VictorJuiz/thesis huggingface dataset:
Statistical algorithms in the study of mammalian DNA methylation

DNA methylation is a dynamic chemical modification that is abundant on DNA sequences and plays a central role in the regulatory mechanisms of cells. This modification can be inherited across cell divisions and generations, providing a ``memory mechanism" for regulatory programs that is more flexible than that coded in the DNA sequence. In recent years, high-throughput sequencing technologies have enabled genome-wide annotation of DNA methylation. Coupled with novel computational machinery, these developments have enabled unperceivable insight to the characteristics, biological function and disease association of this phenomenon. The collaborations between experimental and computational researches who take part in these efforts has been closer than ever before due to the need to involve computational methodologies throughout the entire research pipeline, from experimental design through bias correction to the analysis of large datasets./nIn the first part of this thesis we present contributions to the field of high-throughput DNA methylation. We introduce statistically sound criteria for the detection of methylation signatures in DNA sequence, and present an algorithm for the annotation of an informative non-overlapping subset of such regions that is optimal under biologically motivated assumptions. Our method outputs a sequence-generated list of regions that are of interest with respect to their methylation states. We then present a Bayesian network to infer corrected site-specific methylation states from a favorable but biased experimental method, and describe its incorporation in a software package. Along with site-specific methylation calls our package annotates experiment-specific regions of interest by considering both the methylation state inferences and the genomic sequence. These regions can serve as a basis for comparative methylation studies. In the last chapter of this section we bring results from a genome-scale comparative study conducted on humans, chimpanzees and an orangutan, providing evidence of DNA methylation differences that propagate through generations and distinguish these closely related species./nThe second part of this thesis concerns error correction in high-throughput sequencing datasets. In the course of studying DNA methylation with high-throughput sequencing we discovered a systematic error that results in false-positive variant detection and can significantly affect biological inferences in a variety of genomic studies. We present a classifier to correct for such errors and show that it performs very well with respect to both sensitivity and specificity.

Advisor: Pachter, Lior
Studies of human depth perception in real and pictured environments

Determining the three-dimensional (3D) layout of the natural environment is an important but difficult visual function. It is difficult because the 3D layout of a scene and the shapes of 3D objects are not explicit in the 2D retinal images. The visual system uses both binocular (two eyes) and monocular (one eye) cues to determine 3D layout from these images. The same cues that are used to determine the layout of real scenes are also present in photographs and realistic pictures of 3D scenes. The work described in this dissertation examines how people perceive 3D layout in the natural environment and in pictures. Chapter 1 provides an introduction to the specific 3D cues that will be studied. Chapter 2 describes a series of experiments examining how the visual system's use of binocular cues might be adaptive to improve depth perception in the natural environment. Chapter 3 describes a series of experiments examining how the visual system interprets monocular linear perspective cues, and how this can lead to perceptual distortions in perceived 3D from pictures. Chapter 4, the Conclusion, discusses how the work described in this dissertation might be applied to creating better displays and pictures.

Advisor: Banks, Martin S
Mechanistic insights into the roles of P-TEFb and its novel cofactors in tumorigenesis and HIV transcription

Ongoing research in the field of transcription has given rise to the unappreciated role of elongation control as a rate limiting step for transcription, and the general transcription elongation factor P-TEFb therefore has taken the central stages. P-TEFb is composed of cyclin T1 and the cyclin-dependent kinase Cdk9. It stimulates transcription elongation by releasing the paused RNA Polymerase II (Pol II) through phosphorylating Pol II at Ser2 and antagonizing the effects of negative elongation factors. P-TEFb is not only essential for the transcription of the vast majority of cellular genes, but also critical for the expression of HIV genome. Elucidating how P-TEFb activity is controlled therefore plays a key role in advancing our understanding of cellular and disease-related transcription elongation./nThe first part of this thesis presents my early Ph.D work, which focusing on the identification and characterization of a La-like protein PIP7S (also named as LARP7). I have shown that PIP7S binds and stabilizes nearly all the nuclear 7SK, which leading to sequestration and inactivation of P-TEFb. Consistent with the fact that PIP7S is frequently mutated in human tumors and the Drosophila homolog of PIP7S is a tumor suppressor, loss of PIP7S function disrupts epithelial differentiation and causes P-TEFb-dependent transformation./nThe second part of this thesis introduces the identification of the Super Elongation Complex (SEC) and subsequent characterization of two of its subunits, AFF4 and ELL2. I have shown that through the bridging functions of AFF4 and Tat, P-TEFb and ELL2 combine to form a bifunctional elongation complex that greatly activates basal and HIV-1 transcription, respectively./nThe third part of this thesis continues to dissect the functions of the other two SEC subunits ENL and AF9. I have shown that the homologous ENL and AF9 exist in separate SECs with similar but non-identical functions. ENL/AF9 also exists outside SEC when bound to Dot1L, which is found to inhibit SEC function. The YEATS domain of ENL/AF9 targets SEC to Pol II on chromatin through contacting the PAFc complex.

