10,387 Works

Data from: Notch and Nodal control expression of a forkhead factor in the specification network of a multipotent progenitor population in sea urchin

Stefan C. Materna, S. Zachary Swartz & Joel Smith
Indirect development, where embryogenesis gives rise to a larval form, requires that some cells retain developmental potency until they contribute to the different tissues in the adult, including the germ line, in a later, post-embryonic phase. In sea urchins, the coelomic pouches are the major contributor to the adult but how coelomic pouch cells (CPCs) are specified during embryogenesis is unknown. We here identify the key signaling inputs into the CPC specification network and show...

Data from: Catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes in the ‘anaerobic’ termite gut spirochete Treponema primitia

Kaitlyn S. Lucey & Jared R. Leadbetter
Microorganisms have evolved a spectacular diversity of metabolisms, some of which allow them to overcome environmental constraints, utilize abundant but inaccessible resources and drive nutrient cycling in various ecosystems. The termite hindgut microbial community is optimized to metabolize wood, and in recent years, the in situ physiological and ecological functions of community members have been researched. Spirochetes are abundant in the termite gut, and herein, putative aromatic meta-cleavage pathway genes typical of aerobic pseudomonads were...

Data from: A submersible, off-axis holographic microscope for detection of microbial motility and morphology in aqueous and icy environments

Christian A. Lindensmith, Stephanie Rider, Manuel Bedrossian, J. Kent Wallace, Eugene Serabyn, Gordon M. Showalter, Jody W. Deming & Jay L. Nadeau
Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples...

Data from: Dataset of human medial temporal lobe single neuron activity during declarative memory encoding and recognition

Mailys C. M. Faraut, April A. Carlson, Shannon Sullivan, Oana Tudusciuc, Ian Ross, Chrystal M. Reed, Jeffrey M. Chung, Adam N. Mamelak & Ueli Rutishauser
We present a dataset of 1,576 single neurons recorded from the human amygdala and hippocampus in 65 sessions from 42 patients undergoing intracranial monitoring for localization of epileptic seizures. Subjects performed a recognition memory task with pictures as stimuli. Subjects were asked to identify whether they had seen a particular image the first time (‘new’) or second time (‘old’) on a 1–6 confidence scale. This comprehensive dataset includes the spike times of all neurons and...

Data from: History dependence in insect flight decisions during odor tracking

Rich Pang, Floris Van Breugel, Michael Dickinson, Jeffrey A. Riffell & Adrienne Fairhall
Natural decision-making often involves extended decision sequences in response to variable stimuli with complex structure. As an example, many animals follow odor plumes to locate food sources or mates, but turbulence breaks up the advected odor signal into intermittent filaments and puffs. This scenario provides an opportunity to ask how animals use sparse, instantaneous, and stochastic signal encounters to generate goal-oriented behavioral sequences. Here we examined the trajectories of flying fruit flies (Drosophila melanogaster) and...

Data from: Reconstruction of genetically identified neurons imaged by serial-section electron microscopy

Maximilian Joesch, David Mankus, Masahito Yamagata, Ali Shahbazi, Richard Shalek, Adi Suissa-Peleg, Markus Meister, Jeff W. Lichtman, Walter J. Scheirer, Joshua R. Sanes & Richard Schalek
Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that...

Synaptic organization of cortico-cortical communication in primates

Maria Ashaber, Laszlo Zalanyi, Emese Palfi, Istvan Stuber, Tamas Kovacs, Rob M. Friedman, Anna W. Roe & László Négyessy
In cortical circuitry synaptic communication across areas is based on two types of axon terminals, small and large, with modulatory and driving roles, respectively. In contrast, it is not known whether similar synaptic specializations exist for intra-areal projections. Using anterograde tracing and three-dimensional reconstruction by electron microscopy (3D-EM) we asked if large boutons form synapses in the circuit of somatosensory cortical areas 3b and 1. In contrast to observations in macaque visual cortex, light microscopy...

Insights into the Mechanism of Asparagine-Linked Glycosylation: Kinetic Studies with Substrates and Inhibitors

Tamara Lynn Hendrickson
Investigations into the mechanism of action of oligosaccharyl transferase (OT), the enzyme that catalyzes the first committed step in the biosynthesis of all asparagine-linked glycoproteins, were conducted. Research focused on kinetic studies with small reactive molecules and tripeptide substrates and inhibitors; these experiments were designed to specifically probe the OT active site. Commercially available chemical modification agents were used to identify a reactive cysteine residue in or near the oligosaccharide binding site. Based on this...

