VictorJuiz/thesis huggingface dataset:
What limits a stalled Argentine ant invasion? Effects of human-caused disturbance and resistance from a native ant [electronic resource]

When exotic species invade natural environments, they often cause destruction to native biological communities. In order to conserve native species, it is useful to understand what limits the extent of invasions. It is even more desirable to be able to predict where invasions will and will not occur. In this dissertation, I investigate the limits of an invasion at Jasper Ridge Biological Preserve by the Argentine ant (Linepithema humile). This invasion has been tracked since 1993 through twice-yearly ant surveys. Since 2001, the invasion appears to have stopped, and the interior of the preserve remains uninvaded. I observed how Argentine ants and native ants, particularly the native winter ant (Prenolepis imparis) responded to one another and to habitat, climate, and seasonal factors. At a small scale, weekly changes in Argentine ant presence within a few hundred square meters is limited by winter ant presence and microclimate effects. At the large scale of a whole natural area, the long-term spatial extent of Argentine ant invasion is closely tied to developed areas. Examining seasonal changes in Argentine ant and winter ant distribution on a hectare scale, it is evident that Argentine and winter ants affect one another differently in different habitats, and that Argentine ants have a stronger negative effect in sites closer to development.

Keywords: Biological Sciences.
Advisor: Gordon Deborah (Film producer) primary advisor. Thesis advisor
Dirzo Rodolfo advisor. Thesis advisor
Tuljapurkar Shripad
"The whole earth is our hospital" [electronic resource] : contemporary fictions of eco-sickness

This study defines an emerging narrative mode—what I term "eco-sickness fiction"—and argues that pervasive sickness is a crucial organizing concept of contemporary environmental literature. My readings establish in particular that sickness is a key trope by means of which American fiction figures how individual bodies and global processes of environmental change interrelate. I identify the definition of sickness that emerges from novels and memoirs of the 1990s and early 2000s: it is pervasive and non-causal; it crosses systems; and it joins the social, environmental, and biomedical. This definition is keyed to three developments unique to the late 20th and early 21st centuries: the medicalization of the subject and of space, environmental collapse, and the advance of biotechnologies that raise new ethical dilemmas. I argue that, in imagining sickness in this context, recent narratives offer ways of thinking about the intersection of culture and science in an age of technoscience. In particular, they mobilize various affects to understand the imbrication of humans in their surroundings. This dissertation theorizes these affects of eco-sickness fiction—from wonder and anxiety, to disgust and discord—as mediating awareness of biological change and ethical responses to it. Close analysis of texts by David Foster Wallace, Richard Powers, Leslie Marmon Silko, and AIDS memoirists Jan Zita Grover and David Wojnarowicz reveals the workings of affect. I demonstrate how these writers' narrative strategies elicit feelings that inform responses to environmental and medical issues. This project thus provides an account of how literature molds awareness of and investment and intervention in somatic and ecological dysfunction. In this respect, this dissertation reorients accounts of contemporary literary history. Eco-sickness fiction is continuous with but also diverges from the aesthetic dominant of its time: postmodernism. Consistent with this cultural and theoretical movement, these works diagnose the complexities of etiology and the ubiquity of disorder. Yet they diverge from this paradigm in that they refuse the postmodern ideal of detachment. I show how this literature seeks to recover ethical responsibility and therefore places guarded faith in action and accountability. This project also establishes a framework for the literary analysis of sickness, one that interleaves environmental criticism, social and cultural theories of the body and science, and accounts of affect. Furthermore, it exposes how environmental and biomedical dilemmas generate representational dilemmas that the techniques of postmodernism, realism, or environmental writing alone cannot neatly resolve.

Advisor: Heise Ursula K. primary advisor. Thesis advisor
Jenkins Nicholas (Nicholas Richard)
Jones Gavin Roger
Palumbo-Liu David advisor. Thesis advisor
Winner’s Curse and the Competitive Effect: Measuring Competition in the Viatical Settlement Market

This paper attempts to develop a methodology for measuring competition in markets where the object for sale has a common but unknown monetary value. We do this by conceptualizing transactions in the viatical settlement market as first-price, common value auctions and deriving a parametric model for equilibrium bid functions. Within this model, we then estimate parameters and make observations about bidder behavior. Our analysis finds on average, fewer than five bidders compete for viatical contracts. We believe this is strong evidence of market power. Finally, by simulating comparative statics on the distribution of number of bidders, we conclude that at our estimated levels of competition, any evidence of winner’s curse was completely dominated by the competitive effect.

