VictorJuiz/thesis huggingface dataset:
Microfluidic platforms for single-cell analyses [electronic resource]

This dissertation describes several microfluidic platforms for single-cell analysis. They represent the continuing advance of analytical technologies to provide ever increasingly detailed information of cellular populations. Microfluidics offers several advantages for working with samples at the single-cell level, including the ability to manipulate nanoliter volumes and enhancement of interactions in confined volumes. In order to demonstrate the scientific utility of these new platforms, the devices are used to process and study various strains of cyanobacteria, which represent an important class of organism of interest to the environmental microbiology community. A microfluidic device that incorporates a membrane of conical nanopores is described and used to capture hundreds of single cells, one per pore. The conical nanopores are created using simple chemical etching of a polycarbonate membrane containing heavy-ion damage tracks. The geometries can be tuned to create nanopores capable of capturing single cyanobacteria cells based on size. Capture and observation of single cells, as well as size-based separation of a cellular mixture, is demonstrated. A second method for capture of single cells using a molecular-imprinted film integrated into a microfluidic device is also described. Films are imprinted with target strains of cyanobacteria and used to selectively capture single cells of the same strain as the imprint template. The imprints are shown to be selective even between different strains of the same genus of cyanobacteria. It is thought that this selectivity derives from diverse chemistries present on these organisms, allowing the imprints to prefer template-matching individuals. The separation efficiency of microfluidic molecularly imprinted films, as well as how that efficiency can be tuned with pH, is demonstrated. Microfluidic single-cell genetic amplification is extended to a new class of organisms through the development of chemical lysis protocols for cyanobacteria that remain sufficiently compatible with the amplification reaction. Previously, such methods were limited to organisms susceptible to simple alkaline lysis. Issues of contaminating genetic material and complications of the MDA reaction, such as coverage variance, are also characterized. The utility of the technique is demonstrated by amplifying a heterogeneous sequence of interest, CRIPSR, and sequencing it.

Keywords: Chemistry
Advisor: Zare Richard N. primary advisor. Thesis advisor
Andersen Hans
Fayer Michael D. advisor. Thesis advisor
Micro-patterned polymeric surfaces as directional and selective adhesives [electronic resource]

Nature has recently become a great source of inspiration for researchers in the fields of adhesion and adhesives. A number of biological specimen have inspired impressive advancements as evolution has produced interesting solutions to the problems researchers are looking to solve. This work focuses on a particular type of adhesive, the manufacturing methods used to produce it, and the viability of such adhesives in standard and radiological environments. A novel type of micro-structure based adhesive, the selective adhesive, is introduced. This adhesive utilizes polymer micro-structures to selectively adhere to particles within a desired size range. Two iterations of the micro-structure design are presented and the performance of these adhesives is described. The second generation of the adhesive proves to be effective at sorting large numbers of particles based on their size in a passive manner, without the requirement of gravity or electrical input energy common to other particle sorting methods used in industrial or laboratory settings. Previous production methods used to manufacture the adhesive micro-structures have proven to have a number of limitations that would make the production of the desired micro-structure geometry difficult. To address this, a novel manufacturing method has been presented. This method, called micro-wedge machining, allows for significantly improved control over a number of micro-structure parameters. This improved control has allowed for the production of not only better selective adhesives, but also directional adhesives used for climbing applications, allowing for an improvement in maximum normal adhesion of approximately 100% over adhesives produced via older manufacturing methods. The biologically inspired adhesives discussed previously could foreseeably be used in a large number of environments. In most cases, the polymers that make up the adhesives can be assumed to be mechanically and chemically stable for the usable lifetime of the adhesive. However, this is not the case for a small number of environments. In the case of nuclear facilities or space applications, ionizing radiation fields can be present and have the capability to cause significant changes in the bulk polymer making up the adhesives. Because these effects can be significant, the effects of gamma and alpha radiation on the adhesives has been investigated. The adhesives prove to be quite robust, maintaining their performance out to very high absorbed radiation doses.

Keywords: Mechanical Engineering
Advisor: Cutkosky Mark R. primary advisor. Thesis advisor
Kenny Thomas William advisor. Thesis advisor
Prinz F. B. advisor. Thesis advisor
MicroRNA-mediated induction of neuronal cells [electronic resource]

