/RA downregulates ectoderm, mesoderm, and pluripotency markers while upregulating endoderm and trophectoderm markers; 4) +RA downregulates ectoderm and mesoderm markers. Overall, +BMP appeared to have a more potent effect in positively or negatively regulating gene expression, often with amplified effects in combination with +RA

Keywords:  Department of Biology
stem cells
factors
yamanaka
retinoic acid
BMPs
bone morphogenetic proteins
RA
Stanford
Biology
Thesis
Advisor: Reijo Pera Renee
Dominguez Antonia
Skotheim Jan
Discovering low work function materials for thermionic energy conversion [electronic resource]

The work function is the interfacial parameter of a surface that determines how easily electrons can escape into a vacuum or gas environment, with lower work functions generally facilitating electron emission. This thesis employs density function theory methods to a systematic approach in the discovery of new nanostructured multilayer materials with low work functions. Techniques in density functional theory can enable many promising film coating combinations to be efficiently investigated for the first time. Two main sets of screening studies are described: (1) cesiated transition metal surfaces and (2) alloyed alkali-earth oxide films on tungsten. A model is introduced for the effect of cesium adsorbates on the work function of transition metal surfaces. This model builds on the classic point-dipole equation by adding exponential terms that characterize the degree of orbital overlap between the 6s states of neighboring cesium adsorbates. In addition, the model analyzes the effect of orbital overlap on the strength and orientation of electric dipoles along the adsorbate-substrate interface. This new framework improves upon earlier models in terms of agreement with the work function-coverage curves obtained via first-principles calculations based on density functional theory. All the cesiated metal surfaces have optimal coverages between 0.6 and 0.8 monolayers, in accordance with experimental data. Of all the cesiated metal surfaces considered, tungsten has the lowest minimum work function, also in accordance with experiments. The work function and stability of 570 alloyed alkali-earth oxide films on the (100) surface of tungsten have been calculated within density functional theory. Computational screening of this large phase space is enabled by implementing the virtual crystal approximation, where the degree of freedom in the chemical composition is modeled with virtual atoms of mixed calcium, strontium, and barium character. Low work functions are achieved by doping the films with scandium (1.16 eV) or lithium (~1.2 eV) and alloys containing ~15% to ~20% of calcium. In particular, lithium-doped systems with ~15% calcium also show favorable stability indicated via formation energy calculations. Identification of such film alloys outperforming any of the constituents relies on careful sampling of the chemical composition. Covalent interactions within the film limit the reduction in work function from the dipole normal to the surface. Controlling the electronic screening of these intra-film interactions by oxygen atoms is essential for the design of new low-work function materials.

Keywords: Electrical Engineering.
Advisor: Howe Roger Thomas primary advisor. Thesis advisor
Noerskov Jens
Pianetta Piero advisor. Thesis advisor
A discriminative modeling approach for inferring ancestry and correcting phase in large population genetics data sets [electronic resource]

Local ancestry inference is an important step in both medical genetics studies and demographic studies. This is because many human populations are the result of admixture, or the interbreeding of distinct ancestral populations. The recent drastic increase in sample sizes and marker densities of population genetic data, particularly from whole-genome sequencing, provides an opportunity for computational methods to harness this data to accurately infer fine-scale local ancestry. However, current approaches to inferring local ancestry can only detect continental-level ancestry accurately and are too computationally complex to handle fully sequenced human genomes. Thus there is a need for methods that can utilize massive population genetics data sets to infer fine-scale ancestry in a computationally rapid and robust manner. In this thesis, I describe my contributions toward this goal. First, I describe a method I developed called RFMix, which uses conditional random fields parameterized by random forests to rapidly train on massive data sets, infer fine-scale local ancestry and correct phase. Second, I evaluate RFMix using simulated and real data sets and compare it to other methods. I also apply RFMix to real data sets to infer demographic histories. Finally, I develop a pipeline for generating reference panels from large databases containing mislabeled and unlabeled samples, and apply it to the massive AncestryDNA genetic database to show that using local ancestry inference as an intermediate analysis step gives better global ancestry estimates than traditional direct approaches.

