Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia: Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes.

Here, we report the high-quality draft genome sequences of Opitutaceae sp. strains TAV3 and TAV4, which were isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes Using a combination of Illumina and PacBio sequencing, we constructed nearly complete assemblies totaling 5.84 and 5.91 Mbp in length for strains TAV3 and TAV4, respectively. In addition, we report an in silico analysis of potential lignocellulose-digesting enzymes present in these strains

Improved high-field reliability for a SiC metal-oxide-semiconductor device by the incorporation of nitrogen into its HfTiO gate dielectric

Materials with high dielectric constant (k) have been used in SiC-based metal-oxide-semiconductor (MOS) devices to reduce the electric field in the gate dielectric and thus suppress a high-field reliability problem. In this work, high- k gate dielectrics Hfx Ti1-x O2 and Hfx Ti1-x ON are applied in SiC MOS devices and an ultrathin thermally grown SiO2 is used as an interlayer between SiC and the high- k materials to block electron injection from SiC into the low-barrier high- k materials. Incorporating nitrogen into the Hf-Ti oxide (by adding nitrogen gas during its sputtering) stacked with a SiO2 interlayer (Hfx Ti1-x O SiO2) results in a better gate dielectric for the MOS capacitor, such as smaller frequency dispersion in the capacitance-voltage curve, less oxide charges, and better interface quality. Moreover, the nitrogen incorporation increases the dielectric constant of the oxide, but causes higher dielectric leakage, which can be suppressed by the SiO2 interlayer. High-field stress under constant electric field is performed on the stacked/nonstacked Hf-Ti oxides and oxynitrides, and it turns out that the two oxynitrides show a much smaller flatband shift and a less stress-induced leakage current compared with the two oxides. Based on these results, the Hfx Ti1-x ON SiO2 stack could be a promising high- k gate dielectric for SiC MOS devices with enhanced reliability. © 2007 American Institute of Physics.published_or_final_versio

Effects of NO annealing and GaOxNy interlayer on GaN metal-insulator-semiconductor capacitor with SiO2 gate dielectric

SiO2 was deposited on GaN by radio-frequency sputtering to fabricate metal-insulator-semiconductor (MIS) capacitors. Before the deposition, an ultrathin GaOx Ny interlayer was thermally grown on the GaN wafer to improve the quality of the insulator/ GaN interface. The interface-trap density at 0.4 eV below the conduction bandedge was reduced by one order compared with that of a sample without the GaOx Ny interlayer. Annealing in NO gas at 800°C was conducted on both samples, and turned out to greatly suppress their oxide charges. The NO -annealed sample with the GaOx Ny interlayer achieved the lowest oxide-charge density of 1.7× 1011 cm-2, as compared to 9.5× 1011 cm-2 for its counterpart without the GaOx Ny interlayer and about 8.0× 1012 cm-2 for the two nonannealed samples. Moreover, the NO annealing was found to effectively reduce border traps. Secondary-ion mass spectrometry analysis was performed to explain how the GaOx Ny interlayer and NO annealing affect the performance of the GaN MIS capacitors. © 2007 The Electrochemical Society.published_or_final_versio

Improved I-V characteristics of SiC MOSFETs by TCE thermal gate oxidation

The effects of TCE (trichloroethylene) thermal gate oxidation on the electrical characteristics of SiC MOSFETs are investigated. It is found that TCE thermal gate oxidation can improve the I d-V d characteristics, increase the field-effect mobility, and reduce the threshold voltage and sub-threshold slope of the devices. The better device characteristics are believed to be attributed to the TCE-induced reductions of charges in the gate oxide and traps at the SiO/SiO 2 interface, and also to the gettering of charged impurities and reduction of physical defects by the chlorine incorporated in the gate oxide. ©2005 IEEE.published_or_final_versio

ADVISE: Symbolism and External Knowledge for Decoding Advertisements

In order to convey the most content in their limited space, advertisements embed references to outside knowledge via symbolism. For example, a motorcycle stands for adventure (a positive property the ad wants associated with the product being sold), and a gun stands for danger (a negative property to dissuade viewers from undesirable behaviors). We show how to use symbolic references to better understand the meaning of an ad. We further show how anchoring ad understanding in general-purpose object recognition and image captioning improves results. We formulate the ad understanding task as matching the ad image to human-generated statements that describe the action that the ad prompts, and the rationale it provides for taking this action. Our proposed method outperforms the state of the art on this task, and on an alternative formulation of question-answering on ads. We show additional applications of our learned representations for matching ads to slogans, and clustering ads according to their topic, without extra training.Comment: To appear, Proceedings of the European Conference on Computer Vision (ECCV