Keywords:  Department of Economics
Stanford Department of Economics
winner’s curse
viatical settlement
competitive effect
common value auction
life insurance
Thesis
Advisor: Bhattacharya Jayanta
Wireless mesh networks [electronic resource] : protocol design and performance evaluation

With the increasing interest in multi-hop wireless communications networks, wireless mesh networks (WMNs) have emerged as an affordable and scalable solution to provide broadband packet data communications across wide geographic areas. However, due to the prohibitive complexity of analysis and simulations, studies on WMNs for large-scale applications have often oversimplified the physical and/or networking models. In this thesis, based on more realistic physical and networking models, we study the performance of large-scale WMNs that serve as access networks over large geographic areas. First, we create a new set of medium access control (MAC) protocols that incorporate such models. The protocols are designed within a time division multiple access (TDMA) and time division duplex (TDD) framework. Utilizing separate resources for control and data packets, the protocols provide mechanisms for network entities to explicitly cooperate among themselves for resource allocation in a fully distributed and adaptive manner. We also develop a large WMN simulator that implements the protocols and supports measurement-based models for radio propagation and interference calculation for a large built-in urban area. The simulator also captures the stochastic network behavior resulting from random traffic arrivals, admission control, and queueing. The enormous size and computational complexity of the simulator is addressed using a parallel-processing simulation technique that utilizes multiple processors interconnected with high-speed links and associated with large high-speed memory. Through extensive simulations incorporating such details, the performance of the WMNs is assessed under various simulation scenarios. First, it is demonstrated that an effective admission and congestion control (ACC) policy is critical to support stable user throughput under heavy traffic loads, and one of the ACC policies created in the thesis is shown to stabilize the network even under heavy traffic loads. Then, the scalability of the WMNs is investigated under different scenarios of network topology and routing metrics. The scalability behavior of several fundamental performance metrics is examined including the network throughput, per-session throughput, and blocking and dropping rates. Major factors are identified across the physical, MAC and routing layers that affect the scalability behavior, and the factors are shown to interact with one another in a complicated manner to determine the network performance. With more backbone support to the network, the network throughput and per-session throughput are shown to improve significantly, and the improvement is explained based on the aforementioned interactions across the layers of the network. The overall network performance is shown for two different routing metrics.

Keywords: Electrical Engineering
Advisor: Cox Donald C. primary advisor. Thesis advisor
Cioffi John M. advisor. Thesis advisor
Tobagi Fouad A.
Wolves in sheep's clothing [electronic resource] : understanding modern state-building (and counterinsurgency)

Since the end of the Cold War, the international community has become intimately involved in trying to strengthen weak and failed states. External actors, both multilaterally and unilaterally, have intervened in Europe, Asia, and Africa to bring internally conflicted parties together and to change the domestic authority structures of these countries. This dissertation explains how external actors can successfully contribute to the development of domestic authority structures in conflict-torn or post-conflict countries. Conventional state-building theories follow the Weberian conception of the modern state as an entity that maintains a monopoly over the legitimate use of violent coercion. Further, standard approaches to ending civil conflict recommend the use of population-centric strategies to achieve stability. These prevailing assumptions are problematic as they ignore a credible commitment problem that exists in conflict-torn societies: elites within the government and opposition have no incentive to disarm due to the rational fear that once they do so they will be taken advantage of by the opposing elites. This dissertation proposes a theory of self-enforcing stability to explain, from a rational-choice perspective, how it is possible to overcome this credible commitment problem. The theory contains four testable hypotheses. The first hypothesis is that an elite-centric, rather than population-centric, strategy will lead to greater success in establishing stability in conflict-torn states. Second, external actors contribute to the establishment of stability more successfully when they help nations establish limited access orders created by elite pacts rather than encouraging the creation of liberal democracies, or open access orders. Third, external actors must help internal actors overcome their underlying credible commitment problems by guaranteeing elite pacts. The final hypothesis is that the decentralization, or oligopolization, of violent means and rent-seeking opportunities balances power amongst elites, ensuring that competing elite groups can protect themselves from one another without threatening each other with overwhelming force. This dissertation finds support for the proposed theory's hypotheses in its examination of two cases: the Malayan Emergency from 1948-1960, and the stabilization effort in Iraq between 2006-2008, which includes the "Awakening Movement" and the "Surge. Both cases demonstrate how an external actor can contribute to developing enduring stability in conflict-torn societies by breaking from the standard Weberian conception of the state and population-centric focus. This dissertation concludes with a discussion of policy implications, based on the dissertation's findings, for current state-building efforts in Afghanistan.