Mammalian neurogenesis - an elagant process of producing extraodinarily diversified neuronal propulations - has been largely studied in the context of evoluationarily conserved signalling pathways and neurogenic transcription factors. Yet little is known about the roles of chromatin remodellers and regulatory RNAs, such as microRNAs, in the formation of neurons. We recently discovered that miR-9* and miR-124 instruct compositional changes of SWI/SNF-like BAF chromatin-remodelling complexes during murine nervous development, a process important for neuronal differentiation and function. Here I set out to directly test the neurogenic activity of these microRNAs in human non-neuronal cells. Together with Andrew Yoo, I showed that ectopic expression of miR-9/9* and miR-124 (miR-9/9*-124) in human dermal fibroblasts induces their conversion into neurons (chapter 2). Addition of neurogenic transcription factors such as NEUROD2, ASCL1 and MYT1L enhances the rate of conversion and the maturation of the converted neurons, whereas expression of these transcription factors alone without miR-9/9*-124 appeared ineffective. As a step closer to cell replacement therapy, I next showed that these microRNAs could directly convert human astrocytes into neurons, of which the subtype identity can be further biased by specfic neurogenic factors (chapeter 3). Collectively, these studies indicate that the genetic circuitry involving miR-9/9*-124 and BAF chromatin remodelling complex can have an instructive role in neuronal fate determination, and may form a neuronal ground state that can be further specified by different transciption factors and/or signalling pathways.

Advisor: Crabtree Gerald R. primary advisor. Thesis advisor
Beachy Philip Arden advisor. Thesis advisor
Dolmetsch Ricardo E. advisor. Thesis advisor
Shen Kang
A millimeter-sized wirelessly powered and remotely controlled locomotive implant [electronic resource]

A wirelessly powered and controlled implantable device capable of locomotion in a fluid medium is presented. Two scalable low-power propulsion methods are described that achieve roughly an order of magnitude better performance than existing methods in terms of thrust conversion efficiency. The wireless prototype occupies 0.6mm x 1mm in 65 nm CMOS with an external 2mm x 2mm receive antenna . The IC consists of a matching network, a rectifier, a bandgap reference, a regulator, a demodulator, a digital controller, and high-current drivers that interface directly with the propulsion system. It receives 500 uW from a 2 W 1.86 GHz power signal at a distance of 5 cm. Asynchronous pulse-width modulation on the carrier allows for data rates from 2.5-25 Mbps with energy efficiency of 0.5 pJ/b at 10 Mbps. The received data configures the propulsion system drivers, which are capable of driving up to 2 mA at 0.2 V and can achieve a speed of 0.53 cm/sec in a 60 mT magnetic field.

Keywords: Electrical Engineering
Advisor: Meng Teresa H. primary advisor. Thesis advisor
Poon Ada Shuk Yan
Howe Roger Thomas advisor. Thesis advisor
Minimizing unregulated hazardous chemicals in consumer products [electronic resource] : challenges, strategies, and motivations of proactive companies

Chemical regulations have historically been weak, leading many to argue that human and environmental health is not adequately protected from chemicals that could pose an unacceptable risk. In an environment of regulatory deficits, some proactive consumer product companies are voluntarily exceeding regulatory requirements by restricting from their products unregulated chemicals that could harm human or environmental health, despite the fact that these actions are costly. They do not usually advertise the details of their voluntary programs. This dissertation uses in-depth interviews with senior environmental directors of 20 multinational consumer product companies to examine: (1) consumer product companies' chemicals-related information needs and the challenges they face in obtaining information about the chemicals used in their products; (2) the details of their voluntary strategies to minimize unregulated, but potentially hazardous, chemicals in their products; and (3) their motivations for engaging in voluntary chemicals management. The research results indicate that challenges in obtaining chemicals-related information exist across business sectors. The interviewed companies each designed strategies that attempted to overcome these information challenges, and several strategy elements were common across the sectors studied. The most significant reasons companies reported for trying to minimize dangerous chemicals in their products were to: achieve a competitive advantage and stay ahead of regulations; manage relationships and maintain legitimacy with stakeholders; and put managerial values into practice. The research results may be useful to business and industry representatives who are interested in minimizing chemicals-related product risks and to policy makers who are unfamiliar with companies' challenges in making safer consumer products. Suggestions are offered for policy improvements that increase knowledge, transparency, and information flow about hazardous chemicals and their uses in order to limit the adverse consequences of chemical use and stimulate innovation of safer products.

Advisor: Kennedy Donald
Ortolano Leonard primary advisor. Thesis advisor
Schwarzman Megan advisor. Thesis advisor
Wilson Mike (Michael Perry)
Mixing time of Markov chains on finite and compact lie groups [electronic resource]

This thesis studies the mixing time of three Markov chains on non-abelian groups. The first is a Metropolis Markov chain on the symmetric groups, initially introduced by Hanlon and Diaconis, and the last two are random walks on the special orthogonal groups, known as Rosenthal's walk and Kac's walk respectively. Using input from representation theory and symmetric function theory, it is shown that cut-off phenomena occur under total variation distance for the Hanlon-Diaconis chain and Rosenthal's walk. For the Kac random walk, a combination of functional-analytic and probabilistic techniques are used to establish the first polynomial order upper bound for its mixing time.

