VictorJuiz/thesis huggingface dataset:
Gaining access to the hematopoietic stem cell niche [electronic resource] : novel non-myeloablative conditioning approaches
Keywords: Developmental Biology.

Sickle Cell Anemia, Beta Thalassemia, Severe Combined Immunodeficiency (SCID), and Type I Diabetes share one commonality: these diverse disorders can all be attributed to faulty hematolymphoid effector cells which are largely caused by genetic mutations that alter hematopoietic cell-intrinsic function. These defective blood cells inherit their genetic deficiencies from hematopoietic stem cells (HSC) as they differentiate. Thus, each of these unique diseases should be theoretically curable through the same strategy: replacement of patients' HSCs carrying the problematic mutation with normal HSCs from disease-free donors, thereby generating entire new, healthy hematolymphoid systems. Replacement of disease-causing stem cells with healthy ones has been achieved clinically via hematopoietic cell transplantation (HCT) for the last 50 years, as a treatment modality for a variety of cancers and immunodeficiencies with moderate, but increasing success. However this technique bears high morbidity and mortality severely limiting its utilization. Purified hematopoietic stem cell transplantation is associated with high toxicity primarily attributed to the myeloablative pre-conditioning necessary to facilitate engraftment of the donor HSCs. However the function and mechanistic role of these reagents has been up until now poorly understood. This thesis deconstructs the current barriers in HCT and pure HSC transplantation, and suggests that in addition to the immune barrier, hematopoietic stem cell niche availability is another critical obstacle that needs to be overcome to allow for efficient hematolymphoid replacement. In this thesis I show that in the homeostatic state, most hematopoietic stem cell niches are occupied by host HSCs limiting the ability of incoming HSC engraftment. However, a limited number of HSC niches are vacated by HSC that are egressing from the peripheral blood into the bone marrow in a division independent manner, allowing for true but minimal HSC engraftment without myeloablative pre-conditioning. This thesis illustrates new, up-and-coming strategies to combat the obstacle of HSC niche availability. Here I prove that one non-myeloablative conditioning approach that capitalizes upon physiological HSC egress is repetitive transplantation of purified HSCs. However, this approach is rather laborious and inefficient, and I show that another more efficient novel non-myeloablative conditioning approach to vacate the HSC niche is antibody-mediated depletion of host HSCs. Furthermore, in this thesis I demonstrate that antibody-mediated inhibition of c-kit effectively depletes host HSCs and allows for efficient, non-toxic HSC transplantation. These novel non-myeloablative conditioning methods illustrate new means of overcoming the current barriers to hematolymphoid replacement thereby allowing for the potential expansion of this technique to treat a variety of inherited diseases of hematopoietic and immune function.
Gamma-ray burst observations at high-energy with the Fermi large area telescope [electronic resource]
Keywords: Physics

The Fermi Gamma-ray Space Telescope recently celebrated its two-years anniversary in space. With the Large Area Telescope (LAT), its main instrument onboard, Fermi opened a new era in high-energy astrophysics and in particular for the study of Gamma-Ray Bursts (GRBs), which are short flashes of -rays associated with the brightest and most distant events ever observed in our universe after the Big Bang. My thesis work focused primarily on the observations of this phenomenon with the LAT (20 MeV - 300 GeV) and the Gamma-ray Burst Monitor (10 keV - 40 MeV) onboard the Fermi satellite. After describing the procedure used for detection and analysis of LAT GRBs, I will provide an overview of the temporal and spectral features observed during the prompt emission of these events after one year and a half of operation for Fermi. GRBs can also be used as a tool to probe interesting physics. My focus will be on the detection of very high energy photons (typically above 10 GeV) associated with LAT GRBs and which were used to set significant constraints both on a possible violation of Lorentz invariance - which postulates that all observers measure exactly the same speed of light in vacuum, independently of photon energy - and on the Optical-Ultraviolet extragalactic background light in the Universe.
Gender Bias Under Targeted Transfers: Food for Schooling in Bangladesh
Keywords:  Department of Economics
Stanford Department of Economics
targeted transfers
Bangladesh
gender bias
primary education
development
Thesis