Advisor: Zhou, Qiang
Thermal Transport and Mechanical Properties of Carbon Nanotube Arrays

Electronic Chip cooling has become an important issue with the ever increasing transistor densities and computing power demands. One of the crucial components of the thermal management system is high-performance thermal interface materials (TIMs), the materials connecting various solid-solid interfaces in packaged electronic devices. Ideal TIMs have the characteristics of high mechanical compliance and high intrinsic thermal conductivity. Vertically Aligned Carbon Nanotube (CNT) arrays are promising for advanced TIMs since they possesses both characters yet poor contact to the target surface can limit the overall performance. Recently, indium-assisted bonding has been found to enhance the contact conductance by a factor of 10, which inspires a comprehensive study of the CNT-array thermal transport properties. This thesis presents a systematic study on the thermal transport and mechanical properties of CNT arrays. The CNT array density and length are controlled via the thermal annealing duration and ethylene exposure duration in water-assisted chemical vapor deposition synthesis. The thermal transport properties are measured accurately by phase-sensitive photo thermal reflectance thermometry. The thermal contact conductance between CNT array and Glass increased close to linearly by increasing the volume fraction of the CNT array. The increase of volume fraction can potentially increase the number of contacting tubes which further enhance the contact area. In addition, the effective thermal conductivity increases monotonically with the increase of volume fraction of the CNT array. Quantitatively, it has been found that the increasing trend of thermal conductivity is larger than the increasing trend of volume fraction. The strain and buckling behavior of CNT arrays under compressive stress were systematically studied. It has been verified both experimentally and analytically that buckling in lower density CNT array results in a further decrease of thermal conductivity. The thermal conductivity of CNT array decreases as the structure changes from vertically aligned to buckled, while the thermal conductivity rises back as the buckling structure becomes more compact. The rise of thermal conductivity with the buckling structure is attributed to the rise of the thermal contact conductance between tubes. The thermal contact conductance between CNT array and glass increases as the compressive stress increases to certain degree, while further increase of stress causes fatigue at the contacts, which decreases the contact conductance. These results demonstrate how thermal transport properties vary as a function of CNT array density and as a function of the strain of CNT array. With such trends, the thermal properties can be further increased by understanding the underlying mechanisms for such trends.

Advisor: Majumdar, Arunava
Dubon, Oscar
The Open Book: Digital Form in the Making

This dissertation attempts to put anthropology in conversation with "the book." It does so through an empirical specification of mass book digitization, the industrial-scale, retrospective conversion of books into digital form. Such mass digitization is the work of research libraries, Internet companies, non-profit organizations, national governments, and the computer scientists, digital librarians, and the lawyers and administrators who advise, encourage, and support them./nThe dissertation approaches mass digitization as a venue for plumbing the turbulent waters of what I consider the "contemporary book": an arena of experimentation arising from the productive, seismic encounter of the modern book apparatus with an emergent assemblage in motion around the production, authorization, storage, preservation, circulation, and production of knowledge. By the "contemporary book," I refer to the modern book apparatus (dispositif) as it is being worked upon, reconfigured, and called into question in the early twenty-first century./nThe activities of the digitizers I studied are based upon a shared conviction that the book and its institutions are "closed" and need to be "opened": books are "inaccessible" or "locked up" by virtue of their materiality (their printedness); by the institutions that store and keep them (physical libraries); and by the state's often misguided regulation (copyright). For them, mass digitization is an important development in moving from the closed nature of the modern book apparatus to a remediated knowledge infrastructure, a future book. If it could be achieved, mass digitization would be a breakthrough in the long-anticipated opening of the book./nPrimary research for the dissertation was conducted at the Internet Archive in San Francisco, CA. Additional research took place in a variety of locations in the United States, in specific relation to the public controversy around the Google Book Search Settlement.