Keywords: Mathematics
Advisor: Diaconis Persi primary advisor. Thesis advisor
Bump Daniel
Dembo Amir advisor. Thesis advisor
A model diffractive boundary value problem on an asymptotically anti-de Sitter space [electronic resource]

We study the propagation of singularities (in the sense of smooth wave front set) of the solution of a model case initial-boundary value problem with glancing rays for a concave domain on an asymptotically anti-de Sitter manifold. The main result addresses the diffractive problem and establishes that there is no propagation of singularities into the shadow for the solution, i.e. the diffractive result for codimension-1 smooth boundary holds in this setting. The approach adopted is motivated by the work done for a conformally related diffractive model problem by Friedlander, in which an explicit solution was constructed using the Airy function. This work was later generalized by Melrose and by Taylor, via the method of parametrix construction. Our setting is a simple case of asympotically anti-de Sitter spaces, which are Lorentzian manifolds modeled on anti-de Sitter space at infinity but whose boundary are not totally geodesic (unlike the exact anti-de Sitter space). Most technical difficulties of the problem reduce to studying and constructing a global resolvent for a semiclassical ODE on the real half line, which at one end is a b-operator (in the sense of Melrose) while having a scattering behavior at infinity. We use different techniques near zero and infinity to analyze the local problems: near infinity we use local resolvent bounds and near zero we build a local semiclassical parametrix. After this step, the `gluing' method by Datchev-Vasy serves to combine these local estimates to get the norm bound for the global resolvent.

Keywords: Mathematics
Advisor: Vasy András primary advisor. Thesis advisor
Mazzeo Rafe advisor. Thesis advisor
Ryzhik Leonid advisor. Thesis advisor
Model validation of mixed-signal systems [electronic resource]

Today it is difficult to validate a mixed-signal System-on-Chip, i.e., one which contains analog and digital components. The problem is that the analog and digital subsystems are usually strongly intertwined so they must be validated together as a system, but the validation approach for analog and digital blocks are completely different. We address this problem by creating high-level functional models of the analog components that are compatible with top-level digital system validation, and then providing a method of formal checking to ensure that these functional models match the operation of the transistor level implementations of these blocks. The formal checking of the functional analog models is enabled by observing that the result surface of an analog block is a smooth function of its analog inputs -- that is what makes it an analog block. This smooth result surface means it is not difficult to "explore" the design space of an analog block. We use this insight to create an equivalence checker between two analog descriptions: a SPICE netlist and its Verilog model. This checker exploits the fact that most analog circuits have a linear intent. Lastly we use this same insight to simplify statistical analysis of large mixed-signal systems to ensure that the system is robust to process variations. We describe a way to characterize the statistical behavior of circuits and to map the results to the functional model so one can estimate the parametric yield of the system by running system-level Monte Carlo simulations with analog models instead of circuit netlists.

Keywords: Electrical Engineering
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Murmann Boris primary advisor. Thesis advisor
Wooley Bruce A.
Modeling Gas Production from Shales and Coal-Beds

Development of shale gas has transformed the energy outlook of US in the past decade. Identification of massive global resources and development of technology for economically producing gas from such sources is making a huge impact on the energy picture. According to EIA (EIA, 2011) the total gas resources of the world are estimated to be about 22,600 TCF of which 40% is now contributed by shale plays. Shales have complex pore networks and distinct scales for fluid flow. There are at least four types of porosities present in shales — Inorganic porosity, nano-porosity within organic Kerogen and porosity associated with both natural and artificially created fractures. Also, significant gas is assumed to be adsorbed in the Kerogen. Naturally occurring shales have little matrix permeability though. Horizontal drilling assisted by multi-stage hydraulic fracturing make gas production from shales viable. This increases near well-bore conductivity and also stimulates the network of natural fractures. Modeling fluid transport in shales is challenging. This is due to the combination of multiple porosities, gas desorption and slippage effects. We present two numerical schemes to simulate gas production from such systems. In the Single Porosity Model, we assume that there is only one distinct pore network and the gas desorbs instantaneously from the shale matrix as the reservoir depletes. In the Dual Porosity Model we consider two coupled porous networks with desorption in the organic nano-pores. Langmuir Adsorption Isotherm (Langmuir’s 1916) is used to model the desorption process. Slippage of gas molecules within nano-pores is incorporated using Klinkenberg’s Effect, (Klinkenberg 1941). Single Porosity Model is observed to be less consistent with both pore networks and desorption process in shales. In Dual Porosity Model, natural fractures permeability (kf) significantly affects early stage of gas production and matrix-fracture flux coefficient (Dmf) controls the slow desorbed flux in later half of production. Also, high Langmuir’s Volume (VL) increase production and delay pressure depletion within the reservoir. We also present a scheme to simulate gas recovery from naturally occurring coal seams. Single porosity, two phase gas-water code with instantaneous desorption is developed to model initial-dewatering and depletion phase of a typical Coal-bed Methane well.

Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Thesis
Advisor: Aziz Khalid
Modeling scalar dispersion in urban environments [electronic resource]

The expansion of High Performance Computing (HPC) capabilities is allowing Computational Fluid Dynamics (CFD) methods to be applied to model dispersion in urban areas. The problem of dispersion in such environments is of growing concern to governmental organizations and first responders interested in mitigating the effects of a terrorist attack or intentional release of a harmful substance. The fundamental physical phenomena underlying the dispersion processes to be modeled is that of turbulent mixing and transport. The processes are inherently of a multi-scale nature as releases proceed from localized sources to envelop larger areas. Adding to the modeling challenge within an urban environment is that complex geometries create strong anisotropies which traditional reduced-order modeling approaches fail to capture. In the first portion of this work, the computational infrastructure is assembled to enable simulations of dispersion in real urban environments. An Oklahoma City validation case is presented and compared with available experimental tracer data. Next, high-fidelity Direct Numerical Simulations (DNS) and Large-Eddy Simulations (LES) of dispersion in "building block" geometries are performed. The results are used to study dispersion flow physics within an urban-like canopy from the building to neighborhood scales. Additionally, the high-fidelity datasets are used to evaluate and drive improvements in the Reynolds-Averaged Navier-Stokes (RANS) modeling approach. Algebraic models are shown to yield an improved representation of the turbulent scalar flux as compared to the standard Schmidt number approach. It is shown that these scalar flux models can be combined with eddy-viscosity type turbulence closures when a better representation of normal Reynolds stress anisotropy is provided. The v2-f model is adapted to provide such a representation and improvement is demonstrated in predicting the scalar field from a point source release.

Keywords: Mechanical Engineering
Advisor: Iaccarino Gianluca primary advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Shaqfeh Eric S. G. (Eric Stefan Garrido) advisor. Thesis advisor
Modulation of hepatitis C virus RNA abundance by the liver-specific microRNA miR-122 [electronic resource]

Hepatitis C virus (HCV) is a global health problem, infecting approximately 2% of the world's population. The virus is hepatotropic, replicating in liver cells, and its only known hosts are humans and chimpanzees. HCV is an unusual virus in that it requires the liver-specific host microRNA (miRNA) miR-122 for HCV RNA accumulation. Though the precise mechanism by which miR-122 upregulates HCV RNA is still under investigation, it is known that miR-122 must bind to two adjacent sites in the 5' end of the HCV genome. In this dissertation, a stepwise mutational analysis of the entire sequence of miR-122 was performed to identify residues important for HCV RNA accumulation. All mutant miRNAs were tested in canonical miRNA reporter assays and in HCV RNA accumulation assays. The identities of two nucleotides within miR-122, at positions 15 and 16, were shown to be dispensable for canonical miRNA and siRNA activity but required for HCV RNA accumulation. Compensatory mutations in the HCV genome upstream of the original binding sites uncovered supplementary binding sites for nucleotides 15 and 16 of miR-122. This analysis led to a new model for miR-122-HCV RNA interactions. To further define the requirements of HCV for miR-122, we investigated whether the predecessor of mature miR-122, a long hairpin precursor designated pre-miR-122, was also able to mediate HCV RNA accumulation. The function of pre-miR-122 was tested in miRNA, siRNA, and HCV RNA accumulation assays. Inhibition of pre-miR-122 processing was achieved by substituting deoxyribonucleotides into the loop of pre-miR-122 to prevent Dicer-mediated cleavage. Full-length pre-miR-122 was demonstrated to be functional in miRNA and siRNA assays and to be sufficient for HCV RNA accumulation. Pre-miR-122 also required traditional components of the RNA-induced silencing complex (RISC) for activity. Taken together, this research has uncovered novel requirements of miR-122 for HCV RNA accumulation. Components shown to be dispensable for canonical miRNA interactions were necessary for this unusual microRNA-target RNA interaction. Uncovering hepatitis C virus's stringent requirements for the mature and precursor forms of miR-122 will pave the way for new antiviral therapies targeting a host factor.

Keywords: Microbiology and Immunology.
Advisor: Sarnow P. (Peter) primary advisor. Thesis advisor
Arvin Ann M. advisor. Thesis advisor
Chen Chang-Zheng advisor. Thesis advisor
Fire Andrew Zachary advisor. Thesis advisor