VictorJuiz/thesis huggingface dataset:
Necrolife [electronic resource] : toward an ontology of the corpse in nineteenth century American culture

My purpose was to re-define the concept of the corpse in Western culture through the application of approaches to biological organization patterns particular to the natural sciences that can provide a path to re-describe the relation of self to corpse. This led me to rethink meaning of the terms "life" and life-cycle. I found forms and views of life that transcended ontological categories separating subjects and objects as well as decentering the role of the human in relation to other forms and. I chose nineteenth-century America because I identified a radically different approach to interconnection of life and death in comparison to present times. I argued that the configuration of dying has only altered in the United States within the past 150 years as opposed to other Western countries in which medicalization had been under way since the 18th century. By understanding past conceptualizations of dying, we can better examine current cultural narratives that approach this sensitive and enduring issue, one at the basis of all human experience. The project examined concrete case studies such as: the emergence of the death-care industry in nineteenth-century America; body preservation technology; the management of dying and death through popular discourses and literary genres, both fictional and non-fictional; and the rhetoric of a brand of nationalism grounded on the sacrifice of Civil War soldiers and other major casualties associated with the war.

Advisor: Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Heise Ursula K. primary advisor. Thesis advisor
Lunsford Andrea A.
The negative feelings that people want to avoid [electronic resource] : cultural differences and consequences for compassion

Previous research has documented cultural differences in the positive states that people desire. Less research, however, has examined whether cultural differences exist in the negative states that people want to avoid feeling ("avoided negative affect"). Using a multimethod approach, we examined cultural differences between Americans and Germans in avoided negative affect and whether they are related to different responses to suffering, or compassion. In Study 1, using survey methods, we assessed whether avoided negative affect differs from related constructs, and based on an existing literature, tested our hypothesis that Americans want to avoid negative affect more than do Germans. As predicted, avoided negative affect is distinct from actual negative affect (the negative states people actually feel) and from ideal negative affect (the negative states people ideally want to feel) and European Americans wanted to avoid negative states more than did Germans. In Study 2, we compared the emotional content of American and German sympathy cards to examine cultural differences in responses to suffering. As predicted, American cards contained more positive and less negative content than did German cards. In Study 3, using survey methods, we examined whether cultural differences in responses to suffering were due to cultural differences in avoided negative affect. As predicted, Americans felt less comfortable sending sympathy cards that contained primarily negative content (e.g., "words will not lighten a heavy heart") than did Germans, and these differences were mediated by cultural differences in avoided negative affect. Finally, in a series of experiments, American and German participants were randomly assigned to either "avoid negative affect" or "approach negative affect" conditions. Overall, participants in the "avoid negative affect" conditions preferred sympathy cards with negative content less than those in the "approach negative affect" conditions. These findings suggest that differences in avoided negative affect at least partially drive different responses to suffering (i.e., compassion).

Keywords: Psychology.
Advisor: Tsai Jeanne Ling primary advisor. Thesis advisor
Gross James J. (Professor of psychology) advisor. Thesis advisor
Markus Hazel Rose advisor. Thesis advisor
Negotiating Identities: Gay Catholic Men

Abstract from thesis:
While original research on identity formation located human identity growth and change in discrete (and usually early) stages, contemporary research considers human identity as growing and evolving identity throughout the life cycle. A secondary limitation of earlier research is the narrow population sample. My research uses contemporary theories of identity formation to understand an under-researched (or research-ignored) group: gay Catholic men. Identifying a group of men with two potentially competing identify factors, I ask the research question(s): What common themes exist among gay Catholic men when negotiating their identities? Specifically, what are the common themes for men located in a major US urban center? To answer this question, in 2011 I conducted an exploratory qualitative study of identity formation among 10 gay Catholic men, ages 24 to 68, in the greater New York City area, to illuminate common themes among each participant’s identity formation.
Participants of diverse backgrounds were recruited from DignityUSA for ethnographic interviews averaging one hour in length. Grounded theory practices and deductive analysis were used in this exploratory study. Findings suggest three common themes of identity negotiation and understanding centered on coming out, the institutional and pastoral Church, and acceptance within the family. These themes bring insight to challenges the participants faced when combining two distinct identities.
This is an interdisciplinary Honor Thesis in Feminist Studies and Human Biology.

