VictorJuiz/thesis huggingface dataset:
Membrane-associated RNA-dependent RNA replication of viruses [electronic resource]

Positive strand RNA viruses are major human pathogens that result in significant morbidities and mortalities worldwide. All positive strand RNA viruses induce rearrangement of intracellular membranes to establish a membranous platform where genome replication occurs. This replication factory, or replication complex, contains a collection of host and viral proteins as well as RNAs in organelle-like structures with distinct membrane composition. In this thesis, I aim to dissect the contribution of different components of the replication complex of one important human RNA virus, the hepatitis C virus (HCV). To characterize the importance of RNA secondary structure for viral replication, I utilized and improved a novel chemical mapping method termed 2' selective hydroxyl acylation analyzed by primer extension (SHAPE). This method allowed me to rapidly determine the RNA secondary structure of the HCV 5' untranslated region (UTR) at high resolution and its interaction with the liver-specific microRNA (miR), miR-122. I also utilized a supported lipid-bilayer (SLB) platform coupled with quartz-crystal microbalance with dissipation (QCM-D) to reconstitute and monitor how the interactions of key components of the viral replication complex including the viral proteins, the RNA template, and the membrane phosphoinositides composition affect in vitro RNA-dependent RNA transcription and viral RNA replication inside the cell. The above studies employed a combination of chemical, biophysical, and genetics tools and reveal that 1) the RNA secondary structure of the HCV 5' UTR and the structural integrity of the HCV 5' UTR -- miR-122 complex mediate viral replication; 2) SLB coupled with QCM-D can monitor the reconstitution of RNA synthesis activity of the HCV membrane-anchored RNA-dependent RNA polymerase NS5B and its interaction with other replicase complex proteins; and 3) the replication complex of HCV is enriched with phosphatidylinositol 4,5-bisphosphate (PIP2), PIP2 is a ligand for another replicase component protein NS5A, and NS5A binds PIP2 the basic amino acids PIP2 pincer (BAPPP) domain, and this interaction modulates HCV RNA replication.

Keywords: Microbiology and Immunology.
Advisor: Glenn Jeffrey S.
Greenberg Harry B. advisor. Thesis advisor
Peltz Gary
Sarnow P. (Peter) advisor. Thesis advisor
A MEMS actuator and sensor for the study of cell mechanics and adhesion [electronic resource]

An active area of Microelectromechanical Systems (MEMS) research over the past few years has been to develop tools that can probe the forces generated and sensed by cells. Silicon-based tools developed in this effort have the benefit of being able to apply and sense forces at a greater resolution and in a more repeatable fashion. However, they have been too small to probe more than one or a few cells at a time, and the opaqueness of silicon has prohibited inverted live microscopy, which is important for transferring the technology to biological and medical labs. In addition, while many tools exist that can apply and sense the effects of tension on cells, no devices exist that can apply shear to a sheet of epithelial cells. This is despite the fact that the ability to apply and sense shear is important in understanding how cells interact with each other mechanically, which is essential in studying cell-cell adhesions in biology and medicine. Two types of silicon MEMS devices have been designed, fabricated, and tested, which can strain a sheet of epithelial (2D and skin-like) cells in tension and shear simultaneously. The first set of devices, which have silicon cell-adhesion pads can be used for upright bright-field and fluorescence microscopy. The second set of devices, which have silicon-nitride cell-adhesion pads can be used for both upright and inverted bright-field and fluorescence microscopy. Inverted microscopy has been made possible by spraying the bottom of 50 \um\ deep trenches with photoresist and exposing the area in the shape of cell-adhesion pads. In addition, the Silicon on Insulator (SOI) handle wafer has been backside etched below the cell-adhesion pads. These devices have been integrated with a cell-delivery mechanism that can deliver ~1000 cells to the cells adhesion pads. In addition, an open culture system has been implemented that allows the user to perform live cell microscopy for days without the use of an incubator. With the combination of these devices and experimental methods we have formed single sheets of Madin-Darby Canine Kidney (MDCK) epithelial cells on these devices and observed their reorganization in response to shear and tension. Particle Image Velocimetry (PIV) shows cells in an epithelium move towards the shear plane in response to an applied shear stress. Experiments where blebbistatin, a treatment inhibiting actomyosin contractility, was applied before the application of stress showed no collective cell migration. Therefore, we showed that the collective migration due to shear is an active biological response, as opposed to a passive and purely material one.

