VictorJuiz/thesis huggingface dataset:
From state street to Bilski [electronic resource] : patent protection in the financial industry

Abstract: In the last few years a renewed interest in the validity of patenting business methods has emerged. The issues appeared to have been settled in 1998 with the State Street decision. However, recently the Federal Circuit, following the more restrictive approach toward the patent system adopted by the Supreme Court, has questioned the soundness of the policy of extending patent protection to this type of subject matter. This new scenario occurred explicitly in In re Bilski when the Federal Circuit decided to rehear the case en banc and reconsider the conclusions previously reached in State Street. In so doing, the court significantly restricted the ability of inventors to obtain patents in certain fields. Indeed, to secure a patent on a process, it is no longer sufficient to show that an invention produces "a useful, concrete and tangible result." Now, an applicant also needs to demonstrate that her invention is either tied to a machine or transforms an article into a different state or thing. In June 2009, the Supreme Court decided to granted certiorari on In re Bilski, and the resulting decision is expected to shed light on the proper way to deal with the many questions that this case raises. Ultimately, the issues under consideration revolve around the empirical question of whether the patent system in the specific sector is "doing its job" or, in other words, whether that patent system is fostering the creation of additional business methods. To answer this question, I conducted a two parts empirical investigation of financial methods, as a subset of business methods. Specifically, I studied the innovative types of securities that emerged between 1980 and 2007. Then, I analyzed the patent applications submitted and the patents issued for different types of securities after 1998. Finally, I conducted structured interviews with market participants about the production and consumption of financial methods. The collected results indicate that after 2004 creators of new types of securities have shown less interest in the patent system. Nevertheless, the rate of innovation in this field has remained constant. The structured interviews revile that market participants are ambivalent about the benefits that both the financial market and their companies can derive from having exclusive rights on their inventions. They also provide a description of the financial market and of its dynamics that does not fit well with the patents system's mechanisms. Thus, serious doubts emerge that in the ten years between State Street and In re Bilski patent protection had any impact on innovation in the financial industry.

Keywords: Law.
Advisor: Lemley Mark A.
Bresnahan Timothy F. advisor. Thesis advisor
Cole G. Marcus advisor. Thesis advisor
Dinwoodie Graeme B. advisor. Thesis advisor
Reese R. Anthony advisor. Thesis advisor
A frozen field of dreams, science, strategy, and the Antarctic in Norway, Sweden, and the British Empire, 1912-1952 [electronic resource]

The dissertation examines how actors in Norway, Sweden, and the British Empire conceived the Antarctic as a space for science during the years 1912 to 1952. Instead of tracing a narrative of enlightenment, how science became the dominant form of activity in the Antarctic, I examine a series of episodes with particular attention to why particular kinds of science held sway within specific political, cultural, and economic contexts. Concerned more with how Antarctic science was planned and justified than how it was executed in the field, the project draws upon recent scholarship in geography and geopolitics, as well as the history of exploration. The six case studies involve an aborted Anglo-Swedish Antarctic expedition in 1912; Britain's interwar Antarctic whaling research program; debates among whaling magnates and their associates over the relationship between Antarctic science and whaling in interwar Norway; the culture of polar exploration that emerged at Cambridge (and to some extent Oxford) between the world wars; the approach to polar exploration and quantitative glaciology pioneered by the Swedish geographer Hans Ahlmann; and the complicated history of the Norwegian-British-Swedish Antarctic Expedition (1949-52). I conclude with an epilogue arguing that the rise of international science in the Antarctic during the 1950s reflected the geopolitical dynamics of the Cold War, rather than the triumph of science over politics.

Keywords: History.
Advisor: Proctor Robert
Satia Priya advisor. Thesis advisor
Schiebinger Londa L. advisor. Thesis advisor
Functional analyses of HPH1and HPH2 revealed roles in post-translational protein translocation and nutrient translocation and nutrient signaling [electronic resource]