Keywords: gay
Catholic
church
identity
male
qualitative
interviews
ethnography
religion
Stanford University Program in Feminist Gender and Sexuality Studies
Thesis
Advisor: Robinson Paul
Neural basis of value based decision making [electronic resource]

For many decisions, we must explicitly compare the value of two or more goods being offered. However, often decisions are not between multiple goods, but rather between a single offer and the choice to pass on that offer, such as when deciding to buy a new car, marry a significant other, or read this abstract! For these decisions the relevant comparison is between the expected benefit of the offer and its associated cost. We studied cost-benefit decisions in the macaque monkey while recording from single neurons in the orbitofrontal cortex (OFC), which has been implicated previously in decisions between competing goods. We found that the animal was sensitive to the balance of cost and benefit. That is, his willingness to accept an offer increased monotonically as we increased the benefit while keeping the cost constant. We found that the OFC represented task-relevant information—such as benefit, choice, and expected outcome—in a complex manner. These signals were mixed at the level of single neurons, but by examining the population response, we found separable ensembles of neurons that represented each of these task relevant variables. Moreover, different sets of neurons appeared to represent these signals for discrete temporal epochs within and between trials, which may correspond to distinct functional processes revealed by behavior. Taken together, we offer a novel view of how a population of neurons may collectively represent value and choice information and how that population may transform the representation dynamically over time.

Advisor: Newsome William T. primary advisor. Thesis advisor
McClelland James L. advisor. Thesis advisor
McClure Samuel M. advisor. Thesis advisor
Moore Tirin
Neuronal L-type calcium channels are regulated by FMR1 and SPOPL [electronic resource]

Voltage-gated calcium channels (VGCCs) regulate cellular excitability, differentiation and connectivity. The L-type Ca2+ channel (LTC) CaV1.2 is the most abundant VGCC in the brain, and mis-regulation of LTCs has been linked to bipolar disorder, schizophrenia and autism spectrum disorders. However, how LTC activity is regulated in vivo is incompletely understood. Here we describe a new approach using a high throughput genome-wide screen in Drosophila to identify modulators of CaV1.2 activity. This screen uncovered two novel CaV1.2 regulating proteins, Fragile X Mental Retardation 1 (FMR1) and Speckle-type POZ protein-like (SPOPL). Using biochemistry, calcium-imaging, and electrophysiology in mammalian neurons, we show that FMR1 binds directly to CaV1.2 and regulates its surface expression, while SPOPL alters ubiquitination and electrical properties of the channel. These results reveal new regulatory pathways controlling CaV1.2 activity, and describe a generalizable approach to identifying modulators of LTC function in vivo.

Keywords: Chemical and Systems Biology.
Advisor: Dolmetsch Ricardo E. primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Elias Joshua advisor. Thesis advisor
Mochly-Rosen Daria advisor. Thesis advisor
Neutron star powered nebulae [electronic resource] : a new view on pulsar wind nebulae with the Fermi Gamma-ray space telescope

Pulsars are rapidly-rotating neutron stars born out of the death of stars. A diffuse nebula is formed when particles stream from these neutron stars and interact with the ambient medium. These pulsar wind nebulae (PWNe) are visible across the electromagnetic spectrum, producing some of the most brilliant objects ever observed. The launch of the Fermi Gamma-ray Space Telescope in 2008 has offered us an unprecedented view of the cosmic gamma-ray sky. Using data from the Large Area Telescope on board Fermi, we search for new gamma-ray-emitting PWN. With these new observations, we vastly expand the number of PWN observed at these energies. We interpret the observed gamma-ray emission from these PWN in terms of a model where accelerated electrons produce gamma-rays through inverse Compton upscattering when they interact with interstellar photon fields. We conclude by studying how the observed PWN evolve with the age and spin-down power of the host pulsar.

Keywords: Physics.
Advisor: Funk Stefan
Bloom E. (Elliott)
Romani Roger W. (Roger William) advisor. Thesis advisor
A new incompressibility discretization for a hybrid particle MAC grid representation with surface tension [electronic resource]

This dissertation takes a particle based approach to incompressible free surface flow motivated by the fact that an explicit representation of the interface geometry and internal deformations gives precise feedback to an implicit solver for surface tension. Methods that enforce incompressibility directly on the particles are typically numerically inefficient compared to those that utilize a background grid. However, background grid discretizations suffer from inaccuracy near the free surface where they do not properly capture the interface geometry. Therefore, this dissertation proposes a novel incompressibility discretization which utilizes a particle based projection near the interface and a background MAC grid based projection for efficiency in the vast interior of the liquid domain -- as well as a novel method for coupling these two disparate projections together. It is shown that the overall coupled elliptic solver is second order accurate, and remains second order accurate when used in conjunction with an appropriate temporal discretization for parabolic problems. A similar second order accurate discretization is derived when the MAC grid unknowns are located on faces (as opposed to cell centers) so that Navier-Stokes viscosity can be solved for implicitly as well. Finally, this dissertation presents a fully implicit approach to surface tension that is robust enough to achieve a steady state solution in a single time step. Beyond stable implicit surface tension for the novel hybrid discretization proposed in this dissertation, preliminary results are also demonstrated for both standard front tracking and the particle level set method.