Identification of New OPA1 Cleavage Site Reveals that Short Isoforms Regulate Mitochondrial Fusion

Ruohan Wang
OPA1 is a 120kDa large GTPase belonging to the dynamin superfamily. It is the only known mitochondrial inner membrane fusion protein, mediating fusion of the mitochondrial inner membranes following outer membrane fusion. Additionally, OPA1 also regulates cristae morphology and maintains respiratory chain function. OPA1 has two forms—inner-membrane-anchored long forms (l-OPA1) and cleaved inter-membrane-space only short forms (s-OPA1). L-OPA1 are proteolytically processed by two mitochondrial proteases—OMA1 and YME1L, acting at cleavage sites S1 and S2 respectively,...

High Fidelity Probe and Mitigation of Mirror Thermal Fluctuations

Tara Chalermsongsak
Thermal noise arising from mechanical loss in high reflective dielectric coatings is a significant source of noise in precision optical measurements. In particular, Advanced LIGO, a large scale interferometer aiming to observed gravitational wave, is expected to be limited by coating thermal noise in the most sensitive region around 30–300 Hz. Various theoretical calculations for predicting coating Brownian noise have been proposed. However, due to the relatively limited knowledge of the coating material properties, an...

Dynamic Rupture Simulation Integrated with Earthquake Observations

Yihe Huang
Dynamic rupture simulations are unique in their contributions to the study of earthquake physics. The current rapid development of dynamic rupture simulations poses several new questions: Do the simulations reflect the real world? Do the simulations have predictive power? Which one should we believe when the simulations disagree? This thesis illustrates how integration with observations can help address these questions and reduce the effects of non-uniqueness of both dynamic rupture simulations and kinematic inversion problems....

Seismic Structure along Transitions from Flat to Normal Subduction: Central Mexico, Southern Peru, and Southwest Japan

Sara Lyn Dougherty
The fine-scale seismic structure of the central Mexico, southern Peru, and southwest Japan subduction zones is studied using intraslab earthquakes recorded by temporary and permanent regional seismic arrays. The morphology of the transition from flat to normal subduction is explored in central Mexico and southern Peru, while in southwest Japan the spatial coincidence of a thin ultra-slow velocity layer (USL) atop the flat slab with locations of slow slip events (SSEs) is explored. This USL...

Electronic States in Disordered Topological Insulators

Kun Woo Kim
We present a theoretical study of electronic states in topological insulators with impurities. Chiral edge states in 2d topological insulators and helical surface states in 3d topological insulators show a robust transport against nonmagnetic impurities. Such a nontrivial character inspired physicists to come up with applications such as spintronic devices [1], thermoelectric materials [2], photovoltaics [3], and quantum computation [4]. Not only has it provided new opportunities from a practical point of view, but its...

The Search for Gravitational Waves from the Coalescence of Black Hole Binary Systems in Data from the LIGO and Virgo Detectors. Or: A Dark Walk through a Random Forest

Kari Alison Hodge
The LIGO and Virgo gravitational-wave observatories are complex and extremely sensitive strain detectors that can be used to search for a wide variety of gravitational waves from astrophysical and cosmological sources. In this thesis, I motivate the search for the gravitational wave signals from coalescing black hole binary systems with total mass between 25 and 100 solar masses. The mechanisms for formation of such systems are not well-understood, and we do not have many observational...

Model Predictive Control for Deferrable Loads Scheduling

Niangjun Chen
Real-time demand response is essential for handling the uncertainties of renewable generation. Traditionally, demand response has been focused on large industrial and commercial loads, however it is expected that a large number of small residential loads such as air conditioners, dish washers, and electric vehicles will also participate in the coming years. The electricity consumption of these smaller loads, which we call deferrable loads, can be shifted over time, and thus be used (in aggregate)...

Rational Design of Zinc Phosphide Heterojunction Photovoltaics

Jeffrey Paul Bosco
The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an "earth-abundant" solar absorber, we find zinc phosphide (α-Zn3P2) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>104 cm-1), and long minority-carrier diffusion length (>5 μm), Zn3P2 is composed of abundant Zn and P...

Protein Structure Refinement Algorithms

Mohsen Chitsaz
Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics. Difficulty of the problem stems from two folds: (a) describing the energy...

