Coherence in a transmon qubit with epitaxial tunnel junctions

We developed transmon qubits based on epitaxial tunnel junctions and interdigitated capacitors. This multileveled qubit, patterned by use of all-optical lithography, is a step towards scalable qubits with a high integration density. The relaxation time T1 is .72-.86mu sec and the ensemble dephasing time T2 is slightly larger than T1. The dephasing time T2 (1.36mu sec) is nearly energy-relaxation-limited. Qubit spectroscopy yields weaker level splitting than observed in qubits with amorphous barriers in equivalent-size junctions. The qubit's inferred microwave loss closely matches the weighted losses of the individual elements (junction, wiring dielectric, and interdigitated capacitor), determined by independent resonator measurements

Benthic study of the continental slope off Cape Hatteras, North Carolina

Concern was raised by the NCESRP (1992) that since not much is known about the bottom communities around the Manteo 467 lease block, exploration activities could result in significant environmental disturbance. Therefore, the principal task of this study was to survey the sea floor of the Cape Hatteras continental slope in the vicinity of the Manteo 467 site prior tn any decision on permitting of exploratory drilling. The study objectives as listed in the scope of work are as follows: 1. Define the \u27unusual benthic community\u27 that exists offshore North Carolina which is at its peak in the vicinity of the proposed Manteo drill site and \u27the Point.\u27 The working definition shall be based on species composition and relative abundance. However, the definition must also consider the impact of physical oceanographic processes, oxygen levels, and sediment types and flux. 2. Using the Offshore Operators\u27 Committee (OOC) model (MOEPSO, estimate the area between the 300- and 1,500-m isobaths which could be covered by the deposition of muds and cunings at the proposed drill site. 3. Survey the area of the Manteo site for the \u27unusual benthic community\u27 as defined in objective No. 1. The survey must include benthic mcgafauna as well as the infauna.

Ontological visualization of protein-protein interactions

BACKGROUND: Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO) is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions. RESULTS: GO annotation at Mouse Genome Informatics (MGI) captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data. CONCLUSIONS: Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products

Writ(h)ing Images: Imagination, the Human Form, and the Divine in William Blake, Salman Rushdie, and Simon Louvish

In this paper, we address issues in segmentation Of remotely sensed LIDAR (LIght Detection And Ranging) data. The LIDAR data, which were captured by airborne laser scanner, contain 2.5 dimensional (2.5D) terrain surface height information, e.g. houses, vegetation, flat field, river, basin, etc. Our aim in this paper is to segment ground (flat field)from non-ground (houses and high vegetation) in hilly urban areas. By projecting the 2.5D data onto a surface, we obtain a texture map as a grey-level image. Based on the image, Gabor wavelet filters are applied to generate Gabor wavelet features. These features are then grouped into various windows. Among these windows, a combination of their first and second order of statistics is used as a measure to determine the surface properties. The test results have shown that ground areas can successfully be segmented from LIDAR data. Most buildings and high vegetation can be detected. In addition, Gabor wavelet transform can partially remove hill or slope effects in the original data by tuning Gabor parameters

Gene Ontology annotations: what they mean and where they come from

To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). Here we address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations, in the hope that this will lead both to better representations of biological reality through annotation and ontology development and to more informed use of GO resources by experimental scientists

Nighttime chemistry at a high altitude site above Hong Kong

Nighttime reactions of nitrogen oxides influence ozone, volatile organic compounds, and aerosol and are thus important to the understanding of regional air quality. Despite large emissions and rapid recent growth of nitrogen oxide concentrations, there are few studies of nighttime chemistry in China. Here we present measurements of nighttime nitrogen oxides, NO3 and N2O5, from a coastal mountaintop site in Hong Kong adjacent to the megacities of the Pearl River Delta region. This is the first study of nighttime chemistry from a site within the residual layer in China. Key findings include the following. First, highly concentrated urban NOx outflow from the Pearl River Delta region was sampled infrequently at night, with N2O5 mixing ratios up to 8 ppbv (1 min average) or 12 ppbv (1 s average) in nighttime aged air masses. Second, the average N2O5 uptake coefficient was determined from a best fit to the available steady state lifetime data as γ(N2O5) = 0.014 ± 0.007. Although this determination is uncertain due to the difficulty of separating N2O5 losses from those of NO3, this value is in the range of previous residual layer determinations of N2O5 uptake coefficients in polluted air in North America. Third, there was a significant contribution of biogenic hydrocarbons to NO3 loss inferred from canister samples taken during daytime. Finally, daytime N2O5 mixing ratios were in accord with their predicted photochemical steady state. Heterogeneous uptake of N2O5 in fog is determined to be an important production mechanism for soluble nitrate, even during daytime. Key Points Large (up to 12 ppbv N2O5) but infrequent nocturnal NOx outflow from the Pearl River Delta Average N2O5 uptake coefficients 0.014 ± 0.007, in line with residual layer measurements in the U.S. Daytime N2O5 follows predicted steady state but rapidly produces soluble nitrate in fog.Department of Civil and Environmental Engineerin