Keywords: Mechanical Engineering.
Advisor: Pruitt Beth primary advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Nelson W. J. (W. James)
Metacognizant: Developing Higher Order Thinking Skills

Metacognizant is an application integrated into the middle school classroom, designed to foster metacognitive awareness and positive identity development in a conscious manner. Research suggests that by deliberately exposing students to higher-order thinking strategies, we can begin to close the achievement gap in education. Taking advantage of the affordances of technology for efficiency and personalization, Metacognizant engages students in tailored, bite-size tasks (or ‘cogs’) inspired by current research on metacognitive development. Cogs are structured around concrete artifacts of student learning (including video clips, photos, written work, and class discussions) to help students access these very abstract skills.

Keywords: metacognition
agency
identity
mathematics
higher-order thinking
Learning Design and Technology
Graduate School of Education
Thesis
Methods for monitoring lesion formation during thermal therapies using magnetic resonance imaging [electronic resource]

The first part of this thesis will rely on previously established lesion evaluation modalities such as diffusion to monitor lesion formation. A method to simultaneously monitor temperature and diffusion will be proposed and implemented to remove temperature dependent changes from diffusion measurements in order to highlight the diffusion changes associated with loss of tissue viability. The evolution of how tissue responds to treatment will be analyzed using this new insight on lesion development. The second part of this thesis will introduce a novel contrast mechanism to monitor thermal treatments. This contrast is based on a steady-state sequence called Double Echo in Steady State (DESS); the second echo in DESS is designed to be sensitive to diffusion. A strategy to incorporate this sequence to treatment monitoring will be proposed and implemented through simulations and validated with phantom experiments. Preliminary experiments using this contrast mechanism to monitor and evaluate lesions in vivo will also be presented.

Keywords: Bioengineering.
Advisor: Pauly Kim Butts (Kim Rosemary Butts)
Ghanouni Pejman
Pelc Norbert J. advisor. Thesis advisor
Micro but mighty [electronic resource] : microrobots working in a macro world

The vision of microrobots working together to move human scale objects has long been in the imaginations of science fiction writers, but in practical terms this vision has been hard to achieve. Friction scales unfavorably with size reduction, so the ability to provide shear ground reaction forces is severely limited at small scales. This thesis examines the use of small robots that employ controllable adhesives, i.e., adhesives for which the magnitude of the adhesive pressure can be modulated by varying a quantity such as the applied shear force. The applications include robots for horizontal and vertical surfaces. The thesis also addresses the implications for actuation that accompany a desire to use controllable adhesion in small robots. Finally, the thesis examines the characteristics of small robots, and their mode of locomotion, that make them more or less suited for working in teams to produce much larger forces than each robot can produce individually.

Keywords: Mechanical Engineering.
Advisor: Cutkosky Mark R. primary advisor. Thesis advisor
Kenny Thomas William advisor. Thesis advisor
Prinz F. B. advisor. Thesis advisor
The microfluidic electrokinetic sample holder for serial femtosecond X-ray crystallography [electronic resource]

Serial femtosecond X-ray crystallography (SFX) is sitting at the frontier of a paradigm shift in structural biology. The intense X-rays with short femtosecond pulses available from free electron lasers (FELs) has allowed us to view biological structures with similar, or sometimes better, resolution than current techniques. Refinement of these methods will lead us to structures of macromolecules once not attainable at current generation lightsources or with other imaging techniques. The SFX technique can yield high resolution room temperature data of biological structures. It relies on gathering statistics on tens of thousands of protein crystals, typically on the order of a dozen microns or smaller as opposed to larger millimeter-sized crystals common at synchrotrons. The intense power of the X-rays destroys the sample and thus does not allow for multiple collections on the same crystal. This has required careful consideration on sample delivery techniques. The current sample environments for data collection are in mid-vacuum (10e-6 Torr) and need a constant supply of sample, while not consuming too much sample, remaining stable and minimizing background while keeping the proteins crystalline in solution. This multifaceted optimization has made sample delivery one of the cruxes of the SFX field. This dissertation will outline one of many techniques that have been developed in the past years to address many of the issues of sample injection: the microfluidic electrokinetic sample holder (MESH). This technique leverages the moderate viscosities of the mother liquor and common additives found in crystallization conditions in order to reduce the sample consumption and use an applied electric field in order to focus and stabilize the meniscus to better interact with the incident X-rays probing the sample. This technique, similar to the electrospin process, will be described along with some of the different apparatus designed to interface it at the Coherent X-ray Imaging (CXI) endstation at the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Lab (SLAC). Finally, a new concentric technique will be described, the coMESH, which attempts to address some shortcomings of the first technique, while delivering delicate crystals at low sample consumption. From solution scattering, to protein crystal standards, nanocrystals, large complexes, time-resolved experiments, and experimental phasing, the electrokinetic technique proves quite capable to move between experimental, geometric, and biological constraints in order to leverage the advantages of SFX to the larger structural biology community with it's minimal sample consumption (micro- to milligrams) and simplistic and modular design.