Kinetics of thermal oxidation of 6H silicon carbide in oxygen plus trichloroethylene

In this work, the behaviors of the trichloroethylene (TCE) thermal oxidation of 6H silicon carbide (SiC) are investigated. The oxide growth of 6H SiC under different TCE concentrations (ratios of TCE to O2) follows the linear-parabolic oxidation law derived for silicon oxidation by Deal and Grove, J. Appl. Phys., 36 (1965). The oxidation rate with TCE is much higher than that without TCE and strongly depends on the TCE ratio in addition to oxidation temperature and oxidation time. The increase in oxidation rate induced by TCE is between 2.7 and 67% for a TCE ratio of 0.001-0.2 and a temperature of 1000-1150°C. Generally, the oxidation rate increases quickly with the TCE ratio for a TCE ratio less than 0.05 and then gradually saturates for a ratio larger than 0.05. The activation energy EB/A of the TCE oxidation for the TCE ratio range of 0.001-0.2 is 1.04-1.05 eV, which is a little larger than the 1.02 eV of dry oxidation. A two-step model for the TCE oxidation is also proposed to explain the experimental results. The model points out that in the SiC oxidation with TCE, the products (H2O and Cl2) of the reaction between TCE and O2 can speed up the oxidation, and hence, the oxidation rate is highly sensitive to the TCE ratio. © 2005 The Electrochemical Society. All rights reserved.published_or_final_versio

Genomic Expansion of Magnetotactic Bacteria Reveals an Early Common Origin of Magnetotaxis with Lineage-specific Evolution

The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth’s magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and “Candidatus Lambdaproteobacteria” classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB

Could the compact remnant of SN 1987A be a quark star?

The standard model for Type II supernovae explosions, confirmed by the detection of neutrinos emitted during the supernova explosion, predicts the formation of a compact object, usually assumed to be a neutron star. However, the lack of detection of a neutron star or pulsar formed in the SN 1987A still remains an unsolved mystery. In this paper, we suggest that the newly formed neutron star at the center of SN 1987A may undergo a phase transition after the neutrino trapping timescale (∼10 s). Consequently the compact remnant of SN 1987A may be a strange quark star, which has a softer equation of state than that of neutron star matter. Such a phase transition can induce stellar collapse and result in large amplitude stellar oscillations.We use a three-dimensional Newtonian hydrodynamic code to study the time evolution of the temperature and density at the neutrinosphere. Extremely intense pulsating neutrino fluxes, with submillisecond period and with neutrino energy (greater than 30 MeV), can be emitted because the oscillations of the temperature and density are out of phase almost 180◦. If this is true we predict that the current X-ray emission from the compact remnant of SN 1987A will be lower than 1034 erg s−1, and it should be a thermal bremsstrahlung spectrum for a bare strange star with a surface temperature of around ∼107 K.published_or_final_versio

A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Single-Atom Gating of Quantum State Superpositions

The ultimate miniaturization of electronic devices will likely require local and coherent control of single electronic wavefunctions. Wavefunctions exist within both physical real space and an abstract state space with a simple geometric interpretation: this state space--or Hilbert space--is spanned by mutually orthogonal state vectors corresponding to the quantized degrees of freedom of the real-space system. Measurement of superpositions is akin to accessing the direction of a vector in Hilbert space, determining an angle of rotation equivalent to quantum phase. Here we show that an individual atom inside a designed quantum corral can control this angle, producing arbitrary coherent superpositions of spatial quantum states. Using scanning tunnelling microscopy and nanostructures assembled atom-by-atom we demonstrate how single spins and quantum mirages can be harnessed to image the superposition of two electronic states. We also present a straightforward method to determine the atom path enacting phase rotations between any desired state vectors. A single atom thus becomes a real space handle for an abstract Hilbert space, providing a simple technique for coherent quantum state manipulation at the spatial limit of condensed matter.Comment: Published online 6 April 2008 in Nature Physics; 17 page manuscript (including 4 figures) + 3 page supplement (including 2 figures); supplementary movies available at http://mota.stanford.ed