Calcineurin is a Ca2+/calmodulin-dependent serine/threonine protein phosphatase conserved from yeast to mammals required for cell survival during environmental stress in yeast. It dephosphorylates several proteins located in different cellular compartments. Hph1 is a substrate of calcineurin that together with Hph2, its homolog, is also required for cellular adaptation to environmental stress. Hph1 and Hph2 are novel proteins of unknown function. Hph1 and Hph2 are tail-anchored integral ER-membrane proteins and have no identifiable homologs of in other organisms, except closely related yeast species. The goal of this work was to identify proteins that interact with Hph1 and Hph2 to help us identify their biological function. We show that Hph1 and Hph2 interact with the post-translational translocation machinery and are required for Vph1 stability, suggesting that they function in post-translational translocation at the ER. We have found several additional phenotypes for cells lacking HPH1 and HPH2 that overlap with the phenotypes observed for cells that have defects in vacuolar acidification. Hph1, but not Hph2, interacts with Vam6, a guanine-nucleotide-exchange factor, that regulates homotypic vacuolar fusion (through Ypt7) and TORC1 activation (through Gtr1). Interestingly, hph1[Delta] hph2[Delta] cells are resistant to rapamycin, further suggesting a role for these proteins in nutrient signaling. Structure-function analyses revealed that the coiled-coil motif is required for proper Hph1 localization and function, whereas the transmembrane domain is dispensable. This study has advanced our understanding of Hph1 and calcineurin function in regulating the cell's response to environmental stress and paves the way for a mechanistic understanding of Hph1 and Hph2 function in yeast.

Keywords: Biology.
Academic theses.
Advisor: Cyert Martha S.
Mudgett Mary Beth
Pringle John R
Simoni Robert advisor. Thesis advisor
Functional analysis of YneA, an SOS-induced inhibitor of cell division in Bacillus subtilis [electronic resource]

In both prokaryotic and eukaryotic organisms, the coordination of cell division with DNA replication, segregation, and repair is critical for ensuring that each daughter cell receives an intact copy of the genome. In Bacillus subtilis, DNA damage triggers the SOS response, which activates a host of repair pathways, as well as an inhibitor of cell division, YneA. The mechanism by which YneA inhibits cell division and the processes involved in shutting off YneA activity remain unclear. In this work, we show that YneA is induced under a variety of DNA stress conditions, including replication initiation blocks. We observed that YneA is exported, does not stably associate with the cell wall, and is rapidly proteolyzed. Our results also suggest that YneA may be active prior to signal peptide cleavage. We have isolated mutations that indicate that protein-protein interactions mediated by the transmembrane domain might be required for YneA activity. One possible YneA target may be DivIB, a divisome component that we identified in a screen for suppressors of yneA overexpression.

Keywords: Biological Sciences
Advisor: Burkholder William
Cyert Martha S.
Mudgett Mary Beth
Stearns Tim advisor. Thesis advisor
Functional trait mediation of plant-animal interactions [electronic resource] : effects of defaunation on plant functional diversity in a neotropical forest

This dissertation examines how terrestrial vertebrates, as seed dispersers, seed predators and herbivores, influence plant functional trait composition in tropical forests and thereby diversity. I conducted this work in the Barro Colorado National Monument (BCNM) in Central Panama, where a long term mammal exclosure experiment has been ongoing, and in neighboring Parque Nacional Soberanía, which together with the BCNM forms a defaunation gradient driven by hunting. Seedling communities showed shifts toward higher seed mass in response to exclosure, but no changes in leaf traits or wood density. In contrast, the sapling community did show significant shifts toward higher specific leaf area and lower leaf toughness in response to herbivore exclosure, primarily due to an increased dominance of species with those traits, and secondarily due to differences in the species present in each treatment type. Finally, I tested a model of the seed size responses to changes in mammal abundance by measuring vertebrate seed predation rates in a protected and hunted forest. I found that in Central Panama, in contrast to the model, seed mass does not correlate well with either body size of the seed predator, or vertebrate seed predation rates. This work suggests that terrestrial vertebrates play an underappreciated role in maintaining plant diversity and composition and that pan-tropical levels of unsustainable hunting may indirectly lead to losses of plant biodiversity.

Keywords: Biological Sciences
Advisor: Dirzo Rodolfo primary advisor. Thesis advisor
Ackerly David D. advisor. Thesis advisor
Vitousek Peter Morrison advisor. Thesis advisor
Functionally relevant solvation dynamics in the protein interior

