268 Works

Data from: A double-sided microscope to realize whole-ganglion imaging of membrane potential in the medicinal leech

Yusuke Tomina & Daniel A Wagenaar
Studies of neuronal network emergence during sensory processing and motor control are greatly promoted by technologies that allow us to simultaneously record the membrane potential dynamics of a large population of neurons in single cell resolution. To achieve whole-brain recording with the ability to detect both small synaptic potentials and action potentials, we developed a voltage-sensitive dye (VSD) imaging technique based on a double-sided microscope that can image two sides of a nervous system simultaneously....

Data from: Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease

Timothy R. Sampson, Justine W. Debelius, Taren Thron, Stefan Janssen, Gauri G. Shastri, Zehra Esra Ilhan, Collin Challis, Catherine E. Schretter, Sandra Rocha, Viviana Gradinaru, Marie-Francoise Chesselet, Ali Keshavarzian, Kathleen M. Shannon, Rosa Krajmalnik-Brown, Pernilla Wittung-Stafshede, Rob Knight & Sarkis K. Mazmanian
The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson’s disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in...

Computational Methods for Bayesian Inference in Complex Systems

Thomas Anthony Catanach
Bayesian methods are critical for the complete understanding of complex systems. In this approach, we capture all of our uncertainty about a system’s properties using a probability distribution and update this understanding as new information becomes available. By taking the Bayesian perspective, we are able to effectively incorporate our prior knowledge about a model and to rigorously assess the plausibility of candidate models based upon observed data from the system. We can then make probabilistic...

Fluid Dynamics with Incompressible Schrödinger Flow

Albert Ren-Haur Chern
This thesis introduces a new way of looking at incompressible fluid dynamics. Specifically, we formulate and simulate classical fluids using a Schrödinger equation subject to an incompressibility constraint. We call such a fluid flow an incompressible Schrödinger flow (ISF). The approach is motivated by Madelung's hydrodynamical form of quantum mechanics, and we show that it can simulate classical fluids with particular advantage in its simplicity and its ability of capturing thin vortex dynamics. The effective...

Development of a Synthetic Strategy Toward Trans-Cyclobutane-Containing Natural Products: Enantioselective Total Synthesis of (+)-Psiguadial B

Lauren Marie Chapman
Trans-cyclobutane-containing meroterpenoids are a structurally intriguing class of natural products with a diverse array of pharmacologically interesting properties. Herein, the development of a synthetic strategy for de novo construction of the trans-cyclobutane motif is described, which has enabled the first enantioselective total synthesis of the cytotoxic natural product, (+)-psiguadial B. Specifically, we have developed a photochemical Wolff rearrangement with tandem catalytic, asymmetric addition to a ketene generated in situ. To our knowledge, this work represents...

Insights into Pathways of Nitrous Oxide Generation from Novel Isotopologue Measurements

Paul Macdonald Magyar
The accumulation of nitrous oxide (N2O) in the atmosphere is a significant manifestation of human perturbations of the nitrogen cycle. This thesis reports the development and first applications of a novel isotopic technique for characterizing nitrous oxide sources. Chapter 1 describes the development of methods to use the newly available technology of high- resolution dual-inlet multi-collector mass spectrometry to measure six isotopic parameters in nitrous oxide. It reports the standardization and initial biological application of...

Biophysical Studies of Ligand-gated Ion Channels

Betty Ko Wong
This dissertation describes building a methodology for and the biophysical studies of ligand-gated ion channels (LGICs). The primary focus of the first half of this dissertation is on developing a fluorescence-based assay to broadly study LGICs. Chapter 2 describes the site-selective incorporation of a turn-on fluorophore via unnatural amino acid mutagenesis on the mouse muscle-type nicotinic acetylcholine receptor (nAChR) in Xenopus oocytes as a proof-of-principle study. This method has proven to yield very low levels...

Development of a High-Throughput Protein Interaction Assay and its Applications

Hanqing Li
Protein-protein interactions (PPIs) form the backbone for a vast array of biological processes in an organism, ranging from signal transduction to gene regulation to intercellular signaling. Therefore, mapping out protein interactomes has been a crucial and prolific area of scientific research. In recent years, much progress has been made in generating high throughput protein interaction data in a variety of organisms, including S. cerevisiae, C. elegans, and D. melanogaster, as well as in human cell...