Keywords: Mechanical Engineering.
Advisor: Bucksbaum Philip H. primary advisor. Thesis advisor
Santiago Juan G. primary advisor. Thesis advisor
Bogan Michael A.
Microfluidic manipulation of droplets using synchronous universal logic operations [electronic resource]

From Zuse's thesis, which pioneered digital physics, to Landauer and Wheeler's famous `it from bit', we know that information is fundamentally linked to its physical representations; manipulation of information, for example, represented by the flow of electrons in a microcircuit or biological molecules, intrinsically leads to algorithmic manipulation of matter. Although such algorithmic assembly is commonplace nowadays at the nanoscale, including DNA- based tile nanostructures, its counterpart at the mesoscale is surprisingly missing. Droplets in microfluidic chambers are a growing platform for both physics and biology experiments. Droplets are indeed versatile digital materials; they can be produced in large quantities at high throughput, perform chemical reactions as miniature beakers and carry biological entities. Several manipulation techniques, including electric, optical, acoustic and magnetic forces, have been used for serially manipulating droplets. Because these systems depend on external feedback by the user and lack any inherent computational capability, large scale-up and parallel information-based manipulation is limited. A simple assignment of presence or absence of a droplet as a bit of information can allow us to look at these multi-phase systems as information processing units. Recent work has demonstrated the universal computational capabilities of low-Reynolds-number multi-phase hydrodynamics using pressure-based flow controllers . However, all of these prior systems suffer from a fundamental drawback; they are asynchronous and thus lack the capacity to scale to complex cascaded digital logic. To address this problem, I introduce a new platform that uses a single global clock, that is, a rotating magnetic field to synchronize the motion of arbitrary numbers of droplets and direct or store them in permalloy tracks using digital logic operations. The manipulation of the droplets is magnetophoretic; the rotating magnetic field activates the permalloy tracks to create a dynamic energy landscape that sets the droplets in motion. I demonstrate that the droplets in my platform can either be paramagnetic, that is ferrofluidic, or diamagnetic, for water that is essentially diamagnetic - in practice non-magnetic. Through magnetic and hydrodynamic interaction forces between droplets, we developed OR/AND logic gates, universal XOR/AND and XOR/NAND gates, fanouts, memory loops, flip-flops, a finite-state machine and a full adder that adds droplet `bits'. Our platform demonstrates both combinational and sequential logic and does not rely on pressure-based flow controllers, therefore enabling a unique `non-volatile' conservative physical logic and memory. Our platform enables large-scale integration of droplet logic, analogous to the scaling seen in digital electronics, and opens new avenues in mesoscale material processing.

Keywords: Mechanical Engineering.
Advisor: Prakash Manu primary advisor. Thesis advisor
Santiago Juan G. primary advisor. Thesis advisor
Pease R. (R. Fabian W.) advisor. Thesis advisor
Miniaturized diaphragm-based fiber-tip acoustic sensors for the identification of stem-cell-derived cardiomyocytes [electronic resource]

Historically, acoustic sensors have been used in a variety of applications spanning land, water, and air. This dissertation expands their potential application space into the human body, both figuratively and literally. A diaphragm-based, fiber-tip hydrophone is presented, with the required sensitivity at low frequencies to detect the action potential of a single cardiomyocyte (heart muscle cell).

Keywords: Electrical Engineering.
Advisor: Solgaard Olav primary advisor. Thesis advisor
Digonnet Michel J. F. advisor. Thesis advisor
Melosh Nicholas A. advisor. Thesis advisor
Model-based artifact correction in MRI [electronic resource]

Magnetic Resonance Imaging (MRI) is an imaging modality known for its safety and excellent soft tissue contrast. It is estimated that two out of every hundred Americans have an artificial hip or knee. MRI can serve as a useful tool for postsurgical examination of joint replacement surgeries. However, current techniques that remove image distortion near metallic implants struggle near the metal and also blur the images, potentially making diagnosis harder for radiologists. In this work we present an approach to deblur MRI images near metallic implants. This method consists of improved field-map estimation and spectral bin combination techniques. We also introduce a method to find a good balance between blurring and distortion in regions where the field-map estimation is unreliable. This method is compared in phantoms and in vivo and shown to perform substantially better than current approaches. Additionally, due to its superb soft-tissue contrast, MRI also excels at diagnosis of lesions and cysts. These tissues are often easier to visualize and diagnose when signal from fat, which is often bright in MRI images, is suppressed or separated from that of other "water" tissues. Current techniques for suppressing or separating fat are often unable to do so throughout the entire image and/or lead to long acquisition times. In this work we first present an approach that enables the separation of fat and water while enabling high-resolution imaging and T2-like contrast in short scan times. This approach uses improved signal modeling to enable improved fat/water separation iv using an SNR-efficient balanced Steady-State Free-Precession (bSSFP) two-point Dixon method, while simultaneously reducing the banding artifacts associated with bSSFP sequences. Furthermore, an analysis to assess the viability of a method that combines two-point Dixon fat/water separation with the time-saving benefits of Homodyne reconstructions is also performed. This analysis finds that while the described approach could save time, it's clinical usability may be limited due to artifacts created at fat/water tissue interfaces.

