VictorJuiz/thesis huggingface dataset:
Microfluidic fractionation and analysis of cytoplasmic versus nuclear acids in single cells [electronic resource]

Single-cell gene expression studies have matured and are now widely used to uncover cell-to-cell variability, transcript processing and inhomogeneous response to external stimuli. Despite great progress, significant challenges remain including understanding fundamental questions of human genome transcription, gene expression ranges, localization, and processing destinies of RNAs. Eukaryotic cells make different types of primary and processed transcripts, which are either exclusively found in particular sub-cellular compartments or dispersed throughout the whole cell. These sub-cellular localizations of RNAs are weakly understood at a single-cell level, and are important for fully realizing gene functions. Understanding sub-cellular transcript localization is particularly important for studying the process of splicing, a pathway during which introns of pre-messenger RNA's are excised and exons are stitched together to form mature mRNA transcript. We here introduce a single-cell-isotachophoresis (sc-ITP) method to analyze co-transcriptional and alternative splicing in reference lymphoblastoid cell line (LCL-Snyder), and two sub-lines of CML cells (K562-ATCC and K562-ENCODE). The method is unique in that we physically separate the contents of cell nucleus from those of the cytoplasm and analyze independently. It allows for rapid, electric-field-based selective lysis of cytoplasmic membrane (leaving nucleus intact); and then purification and simultaneous fractionation of total RNA in cytosol (cyt-RNA) and total RNA in the nucleus (nuc-RNA) from single cells with no intra-compartment cross-contamination. We then use our system and state-of-the-art NGS technologies to perform single-cell nuclear and cytoplasmic RNA-seq to study fundamental questions of human genome transcription, differential gene expression, localization, and processing destinies of RNAs for various cell types, disease, and differentiation states. We evaluate the distribution of whole transcriptome gene features and gene expression of precursor and processed transcripts and find that there are considerable differences in expression levels across sub-cellular compartments and among individual cells. We then evaluate cell-to-cell variability of the highly expressed GAPDH housekeeping gene in alternative splicing between the lymphoblastoid and leukaemia cells using sequencing-specific probes and RT-qPCR. The data suggest evidence of significant distinction in splicing patterns. By analyzing nuclear and cytoplasmic compartments of a single cell individually at a whole transcriptome level, we achieve an unprecedented precision in splicing quantification. Together, our results describe an experimental method for single-cell fractionation and an analytical tool for gene and isoform expression analysis in rare cell types, cell differentiation and disease states.

Keywords: Mechanical Engineering.
Advisor: Santiago Juan G. primary advisor. Thesis advisor
Quake Stephen Ronald advisor. Thesis advisor
Snyder Michael
Microfluidic protein bioassays using giant magnetoresistive sensors [electronic resource]

For high performance medical diagnostics, magnetic biosensors have emerged as a suitable platform for fast and accurate protein measurements due to their very low background signal compared to optical methods. Medical applications demand biomarker panels including a larger number of protein analytes, and biosensors with larger and larger numbers of individual sensors enable measuring multiple target analytes in parallel on the same chip. Of these biosensors, Giant Magnetoresistance (GMR) sensors have been identified as one of the most promising technologies for protein detection. As with any solid state biosensor technology, on GMR sensors the effective use of each sensor is limited by its dynamic range and cross-reactivity between analytes used. Each added analyte added onto the sensor needs to be matched in terms of dynamic range of the sensor and using only reagents that do not cross react with other assay reagents. These two constraints limit the target analyte multiplexing capability of the sensor array technology. In order to use large-scale GMR sensor arrays effectively, these constraints need to be overcome. This thesis presents a microfluidic integration approach to GMR sensors which interfaces groups of sensors using individual microfluidic channels as separate compartments and thereby limits the scope of these constraints to only the compartment level and not to the whole array. In addition to overcoming dynamic range and cross-reactivity limitations in protein assays, this compartmentalization approach increases the number of samples that can be measured in parallel on a single chip from 1 up to 8 and enables more precise protein quantification. The use of microfluidics further increases the snr of larger particles with increased magnetic moments. These particles lead to an order of magnitude improvement in detection limit. Furthermore this microfluidic approach enables the integration of sample and reagent reservoirs, actuation elements and automation within the microfluidic chip. Microfluidic compartmentalization is useful for enabling an effective and flexible use of a wide range of surface-based sensor arrays. It enables the deployment of large-scale sensor arrays, which are not limited by cross-reactivity and dynamic range.