Advisor: Bustamante Carlos (Carlos D.) primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Owen Art B. advisor. Thesis advisor
Distant terrains and decorative fictions [electronic resource] : describing Japan in Second-Empire France

This dissertation reveals how Japanese imports participated in a new discourse on objects in 1860s Paris. Looking to the specific political and aesthetic context of the Second Empire, this project reconsiders how the descriptive practices of the 1860s determined the early French encounter with Japanese things. Description places new attention on the communicative properties of inanimate objects and dominates the aesthetic and commercial culture of Second-Empire France. This culture of description materializes in naturalist novels, exhibition catalogs, expansive encyclopedias, republican literature, still-life painting, and portraiture during the 1860s and emerges as the primary framework for ordering and understanding the foreign culture of Japan. Imagined through its objects and inscribed into these various descriptive forms, Japan appeals to a French context that finds new political and aesthetic meaning in the accumulation and representation of things. By mapping the early French encounter with Japan across a variety of material forms, this project complicates the standard narrative of Japonsime to suggest that Japan is both politically and culturally encoded through the description of its objects in 1860s France.

Keywords: Art and Art History.
Advisor: Marrinan Michael primary advisor. Thesis advisor
Guth Christine advisor. Thesis advisor
Vinograd Richard Ellis advisor. Thesis advisor
Wolf Bryan Jay advisor. Thesis advisor
Distributed convex optimization with proximal methods [electronic resource]

This thesis is about a class of optimization algorithms called proximal algorithms. Much like Newton's method is a standard tool for solving unconstrained smooth optimization problems of modest size, proximal algorithms can be viewed as an analogous tool for nonsmooth, constrained, large-scale, distributed, or decentralized versions of these problems. They are very generally applicable, but are especially well-suited to problems of substantial recent interest involving large or high-dimensional datasets. Proximal methods sit at a higher level of abstraction than classical algorithms like Newton's method: the base operation is evaluating the \emph{proximal operator} of a function, which itself involves solving a small convex optimization problem. These subproblems, which generalize the problem of projecting a point onto a convex set, often admit closed-form solutions or can be solved very quickly with standard or simple specialized methods. Here, we discuss many different interpretations of proximal operators and algorithms, describe their connections to many other topics in optimization and applied mathematics, survey some fundamental algorithms, and provide a large number of examples of proximal operators that arise in practice.

Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Koller Daphne advisor. Thesis advisor
Liang Percy advisor. Thesis advisor
Divine institutions [electronic resource] : religious practice, economic development, and social transformation in mid-Republican Rome

In the course of two and a half centuries, the city-state of Rome rose from central Italian dominance to Mediterranean hegemony. Together with this transformation in the scale and extent of Roman power came a revolution in social, economic and cultural practices. My dissertation argues that the success of this imperial project and the nature of the social revolution it triggered must be understood by reference to Roman religious practices throughout this period. I set out the case for why and how religion in mid-Republican Rome and Roman Italy drove meaningful and highly consequential institutional change over time. A primary mover in this institutional change is trust: religious behaviors, observances, and rituals shaped the creation and perpetuation of the forms of trust that anchored the "quasi-voluntary compliance" regime binding together the citizen body of the expanding Republic and its constellation of allies. With the help of insights gleaned from sociology and political science, I isolate several specific areas through which this dialogue of religiously-mediated trust was promoted and enacted: temples and monumental construction; festivals and festival culture; numismatic iconography; and the announcement and expiation of prodigies. I show how these four domains of cultural practice—shaped and orchestrated according to religious considerations—became sites of institutional innovation, with implications for Rome's imperializing project. This characterization of the middle Roman Republic as a distinctive example of how religion interfaces with community-building, economic development, state formation, and imperial expansion aims to be of interest not only to Romanists and ancient historians but to political theorists, comparative historians, economic historians, and sociologists.