Development of Cu- and Ni-Catalyzed C–C and C–N Bond Forming Reactions

Shoshana Bachman
Chapters 1 and 2 describe the development of photoinduced, Cu-catalyzed coupling reactions of unactivated secondary alkyl halides with amide and cyanide nucleophiles. These reactions may be conducted at room temperature under operationally simple conditions. Mechanistic studies are consistent with the intermediacy of alkyl radicals in these processes. Chapter 3 describes progress toward the development of the first enantioselective Ni-catalyzed cross coupling of racemic alkyl halides and heteroatom nucleophiles. Borylation of secondary benzylic chlorides with B2(pin)2...

Discovering Biological Roles of Glycosaminoglycans and Protein O-GlcNAcylation Using Chemical Tools

Matthew Everett Griffin
Carbohydrates surround nearly every cell in the human body. Glycosaminoglycans like chondroitin sulfate and heparan sulfate on the cell surface regulate protein ligand engagement and receptor activation to control a variety of biological processes including development, angiogenesis, and neuronal growth. These polysaccharides exert activity through protein binding to their diverse chemical structures. Therefore, the development of methods to tailor glycosaminoglycan populations at the cell surface with defined structures could provide novel approaches to control biological...

Coding for Security and Reliability in Distributed Systems

Wentao Huang
This dissertation studies the use of coding techniques to improve the reliability and security of distributed systems. The first three parts focus on distributed storage systems, and study schemes that encode a message into n shares, assigned to n nodes, such that any n - r nodes can decode the message (reliability) and any colluding z nodes cannot infer any information about the message (security). The objective is to optimize the computational, implementation, communication and...

Boosting Boosting

Ron Appel
Machine learning is becoming prevalent in all aspects of our lives. For some applications, there is a need for simple but accurate white-box systems that are able to train efficiently and with little data. "Boosting" is an intuitive method, combining many simple (possibly inaccurate) predictors to form a powerful, accurate classifier. Boosted classifiers are intuitive, easy to use, and exhibit the fastest speeds at test-time when implemented as a cascade. However, they have a few...

Aspects of Effective Field Theories from Scattering Amplitudes

Chia-Hsien Shen
On-shell methods offer an alternative definition of quantum field theory at tree-level. We first determine the space of constructible theories solely from dimensional analysis, Lorentz invariance, and locality. We show that all amplitudes in a renormalizable theory in four dimensions are constructible, but only a subset of amplitudes is constructible in non-renormalizable theories. The obstructions to effective field theories (EFTs) are then lifted for the non-linear sigma model, Dirac-Born-Infeld theory, and the Galileon, using the...

Error-Correcting Codes for Networks, Storage and Computation

Wael Halbawi
The advent of the information age has bestowed upon us three challenges related to the way we deal with data. Firstly, there is an unprecedented demand for transmitting data at high rates. Secondly, the massive amounts of data being collected from various sources needs to be stored across time. Thirdly, there is a need to process the data collected and perform computations on it in order to extract meaningful information out of it. The interconnected...

Essays on the Political Economy of Subnational Public Finances

Welmar Eduardo Rosado Buenfil
This dissertation is comprised of three essays addressing the connections between democracy and public finance at the subnational level. Chapter 2 focuses on variation within public expenditure, revenue, and debt at the state level in the United States for the period 1977-2011 seeking to uncover whether there is evidence of efforts by incumbents to manipulate state public finances to influence election outcomes. I find that total public expenditure increased the year before elections, especially during...

Optimal Design of Materials for Energy Conversion

Lincoln Nash Collins
The efficiency of fuel cells, batteries and thermochemical energy conversion devices depends on inherent material characteristics that govern the complex chemistry and transport of multiple species as well as the spatial arrangement of the various materials. Therefore, optimization of the spatial arrangement is a recurrent theme in energy conversion devices. Traditional methods of synthesis offer limited control of the microstructure and there has been much work in advanced imaging for these uncontrolled microstructures and optimizing...

r-Process Nucleosynthesis in Neutron Star Mergers with the New Nuclear Reaction Network SkyNet

Jonas Lippuner
At the Big Bang, only the lightest elements, mainly hydrogen and helium, were produced. Stars synthesize heavier elements, such as helium, carbon, and oxygen, from lighter ones through nuclear fusion. Iron-group elements are created in supernovae (both type Ia and core-collapse). It has been known for 60 years that the slow and rapid neutron capture processes (s- and r-process) are each responsible for creating about half of the elements beyond the iron group. The s-process...