Keywords: Mechanical Engineering.
Advisor: Santiago Juan G. primary advisor. Thesis advisor
Wang Shan
Pruitt Beth advisor. Thesis advisor
Quake Stephen Ronald advisor. Thesis advisor
Micromechanical controls on brittle to plastic fault zone deformation [electronic resource]

This thesis focuses on the applications of experimental rock mechanics and geophysical microanalysis to the study of the structure, physical properties, and deformation mechanisms of geologic fault zones. The motivation for this approach is to connect mechanical and microstructural (micromechanical) data to physical processes occurring on faults in-situ. I examine these relationships in three distinct geologic settings, emphasizing the general interdependence of microstructure, mechanics, and mineralogy. Section 1 (Chapters 1-3) examines the physical properties on and around faults during hydrocarbon production from shale reservoirs. Chapters 1 and 2 focus on the compositional and thermal controls on shale frictional strength and stability, which provide insights into the occurrence of induced fault slip during hydraulic stimulation. Chapter 3 presents multi-scale investigations of shale matrix microstructure, employing electron microscopy and micro-computed tomography to highlight variations in pore networks with composition and reservoir setting. Section 2 (Chapter 4) explores the mechanical behavior of fault gouge from San Andreas Fault Observatory at Depth (SAFOD), which motivates a constitutive law consistent with microstructural evidence of aseismic deformation along the San Andreas Fault creeping section. Section 3 (Chapter 5) presents rheological and textural investigations of peridotite mylonite samples dredged from an oceanic transform fault, which provide new evidence of the depth extent of fluid infiltration and brittle deformation in the mantle lithosphere. Although these sections focus on distinct geophysical applications, they are united in demonstrating the utility of micromechanical studies in furthering our understanding of physical processes in geologic fault zones.

Keywords: Geophysics.
Advisor: Zoback Mark D. primary advisor. Thesis advisor
Segall Paul
Sleep Norman H. advisor. Thesis advisor
Warren Jessica
Microscopic magnetometry with degenerate 1D Bose gases [electronic resource]

This thesis presents a novel scanning probe magnetometer suitable for cryogenic studies, in which the probe is a degenerate 1D Bose gas of 87-Rb. The system is designed for rapid sample changes and operation between 35 K (with possible extension to 5 K) and room temperature while remaining compatible with the UHV requirements of ultracold atom experiments. Using a sample with microscopic fabricated current paths, we demonstrate a spatial resolution (2 [sigma]) of 2.2 ± 0.2 [mu] m and a repeatability of 1.9 ± 1.0 nT, with uncertainties as low as 100 pT attainable with repeated measurements. By separately investigating various noise sources, we show that the system is operating close to the fundamental measurement limits set by photon shot noise and atom shot noise. This scanning quantum cryogenic atom microscope is suitable for fundamental studies of transport and magnetism in condensed matter systems such as high-temperature superconductors and topological insulators.

Keywords: Applied Physics.
Advisor: Lev Benjamin L. primary advisor. Thesis advisor
Mabuchi Hideo advisor. Thesis advisor
Moler Kathryn A. advisor. Thesis advisor
Microsystems to study the mechanobiology of cell adhesion [electronic resource]

Adherent cell functions can be altered by mechanical stimuli through cytoskeleton remodeling and cell-cell junction disruption. Thus, a better understanding of the mechanical response of adherent cells is crucial to the design of pharmacological therapies for cancers and skin blistering diseases. However, a lack of reliable tools to apply mechanical stimuli and probe the cellular response has limited research on the effects of varying strains on adherent cells. Therefore, I develop systems to probe cellular mechanics using microfabrication technology with soft materials specifically designed to exert controlled strain on adherent cells and probe their mechanical response.

