VictorJuiz/thesis huggingface dataset:
Searching for genomic events contributing to brain expansion in the human lineage [electronic resource]

Understanding the genetic changes responsible for the evolution of human traits is a major goal of biology. One of the most distinctive human traits is the dramatic expansion of the forebrain that has occurred over the last six million years. Whole genome sequencing projects have identified millions of genomic differences that separate human and chimpanzee (Chimpanzee Sequencing and Analysis Consortium, 2005). However, connecting particular mutations to evolved human traits such as brain size remains challenging due to the vast number of mutations that have accumulated (Varki and Altheide 2005; Sikela, 2006). Nonetheless, recent evolutionary genetic studies are identifying the most prevalent types of genetic mechanisms contributing to evolved traits in natural populations, and studies of comparative and molecular development are providing an emerging picture for mechanisms by which human brain expansion could have occurred. By combining insights from evolutionary genetics and developmental neurobiology, this thesis aims to identify genomic differences that are particularly likely to have contributed to the evolutionary expansion of the human brain. First, this thesis provides evidence for the role of cis-regulatory mutations in the evolution of natural populations of stickleback fish. Next, this thesis describes a genomic screen we conducted identifying 510 deletions likely to remove cis-regulatory enhancers from the human genome. One of these deletions removes a developmental ventral forebrain enhancer near the tumor suppressor gene GADD45g, the loss of which may release a brake on cell division in particular regions of the brain during neurogenesis. A second deletion removes a developmental dorsolateral neocortex enhancer demonstrating the specificity by which evolution can affect particular regions of the brain. Finally, this thesis identifies a human enhancer near the gene BDNF that drives expression in the nail bed of the digit tips and the stomach, and could influence the distribution and function of mechanoreceptors.

Keywords: Neurosciences.
Advisor: Kingsley David M. (David Mark) primary advisor. Thesis advisor
Fernald Russell D. advisor. Thesis advisor
McConnell Susan K. advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Searching for structured interactions in and between datasets [electronic resource]

This dissertation considers two problems related to finding structured interactions in and between datasets. The first problem is to estimate interaction terms in a regression where the interaction coefficients are assumed to have a particular low-rank structure. The second problem is to identify relationships between datasets using extensions of recent work on regularized canonical correlation analysis. We propose methodologies and computational strategies based on regularized regression techniques that are well-suited to modern datasets where the number of features may be much larger than the number of observations. The final chapter provides a theoretical result on the performance of a low-rank interaction estimation procedure that motivates its use in large-scale problems.

Keywords: Statistics
Advisor: Taylor Jonathan E. primary advisor. Thesis advisor
Hastie Trevor advisor. Thesis advisor
Walther Guenther advisor. Thesis advisor
Security and privacy of client-side isolation on the web [electronic resource]

The modern web browser is very much like a multiple-user operating system, with multiple web sites interacting with each other through designated browser features. As the web platform has grown over time -- adding new features and policies -- security and privacy have not always been preserved. Consequently, there are many features that have resulted in unexpected compromises of the user's security and privacy. This thesis focuses on three different attacks on web features: privacy attacks via the sharing of browsing history, browser cache, and similar incidental bits of state; privacy attacks via the ability to time remote web sites from within the browser, using a user's identity; and security attacks via the non-standard isolation policies of cookies, which are the primary mechanism of access control. For each of these attacks, we will detail the mechanism of the attack and the specific consequences on the security and privacy of the user. We will also explore how to prevent these attacks, from the points of view of the user, web browser developer, and web site developer.

Advisor: Boneh Dan
Dill David L. advisor. Thesis advisor
Mitchell John C. advisor. Thesis advisor
Self-antigen recognition in the pathogenesis of follicular lymphoma [electronic resource]

Follicular lymphoma (FL) is a monoclonal B cell malignancy and each tumor expresses a unique cell surface immunoglobulin (Ig) molecule that can potentially recognize antigens and/or transduce signals into the tumor cell. There is evidence that the functions of antigen binding and signaling are important for maintaining the survival of the FL tumor cells. The Ig variable region genes of these tumors undergo somatic hypermutation and yet functional Ig molecules are preserved. Additionally, the distribution of replacement and silent mutations within the Ig V genes implies a selective force to preserve their ability to bind antigens. We screened the tumor-derived Ig from a large collection of FL tumors and observed a high frequency of reactivity against human tissue antigens. For one FL patient, the recognized self-antigen was identified as myoferlin. This patient's tumor cells bound myoferlin in proportion to their level of surface Ig, and the binding to myoferlin was preserved despite ongoing IgV region somatic mutation. These findings indicate that FL may often be driven by auto-antigens. The preservation of antigen recognition despite ongoing somatic hypermutation suggests a functional positive selective pressure for tumors to maintain the ability to recognize antigens.