Keywords: Classics.
Advisor: Scheidel Walter
Morris Ian
Ober Josiah advisor. Thesis advisor
Trimble Jennifer
Dixie bound [electronic resource] : a cultural biography of an American legend, 1860-1930

Few songs have gained as enduring and contradictory a national legacy as "I Wish I Was in Dixie's Land." The tune was first performed in New York City on the minstrel stage and adapted to new lyrics by Civil War soldiers. President Lincoln requested its performance the day after Appomattox and, though still associated with the Confederate anthem today, it has encouraged generations of Americans to reflect on their national heritage by whistling and wishing that they were in a place called Dixie. But Dixie is not necessarily, or historically, synonymous with the American South. Over the past two centuries, Dixie has played a dominant role in shaping American popular culture, a role derived only in part from Dixie's Southern connotations. By charting Dixie's scandalous and enthralling journey over the turn of the century, Dixie Bound establishes an historical framework for understanding Dixie as a national literary phenomenon that began long before Scarlett and Rhett. Building an archive of previously unexamined tunes, texts, and visual artifacts, this study traces Dixie's circulation from the start of the Civil War through the rise of Tin Pan Alley and Dixieland jazz. These early appearances offer a dramatic counterpoint to present-day notions of Dixie and particularly to our presumptions about Dixie's racial and regional past. Precisely by turning back to the early history of Dixie, Dixie Bound provides necessary insight into the song's unsettling legacy today.

Keywords: English.
Advisor: Jones Gavin Roger
Elam Michele
Rampersad Arnold
Richardson Judith
DMRG studies of ferromagnetic phase diagram of infinite-U hubbard ladders [electronic resource]

The Hubbard model is one of the most important models in theoretical condensed matter physics. The model, which captures the strong interactions among the electrons, has not been solved analytically in more than one dimension. Therefore, over the past tens of year, there has been a tremendous analytic and computational effort to understand the parameter dependent ground state of this model, especially for intermediate strengths of the on-site repulsion U - the regime of parameters relevant to the properties of real material. Possible approaches to understand this model includes perturbative methods which start with the non-interacting kinetic term and treats the potential to low order in an expansion in powers of the interaction strength. A less intuitive approach is to attack the problem from the opposite extreme U> > t, where t is the electron hopping matrix element. In my thesis, I present the results concerning the ground-state phase diagram of Hubbard model in the infinite-U limit with an emphasis on the 2-leg ladder and the extrapolation of these results to the 2D limit. We will show that there is a half metallic ferromagnetic ground state when the density of electrons per site n> =n_c ~ 0.80. When n=0.75, the ground state is a commensurate anti-ferromagnetically ordered plaquette phase with bond density order. We show evidence that in the range of n between n_c and 0.75, the ground state is phase separated between these two states. These properties hold not only for the two-leg ladder, but wider ladders as well, which we assume implies that they continue smoothly to the fully 2D limit. However for 0.75 > n > 0.5 while the ground state is found to be unpolarized for wider ladders, the two leg ladder exhibits a partially polarized ferromagnetic ground state , with a peak in the magnetization density occurring at around n=2/3 where we have demonstrated the existence of another commensurate phase. The ground state of the 2-leg ladder when n=0.5 is an anti-ferromagnetic dimerized phase. A study of the charge carrying elementary excitations in the various commensurate phases suggests that there are further intermediate phases rather than direct first order transitions between them. Moving from infinite to large but finite U, we trace out the boundary of half metallic ferromagnetic phase of the 2-leg ladder as a function of n and U. As the transition seems to be everywhere first order, we propose that outside this phase gives way to a phase-separated ground state between such boundary and the two commensurate phases at n=1 and n=3/4 respectively. The plaquette phase is observed to be stable down to at least values of U~20t, but below a smaller critical value of U/t the ground state enters a stripe ordered phase. We also test the correspondence between Hubbard and t-J at least down to values of U~100t.