Keywords: Mechanical Engineering.
Advisor: Pruitt Beth primary advisor. Thesis advisor
Dunn Alexander Robert advisor. Thesis advisor
Nelson William advisor. Thesis advisor
Mimetic materialities [electronic resource] : spatial representation in mid-20th century Latin American regionalist fiction

In the past decades, materiality has been a constant topic in media studies, philosophy, and poetry. In this context, how can materiality be mimetically understood in prose fiction? This dissertation investigates precisely what I call mimetic materialities in novelistic writing. In other words, I demonstrate that, in certain novels and to different degrees, aspects such as length and internal subdivisions matter, as well as punctuation, chapter organization, use of footnotes, and rewritings. Materially mimetic novels find ways of representing space, sounds, and bodies not only through actual descriptions in the text, but through their very textual tangibility. In this sense, such novels are akin to models of the spaces they represent, whose presence is mimetic without depending solely on the interpretational operations of their content to emerge. They do keep a constant connection with the novels' plots, settings, themes and descriptions, but work under a particular dynamic. I develop the concept of mimetic materialities through a careful examination of a specific body of works, comprised of Latin American novels published in the 1950s. This corpus comprises novels by the Brazilian João Guimarães Rosa, the Mexican Juan Rulfo, the Cuban Alejo Carpentier, the Peruvian José María Arguedas and the Paraguayan Augusto Roa Bastos. I propose that these works make consistent albeit diverse uses of their textual materialities in order to represent the rural or forested areas where their plots are set. I also show that these texts occupy a significant position in the Latin American literary canon, insofar as they do not belong to the regionalist fiction from the 1920s and 1930s, heavily read through a realist paradigm; nor to the Latin American boom from the 1960s and 1970s, when aesthetic experimentalism would have become one of the defining features of Latin American novel. Besides their constant exploration of material mimesis, their intermediary position between these two paradigmatic moments offers a special vantage point: it prevents this study from falling into the conflict between realism and experimentalism that dominated Latin American literary historiography in the 20th century. Without ignoring such tension, I offer an alternative way of understanding some of the fundamental novelistic moves in 20th-century Latin America.

Keywords: Iberian and Latin American Cultures.
Advisor: Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Rocha Marília Librandi primary advisor. Thesis advisor
Hoyos Ayala Héctor advisor. Thesis advisor
Moreira Paulo
Ruffinelli Jorge advisor. Thesis advisor
Mind the gap? [electronic resource] : the international sources of sovereignty and state weakness

Why do some developing countries fail to govern parts of their territory? The consequences of incomplete sovereignty are often severe in terms of order, public goods, and economic growth, which raise the question of why ungoverned spaces remain without effective authority. Although there are many reasons why states leave broad swathes of their territory partially or fully ungoverned, I identify the impact international factors have on domestic sovereignty. I argue that ``bad'' regional neighborhoods - those populated by hostile states - can reduce state administration and control. Neighboring enemy states can reduce domestic sovereignty in target states through subversion, in which they support third party proxy groups hostile to the target state, or through coercion, in which they deter or compel the target into leaving some parts of their territory ungoverned. This practice of external interference creates or sustains ungoverned spaces in the target state, and sometimes generates weak state authority in the enemy state's own territory through a blowback effect. Drawing on an innovative new measure of state authority and evidence from a cross-national statistical analysis, a natural experiment, and two qualitative case studies, I show that bad neighborhoods weaken the state.