Advisor: Levy Ronald
Herzenberg Leonore A. advisor. Thesis advisor
Levy Shoshana advisor. Thesis advisor
Martinez Olivia
Utz Paul advisor. Thesis advisor
Self-calibrating on-chip interconnects [electronic resource]

This dissertation covers the conception, design and evaluation of the self-calibrating interconnect, a new type of capacitively-driven on-chip interconnect that uses feedback and charge-pumps to automatically neutralize receiver offsets caused by device mismatch. It can operate with extremely low signal swings, which minimizes energy, without compromising reliability. A 2 mm long prototype built in a 90 nm low-power CMOS process consumes 77 fJ/bit of energy at 1.5 GHz, and sustains a bit-error rate (BER) below 10^-30 with just 32 mV of swing. We also present a new way to reduce the noise level of comparators by adjusting the size of the precharge devices. For a given energy budget, we demonstrate that by upsizing the precharge devices we can reduce the input-referred thermal noise of the popular StrongARM latch by up to 30% over previously known sizing techniques.

Keywords: Electrical Engineering
Advisor: Dally William
Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Wooley Bruce A.
Semantic-based information extraction of biomedical definitions [electronic resource]

It is well known that the volume of biomedical literature is growing exponentially and that scientists are being overwhelmed when they sift through the scope and diversity of this unstructured knowledge to find relevant information. Prior work on addressing this problem has focused on methods to search for relevant publications and to identify relevant parts of publications. There has been much less research on methods that assist in extracting knowledge from biomedical literature. To tackle this challenge, I present a novel method to support the acquisition of structured knowledge from unstructured text. I have applied my method to support the challenge of identifying rule-based definitions of disease phenotypes. Because background knowledge of complex and diverse medical conditions is critical to undertaking information extraction, I have developed a semantic-based approach. Specifically, I use existing background knowledge to incorporate domain-relevant semantics, such as semantic similarity and rules, into a method for finding publications and the parts of texts within that contain knowledge about phenotype definitions and for identifying the rule or rule format that correctly encodes a phenotype. I have evaluated my method in the autism phenotyping domain, and found that incorporating structured domain knowledge into information extraction provides better accuracy and higher relevance of results than alternative term-based approaches. My novel method can help scientists to rapidly identify and formalize the complex domain knowledge that is emerging in published research findings. My method is also widely applicable to other information extraction challenges where there is a need to accurately extract computer-interpretable definitions, constraints, and policies from text.

Keywords: Electrical Engineering
Advisor: Das Amar K. (Amar Kumar) primary advisor. Thesis advisor
Garcia-Molina Hector primary advisor. Thesis advisor
Musen Mark A. advisor. Thesis advisor
Napel Sandy advisor. Thesis advisor
Separable problems in optimal cooperative control of networked systems [electronic resource]

This thesis characterizes a class of separable optimal cooperative control problems. We show that a simple factorization condition provides a unified technique that allows the problem to separate into several independent subproblems. The technique generalizes many of the previously known computational approaches and further enables us to solve a new class of previously unsolvable problems. The optimal solutions are computed explicitly in a distributed fashion via a series of Riccati equations whose size grows linearly with the problem size, therefore the optimal cooperative control can be easily computed via standard techniques for conventional optimal control problems. Furthermore, the separated problems provide a better understanding of the dynamics of the optimal controller. We illustrate two application examples including a salvo guidance problem and a network design problem for a team of networked missiles.

Keywords: Aeronautics and Astronautics
Advisor: Lall Sanjay primary advisor. Thesis advisor
Boyd Stephen P. advisor. Thesis advisor
Rock Stephen M. advisor. Thesis advisor
Sex differences in a mouse model of neonatal brain injury associated with preterm birth [electronic resource]

Male sex is a well-established clinical risk factor for poor neurodevelopmental outcome following preterm birth. The mechanisms responsible for this sex-related difference are unknown. The damage associated with prematurity can be mimicked in rodents by prolonged exposure to sublethal, postnatal hypoxia. This chronic, sublethal hypoxia (CSH) leads to anatomical changes in mice that strongly resemble the loss of volume, decreased myelination and ventriculomegaly seen in preterm newborns. However, no sex differences have been previously explored in this rodent model. We hypothesized that sex comparisons in hypoxic mice would show sex-related differences in the brain's response to the same degree of hypoxic insult. The hippocampal formation is a brain region that is notably affected in clinical studies and we found in mice that the male hippocampus, normally larger than the female, undergoes a greater volume loss compared to females. Myelination, generally greater in males, was significantly disrupted by hypoxia in neonatal male forebrain. The numbers of oligodendrocytes were significantly reduced in male hippocampus by the end CSH treatment. Females also experienced oligodendrocyte losses, but these occurred earlier than in males and numbers recovered to normal by the end of treatment. Sex-specific oligodendrocyte losses could not be attributed to caspase-dependent cell death or to differences in proliferation. Sex hormones play a complex role in the oligodendrocyte losses, leading us to hypothesize a differential effect of estrogen and testosterone on male versus female brain. We conclude that males show greater vulnerability to myelin loss and that females show greater resilience and recovery following the initial damage. Together, these results 1) illustrate at least two mechanisms that contribute to sex differences in neurological outcome; 2) support the use of this rodent model to investigate the basis of sex-related susceptibility to brain damage, and 3) provide insights into the cellular and hormonal mechanisms that may play a role in producing sex bias in neonatal brain injury.