Keywords: Physics.
Advisor: Kivelson Steven primary advisor. Thesis advisor
Qi Xiaoliang advisor. Thesis advisor
Raghu Srinivas
Do implicit theories of happiness and well-being predict adaptive responses to stress? [electronic resource]

An accumulating body of research shows that stress negatively impacts individuals' mental and physical health, heightening depression and anxiety (e.g., Sapolosky, 1994; Willner, 1997); vulnerability to viral infections (e.g., Slavich & Cole, 2013); and inflammation, unfavorable gene expression, and impaired immune functioning (e.g., Spools, 1994; Slavich & Cole, 2013). Research suggests that coping strategies are an important predictor of the effect of stressors on an individual (e.g., Dumont & Provost, 1998; Folkman & Lazarus, 1985; Seiffge-Krenke, 2000). This dissertation investigates whether differences in implicit theories of well-being (or beliefs that well-being is malleable or fixed) are related to the coping strategies that individuals endorse. Specifically, it was hypothesized that holding a malleable theory of psychological well-being would lead people to endorse and engage in more adaptive coping behaviors in the face of stress. It was also hypothesized that believing that well-being is malleable would make people more interested in learning about and improving their well-being and happiness. The present research investigated these hypotheses in a series of three studies. Study 1 investigated whether those with a more malleable conception of well-being would be more likely to endorse adaptive responses to stressful scenarios. Building on Study 1, Study 2 investigated whether those taught to have a more malleable vs. fixed conception of well-being would be more likely to 1) endorse adaptive responding to stressful situations and 2) show interest in learning about well-being, stress and happiness. Study 3 investigated whether those given a more malleable vs. fixed conception of well-being would be more likely to embrace goals and priorities allowing them to improve their levels of happiness and well-being and take advantage of an opportunity to relieve situationally-induced stress with a mindfulness exercise. Implications for fostering greater overall well-being and more adaptive responses to stress are discussed.

Keywords: Psychology.
Advisor: Dweck Carol S.
Carstensen Laura L. advisor. Thesis advisor
Cohen Geoffrey L. (Geoffrey Lawrence) advisor. Thesis advisor
Heaney Catherine (Catherine Ann) advisor. Thesis advisor
Mueller Claudia Meta
Robinson Thomas (Thomas N.) advisor. Thesis advisor
Drawing from life [electronic resource] : mass sketching and the formation of socialist realist Guohua in the early People's Republic of China (1949-1965)

This dissertation examines how traditional Chinese landscape painting, often the site of an inward-turning private subjectivity, was revolutionized through mass sketching campaigns during the early years of the People's Republic of China (1949-1965). One of the most comprehensive programs to reform artistic practice in the history of Chinese art, state-sponsored sketching campaigns developed amid institutional, ideological, and aesthetic changes. Based on sketchbooks and paintings by the ink painters Fu Baoshi (1904-1965), Li Keran (1907-1989), and Guan Shanyue (1912-2000), this study tracks sketching tours that were designed to reform elite artists into cultural workers, to provide experiential knowledge of the essence of socialist reality, and to transform their observations into landscapes that would give shape to and embody the national culture of new China. The sketching tour routes mapped the industrial, revolutionary history, and cosmopolitan geographies constitutive of socialist landscape that, in turn, served as affective journeys for artists to conceive of themselves personally bound to the conceptualization, articulation, and practice of cultural work as a collective endeavor. Tracing the signal importance placed upon drawing and sketching under Maoist ideas of knowledge, consciousness, and practice, I argue that the practice of sketching in art education allowed for the discursive incorporation of previous historical approaches to painting, while inaugurating a critical emphasis on experiential authenticity and artistic participation that is central to socialist cultural production.

Keywords: Art and Art History.
Advisor: Vinograd Richard Ellis primary advisor. Thesis advisor
Andrews Julia Frances
Ma Jean
Wang Ban
Duality and linear approximations in Hochschild homology, K-theory, and string topology [electronic resource]

This thesis encompasses at least three separate but related projects. The first project is a treatment of twisted Poincare duality for manifolds with coefficients in spectra, and is included as an appendix. The second project investigates the map from the stabilization of the gauge group of a certain principal bundle over a manifold M to the Cohen-Jones string topology spectrum of M. This map is a linear approximation in the sense of Goodwillie and Weiss's embedding calculus. The third project is an ongoing and open-ended exploration of contravariant forms of algebraic K-theory of spaces, with a focus on topological Hochschild homology.

Keywords: Mathematics.
Advisor: Cohen R. L. (Ralph L.)
Carlsson Gunnar
Galatius Søren
Ganatra Sheel advisor. Thesis advisor