Fundamental Studies of Carbon Oxygen Bond Activation in Nickel Diphosphine Ether Complexes. And, Metallomacrocycles as Ligands: Synthesis and Characterization of Aluminum-Bridged Bisglyoximato Complexes of Iron and Cobalt

Paul Kelley
In order to develop better catalysts for the cleavage of aryl-X bonds fundamental studies of the mechanism and individual steps of the mechanism have been investigated in detail. As the described studies are difficult at best in catalytic systems, model systems are frequently used. To study aryl-oxygen bond activation, a terphenyl diphosphine scaffold containing an ether moiety in the central arene was designed. The first three chapters of this dissertation focus on the studies of...

Microstructure Control and Iodine Doping of Bismuth Telluride

Nicholas A. Heinz
On the materials scale, thermoelectric efficiency is defined by the dimensionless figure of merit zT. This value is made up of three material components in the form zT = Tα2/ρκ, where α is the Seebeck coefficient, ρ is the electrical resistivity, and κ is the total thermal conductivity. Therefore, in order to improve zT would require the reduction of κ and ρ while increasing α. However due to the inter-relation of the electrical and thermal...

Search for Color Transparency in A(e,e'p) at High Momentum Transfer

Thomas Germano O'Neill
Rates for A(e, e'p) on the nuclei 2H, C, Fe, and Au have been measured at momentum transfers Q2 = 1, 3, 5, and 6.8 (GeV fc)2. We extract the nuclear transparency T, a measure of the importance of final state interactions (FSI) between the outgoing proton and the recoil nucleus. Some calculations based on perturbative QCD predict an increase in T with momentum transfer, a phenomenon known as Color Transparency. No statistically significant rise...

GPU-Accelerated Fourier-Continuation Solvers and Physically Exact Computational Boundary Conditions for Wave Scattering Problems

Timothy James Elling
Many important engineering problems, ranging from antenna design to seismic imaging, require the numerical solution of problems of time-domain propagation and scattering of acoustic, electromagnetic, elastic waves, etc. These problems present several key difficulties, including numerical dispersion, the need for computational boundary conditions, and the extensive computational cost that arises from the extremely large number of unknowns that are often required for adequate spatial resolution of the underlying three-dimensional space. In this thesis a new...

Randomness and Noise in Information Systems

Hongchao Zhou
This dissertation is devoted to the study of randomness and noise in a number of information systems including computation systems, storage systems, and natural paradigms like molecular systems, where randomness plays important and distinct roles. Motivated by applications in engineering and science we address a number of theoretical research questions. In a computation system, randomness enables to perform tasks faster, simpler, or more space efficient. Hence, randomness is a useful computational resource, and the research...

Polarization-Based Navigation in Drosophila

Peter Thomas Weir
Insects maintain a constant bearing across a wide range of spatial scales. Monarch butterflies and locusts traverse continents (Williams, 1957; Wehner, 1984), and foraging bees and ants travel hundreds of meters to return to their nests (Dyer, 1996; Wehner, 1984, 2003), whereas many other insects fly straight for only a few centimeters before changing direction. Despite this variation in spatial scale, the brain region thought to underlie long-distance navigation is remarkably conserved (Loesel et al.,...

Measurement of Thermo-Optic Properties of Thin Film Dielectric Coatings

Gregory H. Ogin
We have carried out an experiment to test the theory of the thermo-optic response of a dielectric stack mirror coating and to measure parameters of interest in calculating thermo-optic noise. Specifically, we measured the coefficient of thermal expansion and the change of index of refraction with temperature (dn/dT ) for thin film silica (SiO2) and tantala (Ta2O5) in mirror coatings. These measurements were achieved by driving thermal fluctuations in such mirrors in one arm of...

A Novel Method for Studying Nucleated Pathways in Membranes: Development and Applications for Gene Delivery

Christina Lei Ting
The development of a safe, selective, and efficient gene delivery system is key to the success of human gene therapy. In polymer-based gene delivery systems, biocompatible polymers electrostatically bind and condense the genetic material into protective nanoparticles. These nanoparticles must subsequently overcome several challenges, which remain poorly understood. In particular, once internalized by the cell, the nanoparticles are trapped inside a membrane-bound compartment called the endosome. In the proton sponge hypothesis, the buffering capacity of...

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