Advisor: Fedkiw Ronald P.
Levis Philip
Savarese Silvio
New rounding techniques for the design and analysis of approximation algorithms [electronic resource]

We study two of the most central classical optimization problems, namely the Traveling Salesman problems and Graph Partitioning problems and develop new approximation algorithms for them. We introduce several new techniques for rounding a fractional solution of a continuous relaxation of these problems into near optimal integral solutions. The two most notable of those are the maximum entropy rounding by sampling method and a novel use of higher eigenvectors of graphs.

Keywords: Management Science and Engineering.
Advisor: Saberi Amin primary advisor. Thesis advisor
Diaconis Persi advisor. Thesis advisor
Trevisan Luca advisor. Thesis advisor
A new system architecture for green enterprise computing [electronic resource]

Computing systems account for at least 13% of the electricity use of office buildings. This translates to about 2% of the electricity consumption of the entire US or the equivalent of the State of New Jersey! As computing becomes pervasive, making these systems more efficient is an opportunity to reduce operational costs and have a positive environmental impact. Unfortunately, current understanding of energy consumption in office buildings is limited and coarse-grained. Without better visibility into how electricity is spent and how much of it is wasted, it is difficult to find ways to reduce it. Powernet -- a multi-year power and utilization study of the computing infrastructure in the Computer Science Department at Stanford University -- begins to address the visibility problem in one building. Powernet's data is collected via a large network of plug-level wireless power meters and software sensors that cover a significant portion of the 2nd, 3rd, and 4th floors of the Gates building at Stanford. The Powernet data show that at least 25% of Gates's electricity is wasted on idle and over-provisioned devices. At the extreme, many desktops operate at near-idle for 75% of the time. The combination of high idle power and low utilization means that a large chunk of energy is wasted. This highlights an opportunity to improve on current computing systems. This dissertation presents a novel system architecture for office computing, Any- ware. To save energy, Anyware leverages two observations. First, an increase in energy use does not translate to the same increase in performance. Second, there is a range of resources one can have for a fixed power budget. Anyware's hybrid design splits workload execution between a local low-power client device and a virtual machine (VM) on a backend server. Applications that benefit from hardware optimizations, such as video and graphics, remain local; other tasks (document and picture editing, PDF viewing, etc.) are offloaded to the server. Anyware reduces the energy cost of computing by 70%--80% because the client has power draw comparable to that of a thin client or a laptop (15 to 20 watts) while the server can host multiple user VMs. Fast I/O, the availability of network resources in a LAN environment, and the increased CPU and memory on the server mean that users can get comparable performance at the fraction of the energy cost. Anyware demonstrates that with a new computing architecture, it is possible to have the best of two worlds: desktop performance at the energy costs of thin clients.

Advisor: Levis Philip primary advisor. Thesis advisor
Kozyrakis Christoforos
McKeown Nick advisor. Thesis advisor
The non-coding genome [electronic resource] : lncRNA and enhancer function in epidermal homeostasis and melanoma drug resistance

Information encoded within the ~3 billion base pairs of the human genome is processed to coordinate diverse biological functions. While ~2% of the human genome is well characterized as coding for canonical proteins, the function of the vast majority of non-coding DNA is unknown (discussed further in Chapter 1). The central aim of this thesis has been to identify functional non-coding regions of the genome and determine their role in human epidermal biology. The epidermis, or skin, maintains a tight balance between its regenerative capacity and its function as a protective tissue barrier. Progenitor cells located in the basal layer of the epidermis continually self-renew, while epidermal cells that divide and migrate outwards engage a terminal differentiation program to form a barrier. Transcriptome profiling of this differentiation process led to the identification of the long non-coding RNA (lncRNA) ANCR, which was then shown to regulate progenitor function of the epidermis (Chapter 2). A novel technology was developed to investigate the protein-binding partners of RNAs (Chapter 3), and this technique was used to uncover the functional significance of a second discovered lncRNA, TINCR, that regulates terminal differentiation of the epidermis in part by binding the protein STAU1 (Chapter 4). The most deadly cancer derived from the epidermis is malignant melanoma. While treatments targeting the mutated BRAF oncogene are initially effective against a subset of melanomas, drug resistance rapidly develops. A region of non-coding DNA was discovered that acts as a lineage-specific enhancer for the drug resistance gene, MET, and disruption of this enhancer by genome editing of < 7bp of DNA within an MITF motif can selectively block drug-induced MET expression and innate resistance to BRAF inhibition (Chapter 5). Taken together, this work demonstrates a framework for identifying functional non-coding RNA and DNA that regulate a diverse set of biological processes.