Since the creation of the Millennium Development Goals (MDG), achieving universal education (MDG #2) has grown in popularity. One of the most successful policies addressing the problem of primary schooling came first as a national program in Bangladesh. In 1993, Bangladesh began Food For Schooling (FFS) to address growing issues of poor education and rural poverty. The program drew dramatic success in its targeted dimensions. Student absences decreased, and food security of impoverished households improved. The headline statistic for the first two years of the program was school enrollment. Over this period, primary school enrollment increased 35%, with a much higher rate for girls rather than boys. This success is notable for the raw increase but particularly for the increase in girls over boys. South Asia’s gender bias is well known, which makes this observed favoritism towards girls unusual. This paper analyzes this observed increase. Is there a relationship between the gender bias of school enrollment and the criteria families must meet to be eligible for the FFS program? The families are defined by occupations, employment time, head of household gender, and land assets, and the understanding of such a correlation would carry consequences for targeted transfer programs in other developing countries.
Gender Homophily across Types of Social Networks in Rural India
Keywords:  Department of Economics
Stanford Department of Economics
informal credit
gender preference
homosocial norm
social network formation
Thesis

In this paper, I search for evidence that women in 75 Indian villages are somehow constrained in their ability to make instrumental social connections necessary to start or run businesses. I compare gender homophily across ten different types of social networks, and find it to be relatively high in both genders and in most all of networks. It appears that both genders are similarly discouraged from relationships with people of the other gender, but less so when there is a transaction involved than when the association is entirely social in nature. Women in higher castes do not appear to be any more constrained than their lower caste counterparts. There is evidence that a homosocial norm discourages other-gender relationships, but it appears to be uniformly enforced across groups.
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genomic stability [electronic resource]
Keywords: Chemical and Systems Biology.

Genome instability has long been known to be a hallmark of cancerous cells, but the cellular causes and consequences of such instability are still not fully understood. Mutations, translocations, DNA rearrangements, as well as chromosomal loss can all result in the loss of genomic integrity. To prevent the disruption of cellular homeostasis due to DNA damage accumulation, cells contain pathways to sense and respond to DNA damage including cell cycle checkpoints and numerous DNA repair processes, collectively known as the DNA damage response (DDR). Mutations in many of the genes involved in the DDR are linked to several diseases, including premature aging, neurodegeneration and cancer. These signaling pathways are especially critical during DNA replication when the DNA is unwound and vulnerable to processing. Here, the cell relies on the S-phase checkpoint to sense DNA damage at the sites of replication forks and to facilitate a number of downstream pathways to maintain genomic stability. These processes include blocking further origin firing, facilitating DNA repair, preventing cell cycle progression, and stabilizing stalled replication forks. Here, two genome-wide siRNA screens were employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. The first screen looked at H2AX phosphorylation that occurred simply by individual protein depletion, and the second screen used a low level of a replication inhibitor, aphidicolin, to specifically identify genes that were needed to prevent DNA damage during S-phase, potentially due to the loss of replication fork stabilization mechanisms. While the results from the second screen are still undergoing further characterization, we did discover hundreds of genes whose down-regulation led to elevated levels of H2AX phosphorylation in the absence of any external stress. From this gene set, we identified many gene networks that were significantly enriched amongst our screening hits as well as several intriguing individual genes that were chosen for follow up study. These included genes involved in mRNA processing, the pathology of Charcot-Marie-Tooth syndrome, and the histone methyl transferase protein, Set8.
Genomic convergence association studies of expression and aging in the human kidney [electronic resource]
Keywords: Genetics

Although family studies have shown that genes play a role in longevity and tissue aging, it has proven difficult to identify the specific genetic variants involved. Kidneys age at different rates, such that some people show little or no effects of aging whereas others show rapid functional decline. We developed a sequential transcriptional profiling and expression quantitative trait loci (eQTL) mapping approach known as genomic convergence to find genes associated with aging in the kidney. We first performed whole-genome transcriptional profiling to find 630 genes that change expression with age in the kidney. Next, we used two methods to determine which of these age-regulated genes are eQTLs, which means they contain SNPs whose alleles associate with expression level. We found that 101 of the age-regulated genes are eQTLs. We also found that the allele-specific eQTL detection method, which compares the mRNA levels of the two alleles within heterozygous individuals, was more sensitive than the total expression method in detecting allelic expression differences. We tested the eQTLs for association with kidney aging, measured by glomerular filtration rate (GFR) using combined data from the Baltimore Longitudinal Study of Aging (BLSA) and the InCHIANTI study. We found a SNP association (rs1711437 in MMP20) with kidney aging (uncorrected p = 3.6E-05, empirical p = 0.01) that explains 1-2% of the variance in GFR among individuals. The results of this sequential analysis may provide the first evidence for a gene association with kidney aging in humans. Our approach of combining both expression and genotype data can be applied to any phenotype of interest to increase the power to find genetic associations.
Given-before-new, the effects of discourse on argument structure in early child language [electronic resource]
Keywords: Linguistics