Lethal Mutagenesis of Poliovirus Mediated by a Mutagenic Pyrimidine Analogue

Lethal mutagenesis is the mechanism of action of ribavirin against poliovirus (PV) and numerous other RNA viruses. However, there is still considerable debate regarding the mechanism of action of ribavirin against a variety of RNA viruses. Here we show by using T7 RNA polymerase mediated production of PV genomic RNA, PV polymerase-catalyzed primer extension and cell-free PV synthesis that a pyrimidine ribonucleoside triphosphate analogue (rPTP) with ambiguous basepairing capacity is an efficient mutagen of the PV genome. The in vitro incorporation properties of rPTP are superior to ribavirin triphosphate. We observed a log-linear relationship between virus titer reduction and the number of rPMP molecules incorporated. A PV genome encoding a high-fidelity polymerase was more sensitive to rPMP incorporation, consistent with diminished mutational robustness of high-fidelity PV. The nucleoside (rP) did not exhibit antiviral activity in cell culture owing to the inability of rP to be converted to rPMP by cellular nucleotide kinases. rP was also a poor substrate for herpes simplex virus thymidine kinase. The block to nucleoside phosphorylation could be bypassed by treatment with the P nucleobase, which exhibited both antiviral activity and mutagenesis, presumably a reflection of rP nucleotide formation by a nucleotide salvage pathway. These studies provide additional support for lethal mutagenesis as an antiviral strategy, suggest that rPMP prodrugs may be highly efficacious antiviral agents, and provide a new tool to determine the sensitivity of RNA virus genomes to mutagenesis as well as interrogation of the impact of mutational load on the population dynamics of these viruses

An en masse phenotype and function prediction system for Mus musculus

Background: Individual researchers are struggling to keep up with the accelerating emergence of high-throughput biological data, and to extract information that relates to their specific questions. Integration of accumulated evidence should permit researchers to form fewer - and more accurate - hypotheses for further study through experimentation. Results: Here a method previously used to predict Gene Ontology (GO) terms for Saccharomyces cerevisiae (Tian et al.: Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 2008, 9(Suppl 1):S7) is applied to predict GO terms and phenotypes for 21,603 Mus musculus genes, using a diverse collection of integrated data sources (including expression, interaction, and sequence-based data). This combined 'guilt-by-profiling' and 'guilt-by-association' approach optimizes the combination of two inference methodologies. Predictions at all levels of confidence are evaluated by examining genes not used in training, and top predictions are examined manually using available literature and knowledge base resources. Conclusion: We assigned a confidence score to each gene/term combination. The results provided high prediction performance, with nearly every GO term achieving greater than 40% precision at 1% recall. Among the 36 novel predictions for GO terms and 40 for phenotypes that were studied manually, >80% and >40%, respectively, were identified as accurate. We also illustrate that a combination of 'guilt-by-profiling' and 'guilt-by-association' outperforms either approach alone in their application to M. musculus.Molecular and Cellular Biolog

Imaging the Disk around TW Hydrae with the Submillimeter Array

We present ~2"-4" aperture synthesis observations of the circumstellar disk surrounding the nearby young star TW Hya in the CO J = 2-1 and J = 3-2 lines and associated dust continuum obtained with the partially completed Submillimeter Array. The extent and peak flux of the 230 and 345 GHz dust emission follow closely the predictions of the irradiated accretion disk model of Calvet et al. The resolved molecular line emission extends to a radius of at least 200 AU, the full extent of the disk visible in scattered light, and shows a clear pattern of Keplerian rotation. Comparison of the images with two-dimensional Monte Carlo models constrains the disk inclination angle to 7° ± 1°. The CO emission is optically thick in both lines, and the kinetic temperature in the line formation region is ~20 K. Substantial CO depletion, by an order of magnitude or more from canonical dark cloud values, is required to explain the characteristics of the line emission