Keywords: Political Science.
Advisor: Krasner Stephen D.
Fearon James D. advisor. Thesis advisor
Laitin David D. advisor. Thesis advisor
Schultz Kenneth A. advisor. Thesis advisor
A miniature, energy harvesting, scalable data rate, and fully integrated mmWave radio for near range communication [electronic resource]

In this thesis, an integrated 2×2 CMOS transceiver at 60GHz with energy harvesting capability in the transmitter mode is demonstrated. The two dipole antennas are implemented on-chip and are shared between the receiver and transmitter modes using a T/R switch. The radio supports On-Off-Keying (OOK) modulation and a programmable data rate of 38 to 2450Mb/s at a BER of less than 5×10−4. The power consumption of the transmitter scales with data rate. For a communication distance of 5cm, the transmitter consumes 100μW to 6.3mW for a data rate of 38 to 2450Mb/s, respectively. For a communication distance of 10cm, the transmitter consumes 260μW to 11.9mW for a data rate of 38 to 2450Mb/s, respectively. This yields an energy efficiency of 2.6pJ/b at 5cm and 4.9pJ/b at 10cm. The energy harvesting circuits operate at 2.45GHz with an average efficiency of 33%. The harvesting antenna and its matching components are off-chip. The complete transceiver including the energy harvesting block and on-chip antennas occupies 1.62mm2 in 40nm CMOS, which is the smallest 60GHz radio with on-chip antennas to date. This work is the first implementation of a 60GHz transmitter with scalable data rate and power that has the energy harvesting capability.

Keywords: Electrical Engineering.
Advisor: Poon Ada Shuk Yan
Howe Roger Thomasr
Wong S.
Misfolding, not ubiquitylation, underlies protein targeting to inclusion bodies [electronic resource]

Inclusion bodies (IB) containing aggregated forms of disease-associated proteins and polyubiquitin conjugates are universal histopathological features of neurodegenerative disease, but the mechanisms that govern recruitment of ubiquitinated proteins to IB are not well understood. Ubiquitin (Ub) has previously been proposed to target proteins to IB for degradation. In this study, we use conditionally destabilized reporters that undergo misfolding and ubiquitination upon removal of stabilizing ligand to examine the role of Ub conjugation in targeting proteins to IB composed of an N-terminal fragment of mutant huntingtin (htt), the causative protein in Huntington's disease (HD). We show that reporters are excluded from IB in the presence of stabilizing ligand, but are recruited to IB following ligand washout. However, we find that Ub conjugation is not necessary or sufficient to target reporters to IB. Moreover, misfolded reporters and Ub conjugates are stable at IB. These data indicate that compromised folding states, not conjugation to Ub, specifies IB recruitment.

Keywords: Biology.
Advisor: Kopito Ron Rieger
Skotheim Jan
Wandless Thomas advisor. Thesis advisor
The mode and tempo of adaptation in natural populations of Drosophila [electronic resource]

Evolutionary adaptation is a process in which beneficial mutations increase in frequency in response to selective pressures. If these mutations were previously rare or absent from the population, adaptation should generate a characteristic signature in the genetic diversity around the adaptive locus, known as a selective sweep. Such selective sweeps can be distinguished into hard selective sweeps, where only a single adaptive mutation rises in frequency, or soft selective sweeps, where multiple adaptive mutations at the same locus sweep through the population simultaneously. In my second chapter, I propose two new statistics, H12 and H2/H1, which can identify and differentiate hard and soft sweeps in population genomic data. I apply this method to a Drosophila melanogaster population genomic dataset consisting of 145 sequenced strains collected in North Carolina and find that selective sweeps were abundant in the recent history of this population. Interestingly, I also find that practically all of the strongest and most recent sweeps show patterns that are more consistent with soft rather than hard sweeps. In my third chapter, I demonstrate an inverse relationship between H12 and H2/H1 and develop an upper bound for H2/H1 as a function of H12. This upper bound can be used to normalize H2/H1, which can facilitate the interpretation of the application of H12 and H2/H1 to heterogenous data. Finally, in my fourth chapter, I find that the patterns of abundant soft selective sweeps are not unique to the North Carolina data set and are present in a population sample of 200 individuals from Zambia. These results together suggest that adaptation can be rapid in multiple populations of D. melanogaster.

