VictorJuiz/thesis huggingface dataset:
Writing in time [electronic resource] : labor and work in English poetry, 1557-1674

"Writing in Time: Labor And Work In English Poetry, 1557-1674" proposes a new literary historical and theoretical lens for understanding poetry written in English during the early modern period, based on the temporal situation of writing, or what I term "compositional temporality." I argue that the time and rate of writing form a key aspect of poets' self-conceptions and their view of literary writing as a vocation. I argue that poets represented their own circumstances of composition largely in response to two influencing factors: his or her socioeconomic situation, and self-conceptualized place within the literary tradition. I identify two major self-representational modes in this period: one of dedicated writing exemplified by temporal commitment, and the other a casual image of writing quickly and with ease associated with sprezzatura. This dissertation draws upon authorial self-representations of writing, with the understanding that this evidence is often fictional. I argue that placing such fictions of composition next to each other reveals the values motivating these statements. The Introduction provides a theoretical foundation and linguistic context for analyzing how early modern poets articulated their temporal investment in their writing, and what values these self-representations expressed. Chapter One argues that Elizabethan poets, notably Edmund Spenser, refer to the temporal circumstances of writing as a tool to bolster their economic control over their writing and promote the legitimacy of the poetic profession. Chapter Two posits that Ben Jonson distinguishes between literary "work" and "labor" to promote slow, dedicated writing, and to elevate his role as a poet. Chapter Three argues that John Milton's concern with the temporal circumstances of writing is a fundamental part of his negotiation with his literary forebears.

Keywords: English.
Advisor: Greene Roland
Orgel Stephen primary advisor. Thesis advisor
Hoxby Blair
Yndios bàrbaros [electronic resource] : nomadic archaeologies of Spanish New Mexico

This dissertation investigates the encampment practices of the Ute, Comanche, and Apache in New Mexico during the seventeenth and eighteenth centuries. This research draws on archaeological data, archival research, and collaboration with tribal representatives, in order to analyze spatial and material patterns across nomadic communities. Through a comparative analysis of Ute, Comanche, and Apache material culture I demonstrate that New Mexico was a strategic space in the formation of new mobile life-ways during the Spanish colonial period. This research offers one of the first systematic investigations of nomadic material culture in a region dominated by scholarship on Pueblo archaeology and cosmology.

Keywords: Anthropology.
Advisor: Wilcox Michael V. (Michael Vincent)
Meskell Lynn advisor. Thesis advisor
Voss Barbara L.
You are only as old as you feel [electronic resource] : the influence of subjective age on consumer behavior

This dissertation explores the impact of subjective age (how old people feel) on consumer behavior. First, I develop the construct of subjective age by exploring what it means to people, and find that it is possible to experimentally manipulate subjective age. In the first chapter of the dissertation, I find that when people are made to feel older, rather than younger, they act in more pro-social ways. In the second chapter of my dissertation, I find that when people are made to feel older, rather than younger, they display a positivity effect, which leads them to feel less regret about negative outcomes, and increases their willingness to take risks.

Keywords: Business.
Advisor: Levav Jonathan
Huang Szu-chi advisor. Thesis advisor
Wheeler S. Christian advisor. Thesis advisor
β-catenin Stabilization Promotes Proliferation and Fate Change of Cochlear Axin2+ Cells