Child language researchers, particularly those studying the acquisition of syntax, have often viewed young children's utterances as isolated and self-contained units of analysis. But "language does not exist in a vacuum" (Clark & Clark 1978:227), and utterances don't either. This dissertation explores the influence of conversational context on early word order. Specifically, I consider how discourse givenness affects the order of postverbal arguments in the speech of preschool children. In three elicited production studies, I systematically varied the structure of the discourse children heard just before they were asked to describe a filmed vignette. Study 1 targeted verbs of locative transfer, both alternating locative verbs (cf. She squirted the hotdog with the ketchup. vs. She squirted the ketchup on the hotdog.) and non-alternating ones (cf. She filled the cup with sand. vs. *She filled sand into the cup.). Studies 2 and 3 targeted alternating dative verbs (cf. She gave the man the hat. vs. She gave the hat to the man.). These studies provide converging evidence that (i) givenness has a robust effect on early argument ordering—like adults, children tend to use given-before-new ordering, (ii) this discourse effect can be largely, but not fully, attributed to the effect of discourse on referring expressions (viz. that given arguments tend to be pronominal and new ones tend to be lexical), (iii) givenness does not influence all verbs and all arguments equally. I argue that several factors are needed to explain the asymmetrical effects of givenness across verbs and arguments. These include patterns of distribution in the input, conceptual biases, and semantic and pragmatic properties of the verbs. I also evaluate several mechanisms that might drive early given-before-new ordering: those that are addressee-based, speaker-based, or experience-based. My data do not decide between these, but they do offer preliminary evidence in favor of a speaker-based account. Ultimately, my dissertation highlights the importance of approaching syntactic acquisition from several directions simultaneously. Children must learn to attend to cues from form, function, and discourse and use their limited processing capacities to integrate these cues into a larger model of language production. Linguists must do likewise.
Global hepatitis B prevention and treatment [electronic resource] : models and insights
Keywords: Management Science and Engineering

Hepatitis B (HBV) is a vaccine-preventable viral disease that, if untreated, can lead to death from liver disease in 25 percent of patients. Infection with HBV is a major global public health problem, particularly in Asian populations. In an era of limited healthcare budgets, mathematical models can be useful tools to identify cost-effective programs and to support policymakers in making informed decisions. This dissertation describes research on public health policies related to screening, vaccination, and treatment for HBV. It also describe contributions to the theoretical literature on when to stop catch-up vaccination for chronic infectious diseases. In the United States as many as 10% of Asian and Pacific Islander adults are chronically infected with HBV, and up to two thirds are unaware that they are infected. Using Markov models of infection, treatment and disease, I find that screening programs for HBV among Asian and Pacific Islander adults are likely to be cost effective and have clinically significant benefits from identifying chronically infected persons for medical management. Liver disease associated with childhood-acquired HBV is a leading cause of death among adults in China. Approximately 20% of children under age 5 years and 40% of children aged 5 to 19 years remain unprotected from HBV. Using a Markov model of infection and disease progression I find that HBV catch-up vaccination for children and adolescents in China would improve the health of the population and save costs over the long term. Although the 20th century has seen incredible development of safe and effective vaccines, many people remain susceptible to vaccine-preventable diseases. "Catch-up vaccination" for age groups beyond infancy can be an attractive and effective means of immunizing people who were missed earlier. However, as vaccination rates increase, catch-up vaccination may become less attractive. This chapter addresses the question of when to discontinue catch-up vaccination programs as immunization rates increase. I use a cost-effectiveness framework: I consider the cost per quality-adjusted life year gained of catch-up vaccination efforts, as a function of immunization rates over time and consequent disease prevalence and incidence. I illustrate the results with the example of HBV catch-up vaccination in China. I contrast results from a dynamic modeling approach with an approach that ignores the impact of vaccination on disease incidence.
Glop theory [electronic resource] : a new trope ontology
Keywords: Philosophy

The dissertation has two parts, one critical and one positive. Part One presents arguments against bare particulars, zero-dimensional material objects, extended simples, universals, and three-dimensionalist accounts of persistence over time. Part Two posits and defends a novel property—markedness (a Grounding Local Ontological Primitive, or GLOP)—that marks out certain regions of spacetime, thus furnishing a sort of binary code for fundamental ontology. Glop theory is then used to develop new accounts of property exemplification, ontological fundamentality, and persistence. What emerges is an ontology according to which material objects are four-dimensional trope bundles that need not be composed of simple parts. This result is desirable if, as Part One maintains, we should resist commitment to bare particulars, material simples, universals, and three-dimensionalism.
Growth and Characterization of Rubidium Copper Sulfide
Keywords: Physics
RuCu4S3
rubidium copper sulfide
Thesis