Keywords: Genetics.
Advisor: Petrov Dmitri Alex
Bustamante Carlos (Carlos D.)
Rosenberg Noah
Sherlock Gavin
Tang Hua (Geneticist)
Modeling chemistry of copper-based oxygen carriers in chemical looping combustion systems [electronic resource]

Development of a model that can be used to predict oxidation rates of copper to cuprous and cupric oxide (Cu2O and CuO, respectively) in the air reactor of a Chemical Looping Combustion (CLC) system is the primary focus of this thesis. The proposed oxidation model, which is based in Wagner Theory and defect chemistry, describes the fundamental processes occurring during copper oxidation. Consequently, it provides better predictive capabilities over a wide range of temperatures and pressures, as well as characteristic particle geometries (spheres, cylinders and plates) than the phenomenological models that are currently being used to predict oxidation rates of copper-based oxygen carriers used in CLC systems. In addition to developing this oxidation model, cuprous and cupric oxide reduction experiments with gaseous fuels like carbon monoxide, hydrogen and methane, and solid fuels like char, wyodak coal, and corn stover, were performed to characterize reaction rates in the fuel reactor of CLC systems. Oxidation rates obtained from the oxidation model, and measured rates from the reduction experiments were used to estimate the size and oxygen carrier loading for a 10 MWth CLC system.

Keywords: Mechanical Engineering.
Advisor: Gür Turgut M.
Mitchell Reginald primary advisor. Thesis advisor
Zheng Xiaolin
Modeling of micro-Barkhausen-Kurz devices for terahertz applications [electronic resource]

Terahertz frequency band from 300GHz - 3THz has started to gain a fair amount of attention from researchers in the recent past, and several rich potential applications have been identified as a result. As research in this space advances, the number of applications utilizing this frequency band is likely to grow. The lack of appropriate sources is the primary reason that prevents applications in this spectral region from being widely realized. Hence, it is imperative that a highly efficient source of terahertz radiation is identified which can cater to the growing number of applications in this space. The first section of this research explores the limitations of traditional devices to generate terahertz frequency. Traditional CMOS sources start to run out of steam as they are pushed to higher frequencies. The research shows that Moore's law that has governed the scaling of these devices for nearly 50 years is not expected to help bridge this gap. Optical sources have their niche in the infra-red region and above but so far, these technologies have not yielded a compact, room temperature source in the terahertz region. Although vacuum based electron devices exist and span a very wide range from kHz through several THz, their development has been impeded by the lack of efficient CAD tools. This research examines a vacuum based electron device aka Barkhausen-Kurz oscillator as an appropriate source in the terahertz frequency range. In this device, the electrons undergo simple harmonic motion in an ideally parabolic field. With each pass through the device, the electrons lose energy to an appropriately phased RF field. Multiple electron transits allow for high efficiency in DC-to-RF conversion. This research uses theoretical derivations to illustrate the applicability of the Barkhausen-Kurz oscillator as a terahertz source and also highlights the efficiency, and maximum power that can be achieved through it. In addition, this research also shows the usability of the device at odd harmonics of the electron orbital frequency. A key contribution of this research is the development of a particle in cell code from ground up, to cater to the physics of Barkhausen-Kurz oscillator device. The later half of this thesis focuses on numerical validation of the theoretical derivations by simulating the device with this code. Several simulations have been run to qualitatively and quantitatively assess the theoretical derivations, and reconfirm the efficiency that can be achieved through this device in generating terahertz radiation. This particle-in-cell code is expected to bridge the gap that currently exists with respect to the easy availability and accessibility of CAD tools required to develop vacuum based electronic devices.

Keywords: Electrical Engineering.
Advisor: Lee Thomas
Miller D. A. B. advisor. Thesis advisor
Wong S.