Advisor: Rabinow, Paul
The Life and Religious Culture of the Freshwater Boat People of North China, 1700-Present

My dissertation examines how environmental change affected cultural transformation. It investigates the manner in which the mobile, isolated boat people adapted to a boat-dwelling lifestyle and created innovative religious practices and beliefs in order to maintain their relationships with spirits and ancestors, as well as dispersed lineage members, given that they had no fixed base on land to build temples, ancestral shrines or tombs. The subjects of the study are the boat-dwelling people who frequently moved back and forth within the Grand Canal basin between southwest Shandong and north Jiangsu in late imperial and modern China. These boat dwellers were displaced from their land-based estates and became environmental refugees during the eighteenth and nineteenth centuries. The isolation of the boat people protected their unique religious activities from the anti-religious campaigns of the twentieth century. Their ritual tradition Duangu Ceremony was granted the status of National Intangible Cultural Heritage by the Ministry of Culture of the People's Republic of China in 2011. I argue that despite the distinctive lifestyle and religious culture of the floating community, some significant elements of religious belief and practice of boat people remained unchanged, transcending differences in occupation, social status, and environment for centuries. With the assistance of ritualists within the floating community, these boat people endeavored to continue their genealogies and maintain ancestor worship, practices that were equally important to farmers. These shared components can help us rethink core elements of Chinese popular culture, previously based on farmers' experiences, and discern which features are the most significant in Chinese popular religion and how and why they play such vital roles. More importantly, core cultural elements have been resilient and resistant to environmental change./nTo compensate for the scarcity of historical sources, I conducted fieldwork in a fishing community in the Weishan Lakes of Shandong, to document their lifestyle and the complete process of religious ceremonies during 2008-2010. This project not only contributes to our knowledge of Chinese popular religion, previously limited to the farming population, but it also opens up our understanding of voiceless boat people and environmental refugees as subalterns of the past. The lessons learned can be taken forward into possible crises of rising sea levels associated with global warming, which may create more environmental refugees. Learning about ways boat-dwelling changed lifestyle and culture in the past may help us prepare better for the future.

Advisor: Johnson, David G
The Impact of Neighborhood Traffic Density and Deprivation on Lung Function Among Children with Asthma

To investigate the extent to which traffic exposure affects the lung function of children with asthma and how local neighborhood factors may modify this relation, a merge of epidemiologic, environmental health and geographic methods is necessary. People and places are linked; therefore, it is necessary to consider place-effects on health as well as environmental exposures. The Fresno Asthmatic Children's Environment Study (FACES) is a longitudinal cohort study of children with asthma in Fresno, California that followed participants from 2000-2008 to explore short-term and long-term effects of ambient air pollution on lung function (as measured by spirometry, wheeze, and asthma symptoms). With publicly available data on traffic counts in Fresno, CA from 2000-2008, I built a spatial model of traffic exposure that varies both temporally and spatially for the FACES cohort. To capture and quantify neighborhood characteristics, I constructed individual neighborhoods based on global positioning software (GPS) data and walking distances around participant homes. To evaluate neighborhood deprivation, I collected geographic information system (GIS) data on parks, grocery stores, bus stops, etc. from publicly available sources and created an index based on Item Response Theory. To assess the marginal risk difference of lung function among children with asthma exposed to high levels of traffic pollution and those exposed to lower levels of traffic pollution (as measured by traffic density), I apply semi-parametric causal inference methods and use Targeted Maximum Likelihood Estimation (TMLE). More FACES participants who live in high deprivation neighborhoods are also farther away from high traffic areas. Neighborhood deprivation, as defined by a combination of GIS variables in this study, does not track well with US Census poverty. The marginal change in lung function from exposure to high neighborhood traffic to lower neighborhood traffic, without stratification for neighborhood deprivation, is -0.233 (95% CI -0.338, -0.129). The results can be interpreted as--the average decrease of FEV1 is 0.233 L, or there is a 12% reduction in lung function. Either neighborhood deprivation does not modify the effect of traffic on lung function or there is not enough data to evaluate this type of effect modification. The findings indicate that neighborhood exposure to traffic adversely affects lung function among the FACES cohort of children with asthma.

Advisor: Tager, Ira B
The POLARBEAR Experiment: Design and Characterization

We present the design and characterization of the POLARBEAR experiment. POLARBEAR is a millimeter-wave polarimeter that will measure the Cosmic Microwave Background (CMB) polarization. It was designed to have both the sensitivity and angular resolution to detect the expected B-mode polarization due to gravitational lensing at small angular scales while still enabling a search for the degree scale B- mode polarization caused by inflationary gravitational waves. The instrument utilizes the Huan Tran Telescope (HTT), a 2.5-meter primary mirror telescope, coupled to a unique focal plane of 1,274 antenna-coupled transition-edge sensor (TES) detectors to achieve unprecedented sensitivity from angular scales of the experiment's 4 arcminute beam to several degrees./nThis dissertation focuses on the design, integration and characterization of the cryogenic receiver for the POLARBEAR instrument. The receiver cools the ∼ 20 cm focal plane to 0.25 Kelvin, with detector readout provided by a digital frequency- multiplexed SQUID system. The POLARBEAR receiver was been successfully deployed on the HTT for an engineering run in the Eastern Sierras of California and is currently deployed on Cerro Toco in the Atacama Dessert of Chile. We present results from lab tests done to characterize the instrument, from the engineering run and preliminary results from Chile.