Keywords: Electrical Engineering.
Advisor: Hargreaves Brian Andrew primary advisor. Thesis advisor
Daniel Bruce (Bruce Lewis) advisor. Thesis advisor
Nishimura Dwight George advisor. Thesis advisor
Modeling and validation of RNA secondary structures and ensembles through multidimensional chemical mapping [electronic resource]

Ribonucleic acid (RNA) molecules play important roles in many of the core processes of life. The versatility of RNA functions relies on its ability to adopt and interconvert between distinct folding states. However, RNA conformations have largely eluded experimental dissection and validation due to the lack of generally applicable quantitative methods. In this dissertation, I present the recent development of the lock-mutate-map-rescue (LM2R) workflow, which leverages systematic mutagenesis and high-throughput RNA chemical mapping to unambiguously validate or falsify base-pairing models. First, the mutate-map-rescue (M2R) method was established on a small bacterial 16S ribosomal RNA domain, provided incisive evidence falsifying a prior SHAPE-derived model, and instead revealed a structural equilibrium between a crystallographic secondary structure and one with a single-nucleotide register shift. After the initial success, I applied M2R to two novel real-world RNA regulatory elements that possess crucial biological functions. The relevance of M2R-validated secondary structure models was further strengthened by in vivo assays, fueling discoveries of new paradigms in biology. Furthermore, to dissect the solution structures of a paradoxical adenine riboswitch, I advanced the technique into LM2R with an additional layer of mutagenesis to obtain 'locking' mutants that each isolates a single state. With such stabilizers enabling rigorous tests for co-existence of helices within a particular state, LM2R gave rise to a unified ensemble model that resolves discrepancies between previous alternative models. Finally, I made available an algorithm that optimizes PCR assembly design for RNA preparation, and created the Primerize-2D server that greatly simplifies LM2R library synthesis. In sum, as the central component of the multidimensional chemical mapping (MCM) pipeline, LM2R provides a general and practical route to robust validation of RNA secondary structures and ensembles.

Keywords: Biochemistry.
Advisor: Das Rhiju
Greenleaf William James advisor. Thesis advisor
Herschlag Daniel advisor. Thesis advisor
Modeling catalytic properties of metal nanoparticles [electronic resource]

Catalysts are materials that can accelerate chemical reactions, and they are key to creating sustainable processes and a greener environment. Catalysts in the form of metal nanoparticles are ubiquitous in current industrial processes, and they are critical to creating a sustainable energy future. Theory has provided vital insights into the fundamental limitations of various types of processes, and density functional theory (DFT) calculations have inspired the discovery of new active materials. Advancements in supercomputing resources and scalable quantum chemistry codes have enabled us to explore the catalytic behavior of metal nanoparticles from the fundamental atomic level. We present calculated adsorption energies of oxygen on gold and platinum clusters with up to 923 atoms (3 nm diameter) using Density Functional Theory. We find that surface tension of the clusters induces a compression of which weakens the bonding of adsorbates compared to the bonding on extended surfaces. The effect is largest for close packed surfaces and almost non-existent on the more reactive steps and edges. The effect is largest at low coverage and decreases, even changing sign, at higher coverages where the strain changes from compressive to tensile. Quantum-size-effects also influence adsorption energies but only below a critical size of 1.5 nm for platinum and 2.5 nm for gold. We develop a model to describe the strain-induced size effects on adsorption energies, which is able to describe the influence of surface structure, adsorbate, metal, and coverage. Stability of metal nanoparticle is also a great concern in the field of heterogeneous, and a dominant process that degrades the activity of these catalysts is the agglomeration of individual nanoparticles. In order to better understand the sintering mechanism, we propose a kinetic Monte-Carlo (kMC) model for simulating the movement of platinum particles on supports, based on atom-by-atom diffusion on the surface the particle. The proposed model was able to reproduce equilibrium cluster shapes predicted using Wulff-construction. The diffusivity of platinum particles was simulated both purely based on random motion and assisted using a drift velocity. The overall particle diffusivity increases with temperature, however the extracted activation barrier appears to be temperature independent. In addition, this barrier was found to increase with particle size, as well as, with the adhesion between the particle and the support.

Keywords: Chemistry.
Advisor: Nørskov Jens K.
Abild-Pedersen Frank
Martinez Todd J. (Todd Joseph)