Advisor: Penn Anna Asher primary advisor. Thesis advisor
Dolmetsch Ricardo E. advisor. Thesis advisor
Giffard Rona Greenberg
Palmer Theo advisor. Thesis advisor
Shugendō in the Tokugawa period [electronic resource] : Mount Ōmine as imaginary space and place of practice

Shugendō is a Japanese tradition of mountain asceticism co-opted by the schools of Japanese Esoteric Buddhism. This study concentrates on one of the most historically important sites of the tradition, Mount Ōmine, and the stations along the annual, multiple-day 'mountain entry' ritual called the Northern Okugake. Working mainly with the tradition's primary texts, it demonstrates how the tradition reinvented the imaginary landscape, anchoring legends and cosmology onto the rocks, caves, and sources of water that composed the material landscape of the place. The dissertation demonstrates that Shugendō texts present us with a valuable view into Esoteric Buddhism that has been overlooked by scholars of Japanese Esoteric Buddhism in particular, and Japanese religions in general.

Keywords: Religious Studies
Advisor: Bielefeldt Carl primary advisor. Thesis advisor
Faure Bernard primary advisor. Thesis advisor
Harrison Paul advisor. Thesis advisor
Sidewall silicon carbide emitters for microfabricated Barkhausen-Kurz Terahertz vacuum electronics [electronic resource]

The frequency band from 300 GHz to 3.0 THz is rich in potential applications, but there is a lack of efficient sources. This "THz gap" arises from the sharp decrease in the efficiency and power output of solid-state electronic amplifiers at frequencies above 100 GHz along with the unavailability of compact, uncooled optical sources for wavelengths longer than the infrared. Future THz systems hold great promise for leveraging the unique properties of THz waves, which are long enough in wavelength to be penetrating through clothing and skin, but are short enough to be useful for imaging, are resonant with complex molecular bonds, and are low enough in energy to be safe and non-ionizing. In addition to applications in security screening and medical imaging, continuous-wave THz systems would also enable short-range extreme wideband communications. This thesis proposes a micro-fabricated Barkhausen-Kurz ([mu]-BK) oscillator as a promising candidate THz source. The Barkhausen-Kurz concept is a general electronic oscillator principle developed nearly a century ago. The [mu]-BK oscillator has significant advantages over other vacuum electronic devices, promising high DC-to-THz efficiency and low startup current requirements. This device achieves a strong coupling between the resonant cavity structure and the electron beam current, even when operated at harmonics of the electron orbit frequency, by extracting energy over multiple passes of favorably phased electrons confined within a potential well. This enables high space charge, low beam impedance, and efficient energy extraction. The need for an emitter integrated into a parabolic potential well poses a major fabrication challenge. The basic fabrication process for the cavity and integrated poly-silicon carbide thermionic cathode has been demonstrated, providing the foundation for developing stable cathodes for injecting a sheet electron beam and for optimizing the electrode geometry for defining a parabolic potential well. Thermionic emission, in contrast to field emission, has the major advantage of the decoupling the control of electron current intensity (determined by temperature) from the operating frequency (determined by electrode bias). This thesis develops the motivation for the [mu]-BK oscillator as a promising candidate for efficient integrated THz circuits. The fabrication process and results for the sidewall lateral emitter integrated into a silicon [mu]-BK cavity process are detailed. Experimental results on emission current in integrated diode test structures in vacuum are reported, that enable the design of a new vacuum electronic technology that combines electron emitters, coupled resonant cavities, and lithographically shaped electrodes in a single substrate. This new class of efficient THz vacuum electronic integrated circuits promises to bridge the THz gap.