Keywords: Political Science.
Advisor: Krasner Stephen D.
Fukuyama Francis advisor. Thesis advisor
Weingast Barry R. advisor. Thesis advisor
World War I and the remaking of Jewish Vilna, 1914-1918 [electronic resource]

This study argues for the importance of World War I in the history of Jewish life in Russia and Eastern Europe through an analysis of Jewish politics, society, and culture in the city of Vilna/Vilnius from 1914 to 1918.

Keywords: History.
Advisor: Zipperstein Steven J.
Naimark Norman M. advisor. Thesis advisor
Rodrigue Aron advisor. Thesis advisor
Writing lessons [electronic resource] : case studies of beginning teachers

This longitudinal, comparative case study of two large teacher preparation programs investigates how elementary teachers learn to teach writing. I follow nine teachers through their preservice preparation and first year of teaching. Using a cultural-historical activity theory framework (Engeström, 2001), I analyze settings for learning to teach writing in order to illuminate the features within and across settings that support or constrain learning. At the end of the preservice year, differences in teacher learning between cohorts were due to the degree of alignment between the methods course and the field placement and to the quality of instruction in the methods course. Importantly, I found that teachers in the stronger preparation program developed a cohesive set of tools, or conceptual framework for writing instruction, while graduates of the weaker program had a very limited repertoire of tools for teaching writing. This framework remained stable through the first year and guided teachers' decision-making. However, graduates from both programs needed more support in learning to teach writing across the grades and in acquiring the subject-matter knowledge needed to teach writing. Teachers entered the field with a tenuous grasp on how to teach writing, and their teaching quality in the first year depended largely on school and district support. Teachers who had focused grade-level and school/district support fared better than teachers who worked in settings that were unsupportive or settings that were supportive but unfocused. Writing curriculum played a significant role in many teachers' practices, regardless of other supports. Curricular materials varied in terms of the features of practice that were highlighted and the degree to which these features were explained. These differences afforded different opportunities for learning. Directions for future research and implications and for teacher education, administration, policy, and curriculum are discussed.

Keywords: Education.
Advisor: Grossman Pamela L. (Pamela Lynn)
Borko Hilda advisor. Thesis advisor
Juel Connie advisor. Thesis advisor
Murata Aki advisor. Thesis advisor
The X-ray power density spectrum of the seyfert 2 galaxy NGC 4945 [electronic resource] : analysis and application of the method of light curve simulations

The study of the power density spectrum (PDS) of fluctuations in the X-ray flux from active galactic nuclei (AGN) complements spectral studies in giving us a view into the processes operating in accreting compact objects. An important line of investigation is the comparison of the PDS from AGN with those from galactic black hole binaries; a related area of focus is the scaling relation between time scales for the variability and the black hole mass. The PDS of AGN is traditionally modeled using segments of power laws joined together at so-called break frequencies; associations of the break time scales, i.e., the inverses of the break frequencies, with time scales of physical processes thought to operate in these sources are then sought. I analyze the Method of Light Curve Simulations that is commonly used to characterize the PDS in AGN with a view to making the method as sensitive as possible to the shape of the PDS. I identify several weaknesses in the current implementation of the method and propose alternatives that can substitute for some of the key steps in the method. I focus on the complications introduced by uneven sampling in the light curve, the development of a fit statistic that is better matched to the distributions of power in the PDS, and the statistical evaluation of the fit between the observed data and the model for the PDS. Using archival data on one AGN, NGC 3516, I validate my changes against previously reported results. I also report new results on the PDS in NGC 4945, a Seyfert 2 galaxy with a well-determined black hole mass. This source provides an opportunity to investigate whether the PDS of Seyfert 1 and Seyfert 2 galaxies differ. It is also an attractive object for placement on the black hole mass-break time scale relation. Unfortunately, with the available data on NGC 4945, significant uncertainties on the break frequency in its PDS remain.