As sensory hair cells of the mammalian ear lack regenerative capacity, improper development or the loss of these cells can lead to permanent hearing loss. The Wnt pathway plays an important role in the proliferation and differentiation of sensory cells during cochlear development. As a feedback inhibitor of the Wnt pathway, Axin2 reliably reports Wnt-responsive cells. Prior to hair cell differentiation, Axin2-expressing cells are mainly found in the periotic mesenchyme. Although the function of these cells is not well understood, we have shown in in vitro experiments that Wnt agonists and antagonists can regulate the proliferative capacity of Axin2-expressing cells from the late embryonic period. Furthermore, lineage tracing experiments suggest that Axin2-expressing cells can act as precursors to sensory hair cells and adjacent supporting cells. Currently, the biological relevance of these cells and the mechanisms through which they may contribute to cochlear development are unknown. We used transgenic mice to stabilize beta-catenin by deleting exon3, which codes the region important for its degradation, thus augmenting Wnt signaling in Axin2-expressing cells prior to hair cell differentiation. The effects of this manipulation were characterized using markers of proliferation, epithelial cells, mesenchymal cells, hair cells, and supporting cells on whole mounts and cryosections of cochlear tissues obtained one week after activation. Beta-catenin stabilization leads to the formation of proliferative foci in the cochlear duct, with a low but significant percentage of cells displaying markers of cochlear sensory epithelial cells.
These results demonstrate that Axin2-expressing cells can proliferate in response to beta-catenin stabilization and may act as precursors to cochlear ductal cells during cochlear development. This work increases our understanding of the roles of Wnt signaling during cochlear development and will be important in progress towards hair cell regeneration.

Keywords:  Department of Biology
Biology
cochlea
development
Wnt signaling
beta-catenin
Axin2
Department of Otolaryngology Head and Neck Surgery School of Medicine
Thesis
Advisor: Cheng Alan
Bergmann Dominique
A Functional Investigation of the Frequently Mutated Splicing Factor U2AF1 in Non-Small Cell Lung Cancer

RNA splicing is a critical step in manufacturing most human proteins. Regulating the splicing machinery is crucial for normal development, and aberrant splicing can result in diseases such as cancer. Recent studies have uncovered a recurrent mutation of the splicing factor U2AF1 in several human cancers including lung cancer. The lung cancer cell line HCC78 is the only cancer cell line known to harbor this mutation, and it also has a gene fusion involving the ROS1 gene that genetically separates it from other types of lung cancer. This study sets out to both examine splicing effects of the mutated U2AF1 in lung cancer and to clarify the relationship between mutant U2AF1 and the ROS1-fusion, two rare genetic alterations that have been observed to occur together in lung cancers at a significantly higher than expected frequency. Specifically, by genomically editing the HCC78 cell line and repairing the U2AF1 point mutation, an appropriate point of comparison has been created using transcription activator-like effector nucleases (TALENs). Use of TALENs allows for targeting sequence-specific locations in the genome for double-stranded breaks. Taking advantage of endogenous DNA repair machinery, a designed sequence has been inserted into the genome of these HCC78 cells to repair the U2AF1 point mutation.

Keywords: Bioengineering
U2AF1
NSCLC
lung
cancer
splicing
spliceosome
U2AF35
Thesis
Advisor: Diehn Maximilian
A genetic screen to identify novel regulators of adult stem cell maintenance

Adult stem cells are an important class of cells responsible for the maintenance and regeneration of the body’s many tissues. These cells are under heavy investigation for potential therapeutic roles. However, one of the rate limiting steps is an understanding of the exact mechanisms and genes that regulate this class of cells. To better understand the genetic program regulating adult stem cells, a forward genetic screen was utilized involving a two-stage screening process comprising a Flp/FRT primary screen and an EGUF/hid secondary screen . Out of 3,118 mutant males produced, 1,041 were recovered, of which 412 showed loss of germ line clones and one showed overproliferation of germline clones in the primary screen. Of the 412 germ cell loss mutations, 59 passed through a secondary screen for cell lethality (EGUF/hid). 6 mutant strains have been partially or completely mapped, uncovering germ cell loss mutations in DNA Replication-Related Element Factor (DREF), Apoptosis Inducing Factor (AIF), Guanylyl Cyclase 32E (Gyc32E) and two other loci, as well as a germ cell overproliferation mutation in Star. Further research on DREF has shown that the allele we uncovered genetically separates DREF’s role in cell division and DNA-replication from its role in adult stem cell maintenance. Furthermore, I have uncovered a novel antagonistic interaction between DREF and members of the NuRD complex that is essential for the regulation of germline stem cell maintenance. These results suggest that our understanding of the genetic program of adult stem cells can still be enriched by well-designed, classic genetic screens.