Keywords: Electrical Engineering
Advisor: Lee Thomas primary advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Leeson David B.
Sign and signal [electronic resource] : deriving linguistic generalizations from information utility

Why do languages have such different phonological processes even though all speakers share the same cognitive, articulatory and perceptual constraints? American English preserves sounds such as /p/ and /g/ even though they are absent from the sound systems of many of the world's languages, but reduces sounds such as /t/ even though it is one of the most frequently used sounds cross-linguistically. In contrast, Romance languages reduce /s/, which American English preserves. What makes American English have this particular set of phonological processes and not processes that affect other languages? I show that by assuming that speakers attempt to maximize the amount of information they transmit while minimizing the amount of effort required to transmit that information, it is possible to determine which sounds are more likely to be affected by reduction processes and which sounds are more likely to be preserved in each language. Unlike cognitive, perceptual and articulatory constraints, which are the same for speakers of all languages, the amount of information languages assign to linguistic elements, such as individual sounds, varies markedly. The more information a sound carries, the more effort speakers are willing to expend to transmit it faithfully to listeners. The trade-off between maximizing information and minimizing effort forms the basis for a new framework I call MULE (Most information Utility, Least Effort). MULE predicts preservation and reduction patterns in English and Arabic at the levels of performance, competence and change, thereby providing a partial answer to the actuation problem (Weinreich et al. 1968). MULE also predicts cross-linguistic generalizations. I show that in American English, Egyptian Arabic and Spanish, highly informative sounds are more likely to benefit from the perceptual prominence of the onsets of stressed syllables. Similarly the balance between effort and information successfully predicts cross-linguistic asymmetries between the frequencies of less effortful sounds and more effortful sounds. As such, MULE enhances the explanatory power of linguistic theory, and provides a disciplined way to integrate phonetics and information theoretic considerations.

Keywords: Linguistics
Advisor: Jurafsky Dan
Anttila Arto advisor. Thesis advisor
Kiparsky Paul advisor. Thesis advisor
Manning Christopher D. advisor. Thesis advisor
Sumner Meghan advisor. Thesis advisor
A signal processing approach to overcome data integrity challenges in flash SSD design [electronic resource]

Recently, flash-based Solid State Drives (SSD's) have emerged as a faster and more efficient alternative to hard drives. However, their higher cost is still an obstacle for their widespread use. Manufacturers have significantly reduced the cost by aggressively scaling the technology but this reduction has come at a price in lifetime, speed, and reliability. As the cell size shrinks and more bits are programmed into each one of them, interaction between neighboring cells increases significantly leading to noisier writing and unreliable reading of the flash memory. It is thus a signal processing challenge to write and read back reliably. This thesis proposes methods to overcome this challenge.

Keywords: Electrical Engineering
Advisor: Cioffi John M. primary advisor. Thesis advisor
Montanari Andrea primary advisor. Thesis advisor
Agarwal Rajiv
Silicon nanocrystals, dust to gold [electronic resource] : progress in material, devices and synthesis

Over the past half century silicon has become a dominant material for electronics but it has remained a very poor optical material. Bandwidth limitations in electronics are currently being seen as a problem. A similar situation to what happened on the long haul transport where we switched from the copper pair to optical fiber communication, may occur at the chip scale through integration of cheap on-chip optical devices. We consider two ways forward for silicon to remain a relevant material for lightwave communication in this era despite challenges posed by the indirect gap and free carrier absorption. In specific, we look at silicon nanocrystals (Si-NC) as a light emitting material to show progress in turning this indirect gap material into an efficient emitter. First we show through a highly sensitive optical absorption spectroscopy technique (photothermal deflection spectroscopy) that the negative effective mass electron states in Si-NC shift down in energy thereby reducing the energy gap at the direct transition. This effect is responsible for low amounts of visible range emission reported in small crystals; as opposed to the emission from band gap minima at the X valley attributed with majority of the near IR emission. Thus we confirm through a direct measurement the minima in density of states at the [gamma] valley from splitting of the negative and positive effective mass states. We compare the shift in a few of these states with a model for quantum confinement in the nanocrystals surrounded by oxide using a simple parabolic potential well model. We then show how resonant nanocavities should be optimized for low gain broad emitters like Si-NC. These cavities offer reduced mode volumes at the cost of quality factors such that "bad emitters" like Si-NC may couple with the cavity and ultimately offer a higher likelihood of observing Purcell enhancement. FDTD simulations show Q factors above 25000 and mode volumes below 0.6([lambda]/n)3 in silicon rich oxide, which has a refractive index of only 1.7. Finally we show a novel technique to make Si-NCs only on selected areas of the wafer: we direct-write tracks of silicon nanocrystals using a ps UV laser. It is possible to obtain 4 orders of magnitude throughput increase using this process as an alternative to oven annealing while also making localized nanocrystal precipitation a possibility. The tracks show emission enhancement over bare silicon rich oxide films and emission intensity comparable to that observed in conventionally-processed Si-NCs. We study variations in emission spectra, nanocluster phase and film stress across these tracks showing that ultimate limitation in throughput is film densification leading to compressive stress on the clusters that increases interfacial defects leading to emission quenching.

Keywords: Electrical Engineering
Advisor: Salleo Alberto
Harris J. S. (James Stewart)
Miller D. A. B. advisor. Thesis advisor