Functionally relevant solvation dynamics in the protein interior Stanford University, 2010. The role of solvent in the kinetics and thermodynamics of charge transfer reactions in simple solvents is well studied. However, biologically relevant systems often involve chemical reactions not in simple aqueous environments, but within a protein interior that constitutes an organized solvent environment. The role of the protein environment during catalysis and charge transfer reactions continues to be debated. To determine the role of the protein environment during charge transfer reactions, experiments presented in this dissertation were designed to measure the time-resolved response of a protein environment to sudden electronic perturbation. Specifically, time-resolved fluorescence measurements were used to determine the solvation response of a chromophore bound in the protein interior. An unnatural amino acid containing a fluorescent side chain, aladan, was synthetically incorporated into seven sites of a small globular protein, GB1, in order to determine the degree of solvation in different regions of a single protein. In all regions, the solvation dynamics showed an ultra-fast solvation response on the subpicosecond timescale. However, in addition to the subpicosecond dynamics, buried sites also showed relatively long solvation behavior over nanoseconds. mPlum, a variant of the red-fluorescent protein DsRed, was produced by a directed evolution experiment in the Roger Tsien lab. Ultra-fast fluorescence upconversion experiments measured a solvation response in mPlum. Examining the comprehensive library of mutants generated by the directed evolution experiment identified a single hydrogen bond between glutamic acid 16 and the chromophore to be the origin of the solvation process. The possibility of localizing a solvation response to a single interaction is only possible in an organized solvent system like a protein interior. The catalytic relevance of solvation dynamics was studied with a light-driven reaction analog for isomerisation of [delta]5-3-ketosteroids in ketosteroid isomerase. The light-driven analog consists of a photoacid bound to the active site of ketosteroid isomerase. In the ground state, the photoacid electrostatically resembles the reaction intermediate. In the excited state, the photoacid resembles the starting material. The solvation response recorded from the fluorescing photoacid shows a dramatically reduced solvation capacity and slower dynamics than observed with the same fluorophore in solution. Solvation within the protein occurs on the nanosecond timescale compared to picoseconds in solution. The active site of ketosteroid isomerase does show dynamic electrostatic behavior during the simulated reaction; however, the response is among the slowest recorded. The resistance to electrostatic perturbation suggests an electrostatically preorganized environment which does not significantly reorganize during catalysis.

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Dai Hongjie
Zare Richard N. advisor. Thesis advisor
Funding innovation in young firms [electronic resource] : the case of minimally invasive surgical devices

This dissertation explores the impact of different types of investors on invention and innovation in new firms. While prior work has focused primarily on one type of investor, venture capitalists, and has investigated a few long-term outcomes such as exit events, I compare a variety of investor types and consider more immediate innovation-related goals. Drawing from agency and resource dependence theories, I develop and test hypotheses linking different investor types to invention and innovation in new firms. To do this, I construct a novel longitudinal dataset of 198 U.S.-based minimally invasive surgical device firms between 1986 and 2007. The findings indicate that investor type matters for both invention and innovation. Technology-focused investors promote invention while commercially-focused investors are more beneficial to innovation. I also find that although some investors (VCs) help innovation, other investors (the government's SBIR program) hurt it. This difference can be traced to investors' use of monitoring to tailor resources to the specific needs of new firms. These findings suggest that monitoring can be mutually beneficial to both parties as it allows investors to focus their efforts and new firms to receive needed resources at opportune times. My findings also suggest that new firms should be cautious, as there is a potential dark side to the relationships they form with investors: obtaining resources from some investors may prevent new firms from accomplishing their goals.

Keywords: Management Science and Engineering.
Advisor: Katila Riitta primary advisor. Thesis advisor
Byers Thomas (Thomas H.) advisor. Thesis advisor
Eisenhardt Kathleen M. advisor. Thesis advisor
Gamma-ray burst observations at high-energy with the Fermi large area telescope [electronic resource]

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.

Keywords: Physics
Advisor: Kamae Tuneyoshi primary advisor. Thesis advisor
Funk Stefan
Petrosian Vahe advisor. Thesis advisor
Tajima Hiroyasu advisor. Thesis advisor
Gender Bias Under Targeted Transfers: Food for Schooling in Bangladesh

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.

Keywords:  Department of Economics
Stanford Department of Economics
targeted transfers
Bangladesh
gender bias
primary education
development
Thesis
Advisor: Klenow Pete
Gender Homophily across Types of Social Networks in Rural India

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.

Keywords:  Department of Economics
Stanford Department of Economics
informal credit
gender preference
homosocial norm
social network formation
Thesis
Advisor: Jackson Matthew
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genomic stability [electronic resource]

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.

Keywords: Chemical and Systems Biology.
Advisor: Cimprich Karlene primary advisor. Thesis advisor
Meyer Tobias advisor. Thesis advisor
Wang Clifford (Clifford Lee) advisor. Thesis advisor
Wysocka Joanna