Keywords:  Department of Biology
Adult Stem Cells
DREF
Biology
Genetics
Developmental Biology
Stem Cells
Stanford University
Genetic Screen
Thesis
Advisor: Fuller Margaret
Nelson W James
A Rapid and Simple Method for DNA Engineering using Cycled Ligation Assembly

DNA assembly techniques have developed rapidly, enabling efficient construction of complex constructs that would be prohibitively difficult using traditional restriction-digest based methods. Most of the recent methods for assembling multiple DNA fragments in vitro suffer from high costs, complex set-ups, and diminishing efficiency when used for more than a few DNA segments. Here I present a cycled ligation-based DNA assembly protocol that is simple, cheap, efficient, and powerful. The method employs a thermostable ligase and short Scaffold Oligonucleotide Connectors (SOCs) that are homologous to the ends and beginnings of two adjacent DNA sequences. These SOCs direct an exponential increase in the amount of correctly assembled product during a reaction that cycles between denaturing and annealing/ligating temperatures. Products of early cycles serve as templates for later cycles, allowing the assembly of many sequences in a single reaction. In tests I directed the assembly of twelve inserts, in one reaction, into a transformable plasmid. All the joints were precise, and assembly was scarless in the sense that no nucleotides were added or missing at junctions. I applied cycled ligation assembly to construct chimeric proteins, revealing functional roles for individual domains of the Hedgehog signaling pathway protein PTCH1. Simple, efficient, and low-cost cycled ligation assemblies will facilitate wider use of complex genetic constructs in biomedical research.

Keywords:  Department of Biology
Biology
Synthetic Biology
Genetic Engineering
Cycled Ligation
DNA Assembly
Thesis
Advisor: Scott Matthew
Nelson James
A Survey for Hα Pulsar Bow Shocks

Hα emitting pulsar wind bow shock nebulae are rare and beautiful objects whose study has the potential to provide insights into the nature of relativistic shocks, pulsar emission, and the composition of the ISM. We report the results of a large Hα survey of 100 Fermi pulsars to characterize the distribution of Hα pulsar bow shocks, constituting the largest and most sensitive such survey yet undertaken. By reobserving previously known Balmer shocks, we confirm the excellent sensitive of our observations and reveal additional Hα structure not previously documented around PSRs J0742-2822 and J2124-3358. Our survey discovered three additional Hα shocks of interesting morphology around PSRs J1741-2054 (already discussed in a previous publication), J2030+4415, and J1509-5850. Despite our excellent sensitivity, fully 94 of our targets have no convincing evidence of an Hα shock. We develop a novel method to characterize the sensitivity of our imaging for all frames as a function of bow shock angular size that accounts for the essential role played by the characteristic bow shock shape in aiding detections. Combining these measurements with a standard model of the ISM and the expected Hα flux of a bow shock apex, we conclude that the number of confirmed detections around all Fermi pulsars is in reasonable agreement with our model. Our results are inconsistent with a model of the ISM that predicts a significantly larger fraction of neutral material in the ISM, and our data may provide a spot-sample constraint of HI.

Keywords:  Department of Physics
Hα wind nebulae
Fermi pulsars
J1509-5850
J0742-2822
J2030+4415
J1741-2054
H-alpha wind nebulae
H alpha wind nebulae
Thesis
Advisor: Romani Roger
Allen Steve
Ablation of Quiescent Neural Stem Cells for Evaluation of Subsequent Repopulation