Keywords: Physics
Advisor: Kamae Tuneyoshi primary advisor. Thesis advisor
Madejski Grzegorz
Wagoner Robert V.
Algorithms for analysis of multiple biological sequences [electronic resource] : theory and practice

Availability of massive amounts of genomic data from hundreds of species has introduced many challenging computational problems as well as the need for efficient algorithmic tools that leverage multiple species information to facilitate biological analysis. This dissertation discusses two such problems: noncoding RNA multiple structural alignment and constrained element detection. Noncoding RNA genes (ncRNAs) are regions of the genome that are transcribed but not translated into protein, and fold directly into secondary and tertiary structures which can have a variety of important biological functions. Because their function depends closely on the secondary structure, ncRNAs often do not exhibit enough primary sequence conservation to be properly aligned using standard sequence-based methods. I therefore consider the problem of RNA multiple structural alignment, i.e., performing sequence alignment and secondary structure prediction simultaneously. In the first part of this dissertation I introduce a novel graph theoretic framework for analyzing this problem and prove that when the number of sequences is not fixed it is NP-complete. I also provide a polynomial time algorithm that approximates the optimal solution to within a factor of O(log^2 n). Constrained elements are regions of the human genome exhibiting evidence of purifying selection and therefore biological function. Computational identification of such elements is one of the major goals of comparative genomics. In the second part of this dissertation I present GERP++, a new tool for efficient constrained element detection that significantly improves on one of the current leading methods, GERP. While retaining GERP's biological transparency and metric for quantifying position-specific constraint, GERP++ uses a more rigorous method for computing evolutionary rates and a novel algorithm for element identification that uses statistical significance directly to evaluate and rank candidate elements. These algorithmic improvements decrease the running time by several orders of magnitude in practice, enabling high-throughput analysis of large data sets. Furthermore, I present analysis and biological interpretation of constrained elements identified by GERP++ in the human genome from recently available multiple species alignments.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Dill David L. advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Anger in the workplace [electronic resource] : effects of gender and frequency in context on social and job-related outcomes

This dissertation explored expression of anger in the workplace through two experiments that varied in terms of the gender of the person expressing the anger, the frequency of the anger, and the object of the anger. Subjects reviewed resumes and performance reviews that they were told belonged to two consultants competing for the same promotion. Consultants who were said to express anger frequently were less likely to be promoted than neutral consultants. They also suffered social consequences, like being rated as less pleasant. Consultants who expressed anger a single time suffered social consequences (albeit less severe than those experienced by the frequently angry individuals) compared to neutral consultants, but their promotional outcomes were less affected. When respondents were given the option to promote both the neutral consultant and the angry consultant, most subjects chose to do so. The Study 1 results were based on an undirected expression of anger; Study 2 respondents were told that the anger was directed at a subordinate. A single instance of directed anger was more damaging to social and promotional outcomes than a single instance of undirected anger. Few gender effects were observed in either study, and the gender effects that were observed tended to favor females.

Keywords: Sociology.
Advisor: Ridgeway Cecilia L. primary advisor. Thesis advisor
Cook Karen S. advisor. Thesis advisor
Nie Norman H. advisor. Thesis advisor
Are Bad Times Good for the Internet? An Empirical Analysis of the Shift to Internet Advertising During Recessions

Internet advertising has several distinct benefits over more traditional advertising media such as television and newspapers. These include increased flexibility, cost effectiveness, targeting, and measurability. Given these advantages, it seems that internet advertising is ideally suited for times when budgets are constrained, and any marketing initiatives need to be strongly justified. This study explores whether there is a shift in the allocation of advertising expenditure towards online media as a result of recessions. A first step investigates whether the growth in internet advertising can be explained by the growth in sales in the field most closely tied to the medium: e-commerce. Next, the empirical results show that e-commerce does serve as a good baseline for explaining the growth in internet advertising, but that there is a separate, significant, and positive effect of the recession on internet advertising, both in dollar and share terms. A comparison to TV advertising expenditures shows that TV advertising does not exhibit similar behavior.

Keywords:  Department of Economics
Stanford Department of Economics
advertising expenditure
online advertising
business cycles
internet advertising
recessions
e-commerce
Thesis
Advisor: Hanson Ward