In this thesis I describe the synthesis and physical properties of a novel ternary compound RbCu4S3. The material is a bilayer variant of the familiar ThCr2Si2 structure (adopted, for instance, by several members of the iron-pnictide family of superconductors, including BaFe2As2 [1]). Interest in this quasi-low-dimensional compound revolves around its potential to harbor an electronic instability, for example a charge density wave. After establishing a suitable procedure to grow high quality single crystals, my ongoing experiments have probed the nature of the RbCu4S3 ground state via a combination of transport and thermodynamic measurements. The results of these experiments have been compared with band structure calculations performed using the WIEN2K software package. Additional x-ray diffraction and transmission electron microscopy (TEM) structural characterization has been performed by collaborators.
The calculated Fermi surface of RbCu4S3 reveals one three-dimensional pocket and two quasi-two-dimensional pockets with considerable potential for nesting. However, neither single crystal x-ray diffraction refinements nor high resolution TEM measurements indicate the presence of a lattice modulation in this material. The electrical resistivity is that of a good metal, with a very low residual resistivity and a correspondingly high residual resistance ratio (RRR[typical] = [rho](300K)/[rho] naught >=600). Such high quality samples permit the observation of quantum oscillatory effects in high magnetic fields, providing a direct probe of the Fermi surface morphology and the quasiparticle effective mass. Preliminary measurements of Shubnikov-de Haas oscillations in the magnetoresistance for fields oriented along the crystalline c-axis reveal several frequencies corresponding to different extremal orbits of the various Fermi surface pockets. Comparison with the calculated band structure leads to a tentative assignment for at least one of these orbits with the three-dimensional hole pocket, but additional angle-dependent measurements will be necessary to make an unambiguous comparison. Heat capacity measurements yield a Sommerfeld coefficient [gamma] = 13:1 +/- .04 mJ/mol K2, which is larger by a factor of ~ 1.6 over that estimated from our band structure calculations, presumably reflecting mass renormalization due to many-body effects. Taken together, the preponderance of the evidence suggests that RbCu4S3 does not suffer an electronic instability, although further experiments will be necessary to conclusively establish whether or not this is the case.
"Havoc of matter", détournement in the films of Debord, Rouch, Godard [electronic resource]
Keywords: Art and Art History

The dissertation addresses the significance of the practice of détournement in the films of Guy Debord, Jean Rouch, and Jean-Luc Godard. The purpose is threefold: to see détournement 1) as part of a re-conceptualization of montage after World War II; 2) as a critique of the reification of political representation during les trentes glorieuses, the so-called Golden Age of capitalism from 1950's to the 1970's; 3) as a method for the (de)construction of subjectivities. For Debord and the Situtionist International [SI], détournement was a re-conceptualization and radicalization of montage -- a method of appropriating an image, of turning it away and leading it astray from its seemingly natural, normal use. Emphasizing various contemporaneous critiques of the relation between power, knowledge, and subjection/subjectivation (especially, the critiques of Debord, Michel Foucault, Gilles Deleuze), I argue for the practice of cinematic détournement as a deconstruction of the image that not only dissociates it from its source, but also dissociates our habituated modes of perception and experience, action and reaction, of relating to the world and to oneself -- especially those modes through which one constitutes and recognizes oneself as a subject. The dissertation underscores the affective force of such dissociations, especially its implications for the struggles against subjection/subjectivation, that is, the struggles against a form of power in which procedures of subjection become ever more implicated with the processes of subjectivation. Particularly, I point to how détournement is deployed in attempts to respond to the unsettling, disjunctive encounter with the new political subjectivity of the colonized subject in France of the 1950's, 60's -- not only in relation to the struggles for decolonization (for example, the Algerian War, an especially significant example for France at this moment), but also in relation to the struggles against "the colonization of everyday life" (for example, the SI's call to address the problem of the quality of life, of "happiness, " during the period of an aggressive, at times violent, form of state-led modernization). In short, the dissertation aligns the practice of cinematic détournement with a method of analysis that seeks to deconstruct the habituated truths about one's relation to oneself and others (particularly, the psychoanalysis of Jacques Lacan and Jean Laplanche). And it addresses the significance of this method in the films of not only Debord but also his contemporaries, Rouch (cinéma-vérité) and Godard (French new wave, Dziga Vertov group) -- two of the foremost practitioners of a new mode of filmmaking that unsettles the dichotomy between documentary and fiction, objective and subjective, true and false, and poses the question of how truth is articulated, imposed, enacted upon and for whom.