Recent work has established disruption of neurogenesis as a key cause of cognitive decline after use of brain irradiation to treat primary and metastatic tumors in children. Yet though this is widely accepted, little is known about the possibilities of restoration of normal neural stem cell (NSC) function after such a treatment, either through stem cell transplant or by promoting endogenous recovery by enhancing trophic effects. It is yet to be discovered whether endogenous quiescent neural stem cells (qNSCs) that are present in the irradiated brain have the potential to repopulate an injured neurogenic niche or whether resident stem cells are themselves damaged and are unable to repopulate the niche. It is also possible that a niche occupied by defective stem cells may simply block undamaged cells from occupying the niche. In this case, it may be necessary to ablate cells to create space for engraftment. Whereas most prior research has focused on solely anti-mitotic methods that spare rarely dividing quiescent NSCs, this research analyzes effective ablation of neural stem cells, including quiescent NSCs, in the dentate gyrus of the subgranular zone through the use of diphtheria toxin receptor-mediated cell death. My hypothesis was that partial ablation would show that qNSCs could repopulate the affected niche over time. After ablation treatment, it was observed that the number of nestin+ cells in the dentate gyrus (DG) was drastically reduced, and remained that way following a two-month recovery period. Along with this lack of renewal was partial ablation of neurogenesis in the olfactory bulb, evaluated by quantification of IdU+/CldU+ cells two months after ablation treatment. The data shown here provide new insight into the response of the neurogenic niche and surviving cells to effective ablation of local NSCs. This will potentially have a great impact on further research to be done regarding recovery procedures for irradiation-treated children.

Keywords:  Department of Biology
biology
neurosurgery
stem cells
quiescent
ablation
Thesis
Advisor: Palmer Theo
Jones Patricia
Acquisition of 3D knee morphology under weight-bearing conditions using a C-arm CT scanner for the assessment of knee disorders [electronic resource]

A C-arm-based cone-beam computed tomography (CBCT) scanner with a digital flat-panel detector represents a promising imaging system for the evaluation of static 3D joint positions and orientations and cartilage bone stress in vivo under weight-bearing conditions. The C-arm system provides high-resolution (150 [mu] m isotropic) 3D volume images (i.e., a stack of slices) with superior bone contrast and highly flexible trajectories for image acquisition, and has short image acquisition times. With the use of contrast agents in CBCT imaging, accurate visualization of soft tissue structures, including the meniscus and articular cartilage, is possible. In the first part of this dissertation, new technologies that enable weight-bearing imaging using a C-arm CT system are described. First, verification of system trajectory reproducibility in the new horizontal gantry trajectory (i.e., with the axis of rotation perpendicular to the floor) is demonstrated. Image quality of static objects imaged using the new geometry is presented. Second, the impact of limited dynamic range of the detector on image quality is discussed, and a solution to overcome the limitation is provided. Finally, during imaging of a human subject in vivo in weight-bearing positions, involuntary and non-reproducible motion is significant over the 10-20s scan. This motion renders the 3D images non-diagnostic. Three new approaches to correct for knee motion have been developed, and final image quality in in vivo images of volunteers is presented. In the second part of this dissertation, the use of C-arm CT as a diagnostic tool for joint disorders such as patellofemoral pain syndrome, and knee osteoarthritis is described. Workflow for image acquisition and analysis for successful measurement of 3D patellofemoral tracking and for in vivo time-dependent cartilage deformation under full weight-bearing conditions is demonstrated.

Keywords: Mechanical Engineering.
Advisor: Fahrig Rebecca primary advisor. Thesis advisor
Delp Scott advisor. Thesis advisor
Pelc Norbert J. advisor. Thesis advisor
Adaptation and acclimation to temperature in a globally invasive species, Carcinus maenas [electronic resource]