Advisor: Khavari Paul A. primary advisor. Thesis advisor
Chang Howard
Greenleaf William James advisor. Thesis advisor
Oro Anthony
Wysocka Joanna
Novel mechanisms of prevention in models of Alzheimer's disease [electronic resource]

Alzheimer's disease (AD) presents an enormous burden to society that will increase substantially in the next decades as the population ages. Because of this, it is essential to develop a more complete understanding of the underlying disease mechanisms to identify preventive and therapeutic strategies. AD is characterized by synergistic interactions among inflammation, amyloid beta (A[beta]) peptide accumulation, and neuronal network dysfunctions that contribute to eventual cognitive decline and memory loss. In the search for treatment strategies, an emerging consensus holds that preventive intervention before symptoms occur may be most effective. Multiple studies have demonstrated that chronic use of non-steroidal anti-inflammatory drugs (NSAIDs), a class of drugs that inhibit the synthesis of prostaglandins such as PGE2, prevents the onset of AD in normal aging populations. However, later administration in symptomatic AD patients is not effective in reducing cognitive decline. Moreover, the detrimental effects of NSAIDs in some contexts suggest that there is a balance between toxic and protective signaling downstream of NSAID activity. The studies presented in this dissertation aim to identify and characterize the mechanisms underlying this balance between toxicity and protection. The first study presented here investigates mechanisms that promote paradoxically protective effects of PGE2 signaling. Specifically, we find that the EP4 receptor for PGE2 drives a potent anti-inflammatory response in microglia exposed to A[beta], while at the same time promoting the clearance of A[beta] by microglia. Through genome-wide microarray analysis, we identify several novel targets of EP4 signaling that may mediate these protective effects. In a second study, we investigate the mechanism of protection by the NSAID ibuprofen in a mouse model of AD. Here, we show that ibuprofen treatment prevents the earliest memory behavior deficits in this AD model, but that it does so without altering A[beta] levels or the inflammatory response to A[beta]. Instead, another unbiased microarray study demonstrates that ibuprofen selectively reduces the expression of an enzyme involved in tryptophan catabolism, and thus increases the availability of tryptophan for serotonin production. These two studies identify promising new mechanisms in the effort to understand and ultimately prevent AD.

Advisor: Andreasson Katrin
Wyss-Coray Anton primary advisor. Thesis advisor
Palmer Theo advisor. Thesis advisor
Rando Thomas A.
On Nietzsche's historical philosophy [electronic resource]

This dissertation takes up the question of exactly why Nietzsche insisted, as he so often did in his writings, that philosophical enquiry needs to be conducted historically, an insistence that shaped Nietzsche's own turn towards the method of genealogy in his later works. The answer proposed is that in Nietzsche's view, some of our most important philosophical concepts (such as the concept of 'good') have undergone radical changes in meaning over the course of history, and yet, the past meanings of these concepts, rather than having been entirely overwritten by their present meanings, continue to have some residual semantic presence in them today. Consequently, our philosophical attempts to understand these concepts today necessarily require that we pay serious attention to their histories, which is why Nietzsche thought that our philosophical enquiries have to be conducted historically. This is the answer developed in this dissertation through an in-depth study of Nietzsche's theory of conceptual change over history, and an analysis of the practical consequences this theory of conceptual change might have for us today.

Keywords: Philosophy.
Advisor: Anderson R. Lanier primary advisor. Thesis advisor
Hills David James
Hussain Nadeem J. Z. advisor. Thesis advisor
On the variational methods for minimal submanifolds [electronic resource]

In this thesis, we study two problems concerning variational methods for minimal submanifolds. Specifically we consider min-max theory for minimal surfaces. We construct the "saddle point" type critical points for the area functional, and study the geometrical properties of these. In the first part, we consider the mapping problem for the min-max theory. In particular, we prove an existence theorem for min-max minimal surfaces of arbitrary genus g ≥ 2 by variational methods. We show that the min-max critical value for the area functional can be achieved by the bubbling limit of branched minimal surfaces with nodes of genus g together with possibly finitely many branched minimal spheres. We also prove a strong convergence theorem similar to the classical mountain pass lemma. In the second part, we consider the geometric measure theory approach to the min-max theory. We study the shape of the min-max minimal hypersurface constructed by Almgren-Pitts corresponding to the fundamental class of a Riemannian manifold (M, g) of dimension n + 1 with positive Ricci curvature and 2 ≤ n ≤ 6. We characterize the Morse index, area and multiplicity of this min-max hypersurface. Precisely, we show that the min-max hypersurface is either orientable and of index one, or is a double cover of a non-orientable minimal hypersurface with least area among all closed embedded minimal hypersurfaces.

Keywords: Mathematics.
Advisor: Schoen Richard (Richard M.) primary advisor. Thesis advisor
Brendle Simon
White Brian