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

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

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

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

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

The Gene Ontology resource: enriching a GOld mine.

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations

Impact of Redshift Information on Cosmological Applications with Next-Generation Radio Surveys

In this paper, we explore how the forthcoming generation of large-scale radio continuum surveys, with the inclusion of some degree of redshift information, can constrain cosmological parameters. By cross-matching these radio surveys with shallow optical to near-infrared surveys, we can essentially separate the source distribution into a low- and a high-redshift sample, thus providing a constraint on the evolution of cosmological parameters such as those related to dark energy. We examine two radio surveys, the Evolutionary Map of the Universe (EMU) and the Westerbork Observations of the Deep APERTIF Northern sky (WODAN). A crucial advantage is their combined potential to provide a deep, full-sky survey. The surveys used for the cross-identifications are SkyMapper and SDSS, for the southern and northern skies, respectively. We concentrate on the galaxy clustering angular power spectrum as our benchmark observable, and find that the possibility of including such low redshift information yields major improvements in the determination of cosmological parameters. With this approach, and provided a good knowledge of the galaxy bias evolution, we are able to put strict constraints on the dark energy parameters, i.e. w_0=-0.9+/-0.041 and w_a=-0.24+/-0.13, with type Ia supernovae and CMB priors (with a one-parameter bias in this case); this corresponds to a Figure of Merit (FoM) > 600, which is twice better than what is obtained by using only the cross-identified sources and greater than four time better than the case without any redshift information at all.Comment: 12 pages, 6 figures, 6 tables; accepted for publication in MNRA