Temperature plays a vital role in shaping species' biology and biogeography, but the response of marine species to changes in temperature is still poorly understood over time scales relevant to climate change. In this thesis, I use a single species as a case study to explore acclimation and adaptation to temperature at the levels of gene sequence, gene expression, and whole-animal physiology. My study species is the European green crab, Carcinus maenas, a globally invasive temperate species that thrives across a wide range of environmental temperatures. By comparing an invasive species across seven populations in its native and invasive range, I was able to explore both short-term (invasive range) and long-term (native range) impacts of environmental temperature. To lay the groundwork for this project, I first review the literature on adaptation in marine invasive species. While quantitative research strongly suggests a role for adaptation, the dearth of integrated genetic-quantitative work severely limits our understanding of this process. The rest of this thesis attempts to fill this gap with empirical research. First, I describe the thermal physiology of green crabs in detail, and find that green crabs have high inherent eurythermality and acclimatory plasticity. Despite this thermal flexibility, I also observed potentially adaptive differentiation among populations, particularly within the native range. Population genetics supported a role for significant local adaptation between populations in the species' native range. I identified a number of specific genes likely involved in long-term adaptation between northern and southern native range populations, suggesting that innate immunity and muscle function may be under selection. These data also suggested a more limited role for ongoing, rapid adaptation in the species' invasive range. Patterns of gene expression integrate neatly with the genetic and physiological data, and I identified two groups of co-expressed genes whose expression appears related to adaptive differences in intraspecific physiology. Taken together, this project provides detailed, integrative evidence for the importance of acclimatory plasticity and both short- and long-term adaptation in success across a wide range of thermal environments in a high gene flow species. Finally, I discuss the broader implications of this work to species persistence in a rapidly changing ocean.

Keywords: Biology.
Advisor: Palumbi Stephen R.
Fraser Hunter B. advisor. Thesis advisor
Hadly Elizabeth Anne
Somero George N. advisor. Thesis advisor
Adhesion and debonding kinetics in inverted polymer solar cells [electronic resource]

Organic photovoltaic (OPV) devices using materials compatible with flexible plastic substrates, have reached over 10 % power conversion efficiency, one of the critical milestones for market penetration. However, organic materials are often mechanically fragile compared to their inorganic counterparts, and devices containing these materials have a higher tendency for adhesive and cohesive failure. Using a thin-film adhesion technique that enables us to precisely measure the energy required to separate adjacent layers, weak interfaces in OPV devices were identified. For example, the interface of the P3HT:PCBM and PEDOT:PSS in a polymer solar cell with the inverted device architecture has an adhesive value of only ~1.5 to 2 J/m2. Such poor adhesion between adjacent thin-films can contribute to low processing yield and poor long-term reliability. Several strategies to improve the adhesion are proposed and quantified in this work, including chemical and thermal treatments. Pre and post electrode deposition thermal annealing can be used to tune interfacial and film parameters, such as interface chemistry, bonding and morphology to improve the adhesion. Post annealing effectively improved the adhesion at the P3HT:PCBM/PEDOT:PSS interface. Using near edge X-ray absorption fine structure (NEXAFS), we precisely quantified the interfacial composition and P3HT orientation at the delaminated surfaces and correlated the increase in adhesion to changes in the interfacial structure. The structural and chemical reorganizations are correlated with the glass transition and crystallization temperatures of the materials used in the structure and thus the conclusion can be generalized to other materials systems. Understanding the interlayer adhesion and developing strategies to improve the adhesion of OPV materials is essential to improve the overall mechanical integrity and yield general guidelines for the design and processing of reliable OPV devices. We also demonstrate how moisture and temperature accelerate debond propagation at mechanical stresses well below those required for critical failure. Understanding such debonding kinetics is critical for device reliability and lifetime. When environmental species are introduced, the bulk layers and other interfaces in the OPV structure become more susceptible to debonding. The cohesion of the PEDOT:PSS layer is significantly influenced by moisture along with temperature and mechanical loads. Elucidating the kinetic mechanisms using atomistic bond rupture models supports that decohesion is facilitated by a chemical reaction between water molecules from the environment and strained hydrogen bonds. This extensive series of quantitative analysis provides the impact of the different environmental species and most importantly their synergies, leading us to an in-depth understanding of the debonding mechanisms.

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.) primary advisor. Thesis advisor
McGehee Michael
Salleo Alberto