Advisor: Lee, Adrian T
Optical Characterization of Plasmonic Metamaterials

Optical metamaterials are artificially engineered structures composed of subwavelength units. They exhibit exotic optical properties that are unobserved or unattainable in nature. Recent efforts have led to the observation of many interesting phenomena and as well as/npromising applications such as super-resolution imaging and transformation optics. At optical frequencies, the functionalities of metamaterials are achieved through excitation of plasmons as most structures are metal-dielectric composites. The objective of this dissertation is to provide the tools and study the unique properties and novel phenomena of plasmonic metamaterials./nWe first theoretically study a pair of nanobars to properly understand artificial magnetism which is important in most metamaterials. Then we experimentally investigate the optical properties of the "fishnet" metamaterial using a variety of spectroscopic techniques. First, we probe the plasmonic band structure using angle- and polarization- resolved linear spectroscopy. Most interestingly, we observe dark magnetic modes and their coupling to bright modes leading to avoid-crossing behavior typical of quantum systems. The k-dependent effective optical constants are measured through phase measurements confirming the dispersion of the magnetic resonance. Second, second-harmonic generation spectroscopy is carried out showing significant resonance enhancement achieved through the excitation of plasmons. The observations are substantiated with theory to validate our physical understanding of nonlinear wave-mixing processes in metamaterials. Finally, we carry out pump-probe spectroscopy to understand the dynamic behavior. The optical responses are shown to be modulated in femtosecond time scale. The modulation magnitude is greatly enhanced while the dynamics is mainly determined by the constituting dielectric medium.

Advisor: Shen, Yuen-Ron
Wang, Feng
Analyzing the Structure of Informal Transport: The Evening Commute Problem in Nairobi, Kenya

In many parts of the world, particularly in developing countries, informal privately-operated transportation plays an integral role in people's mobility. This study systematically analyzes the development and structure of informal transit systems as a function of the network, user, and modal characteristics for an evening commute problem along a linear corridor where passengers originate uniformly from a central business district and have destinations uniformly distributed along the corridor. The model jointly takes into account user mode choice and operator fare and frequency decisions. Three types of operators each with different objectives are analyzed: (1) informal transit with competing operators, (2) a welfare-maximizing government, and (3) a private monopoly or company. Policies, such as fare regulation and vehicle licensing schemes, are presented to help rationalize private and informal transit service using a government-operated service as the baseline. The use of continuum approximation tools allow for a 2-D graphical representation of the regulatory environments. Using Nairobi, Kenya as a case study, it was concluded that with proper regulation and oversight informal transit can perform similar to publicly provided transit.

Advisor: Daganzo, Carlos
The Electronic Structure of Single-Layer Graphene

Single-layer graphene has been widely researched in recent years due to its perceived technological applicability and its scientific importance as a unique model system with relativistic Dirac Fermions. Because of its unique geometric and electronic structure, the properties of graphene can be tuned or manipulated in several ways. This tunability is important for technological applications in its own right, and it also allows us to study the fundamental properties of Dirac Fermions, including unique many-body interactions and the nature of the quasiparticles at half-filling. This thesis is a detailed examination of the electronic and structural properties of graphene, studied with angle-resolved photoemission spectroscopy (ARPES) and other surface science techniques like low-energy electron microscopy and diffraction./nThis thesis is organized as follows. Chapter 1 gives an introduction to the electronic and structural properties of single-layer graphene. It provides a brief historical overview of major theoretical and experimental milestones and sets the stage for the important theoretical and experimental questions that this thesis addresses./nChapters 2 and 3 describe the experimental setup. Chapter 2 discusses the experimental techniques used in this thesis with particular focus on the mechanics of ARPES. Chapter 3 discusses the different graphene growth techniques that were used to create our sample with particular focus on our characterization of epitaxial graphene on SiC(0001)./nChapters 4 and 5 form the meat of this thesis: they provide a thorough discussion of the electronic properties of graphene as studied by ARPES. Chapter 4 describes how various perturbations can result in the manipulation of the bare electronic band structure, including the deposition of atomic or molecular species on top of an epitaxial graphene sheet as well as the interactions between graphene and its substrate. Chapter 5 describes the many-body physics in single-layer graphene. It begins with a discussion of the electron-electron interaction in undoped graphene, demonstrating that these interactions qualitatively differ from ordinary metals and semiconductors and depart from the standard Fermi liquid picture for quasiparticles; it then continues by describing how screening the electron-electron and electron-impurity interactions can impact the electronic properties of graphene. Chapter 5 ends with a discussion of the doping-dependent coupling strength of the electron-phonon interaction.

Advisor: Lanzara, Alessandra