Cell-Selective Chemoproteomics for Biological Discovery

Shannon Elizabeth Stone
Cellular protein synthesis changes rapidly in response to internal and external cues in ways that vary from cell to cell. Global proteomic analyses of microbial communities, tissues, and organisms have provided important insights into the behavior of such systems, but can obscure the diversity of responses characteristic of different cellular subpopulations. Recent advances in cell-specific proteomics—fueled in part by the development of bioorthogonal chemistries, more sensitive mass spectrometers and more advanced mining algorithms—have yielded unprecedented...

Engineering Biosynthetic Pathways in Cell-Free Systems for Sustainability and Chemical Innovation

Yong Yi Wu
This work presents the cell-free transcription-translation (TX-TL) system as a research and development platform for renewable synthesis and molecular discovery. TX-TL is easy to use and provides a biomolecular breadboard for the rapid prototyping and engineering of biosynthetic pathways. This work has validated the capabilities of the cell-free TX-TL system for simultaneous protein expression and chemical synthesis. Specifically, this work shows that TX-TL supports the conversion of intermediates from carbohydrate metabolism and amino acids into...

Visualizing mRNA Translation in situ in Single Cells

Kelly Suzanne Burke
Translation of mRNA is tightly regulated in cells to ensure that proteins are synthesized at the right time, in the right location, and at appropriate levels. Single-molecule fluorescence in situ hybridization (smFISH) is a simple and widely used method to measure mRNA transcription through determining the abundance and localization of mRNAs in single cells. A comparable single-molecule in situ method to measure mRNA translation would enable a more complete understanding of gene regulation. In this...

Numerical Simulations of Three-Dimensional Instabilities in Cavity Flows

Guillaume Alain Brès
Direct numerical simulations are performed to investigate the stability of compressible flow over three-dimensional open cavities for future control applications. First, the typical self-sustained oscillations, commonly referred as shear-layer (Rossiter) modes, are characterized for two-dimensional cavities over a range of flow conditions. A linear stability analysis is then conducted to search for three-dimensional global instabilities of the 2D mean flow for cavities that are homogeneous in the spanwise direction. The presence of such instabilities is...

Analysis and Characterization of Titan Aerosol Simulants by Mass Spectrometry

Kathleen Tiffany Upton
Saturn’s large moon of Titan is unique as the only solid body in the outer solar system to possess a dense atmosphere, which is comprised of mostly nitrogen and methane. Atmospheric chemistry on this moon creates aerosols comprised of carbon, hydrogen, and nitrogen. Laboratory based synthesis of simulated Titan aerosols, also called tholins, led to molecules with rich chemical diversity, functionalities, and molecular weights. While this diversity has intriguing implications for Titan, it complicates the...

On the Evolutionary Pathways of Stars and Extrasolar Planets

Trevor Justin David
In this thesis, I present several studies aimed at determining the evolutionary states of stars and the planets that orbit them. Multiple approaches are undertaken to determine the physical parameters of stars over a wide range of masses, and in the process I evaluate current theoretical models which are commonly used to indirectly determine the properties of stars and planets. Chapter II concerns the ages of nearby stars more massive than the Sun. These stars,...

Transition Metals as Catalysts for Cross-Coupling and Dinitrogen Fixation

Trixia Marie Buscagan
Transition metals are used as catalysts in the laboratory and by nature to facilitate difficult chemical transformations. Herein, three different metal containing catalysts are discussed: Pd and Ni catalysts towards the formation of carbon-carbon (C-C) bonds and Fe catalysts towards the reduction of N2 to NH3. In Chapter 2, mechanistic studies of Pd- and Ni-catalyzed cross-coupling reactions are discussed. The mechanism of transmetalation of a Pd-catalyzed Suzuki cross-coupling reaction is studied using a stereochemical probe,...

Shielding Theory of Enclosures with Apertures

Horacio Augusto Mendez
Present methods for computing the shielding efficiency of metallic plates with apertures are based on the analysis of a plane wave incident on an infinite conducting sheet. When applied to actual enclosures with internal radiation sources, these methods lose all validity, and obviously fail to predict the measured results. Semi-empirical formulas are available for special cases, but no serious analytic investigation has ever been conducted. This dissertation develops the theory of electromaqnetic radiation from metallic...

Registration Year

  • 2017

Resource Types

  • Text
  • Dataset


  • California Institute of Technology
  • University of Washington
  • Stanford University
  • University of California System
  • University of Groningen
  • University of Otago
  • Rush University
  • University of Wisconsin-Madison
  • Arizona State University
  • Chalmers University of Technology