| 1. |
- Thiele, I., et al.
(författare)
-
A community-driven global reconstruction of human metabolism
- 2013
-
Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 31:5, s. 419-
-
Tidskriftsartikel (refereegranskat)abstract
- Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including similar to 2x more reactions and similar to 1.7x more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.
|
|
| 2. |
- Bower, G. C., et al.
(författare)
-
THE ALLEN TELESCOPE ARRAY Pi GHz SKY SURVEY. I. SURVEY DESCRIPTION AND STATIC CATALOG RESULTS FOR THE BOOTES FIELD
- 2010
-
Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 725:2, s. 1792-1804
-
Tidskriftsartikel (refereegranskat)abstract
- The Pi GHz Sky Survey (PiGSS) is a key project of the Allen Telescope Array. PiGSS is a 3.1 GHz survey of radio continuum emission in the extragalactic sky with an emphasis on synoptic observations that measure the static and time-variable properties of the sky. During the 2.5 year campaign, PiGSS will twice observe similar to 250,000 radio sources in the 10,000 deg(2) region of the sky with b > 30 degrees to an rms sensitivity of similar to 1 mJy. Additionally, sub-regions of the sky will be observed multiple times to characterize variability on timescales of days to years. We present here observations of a 10 deg(2) region in the Bootes constellation overlapping the NOAO Deep Wide Field Survey field. The PiGSS image was constructed from 75 daily observations distributed over a 4 month period and has an rms flux density between 200 and 250 mu Jy. This represents a deeper image by a factor of 4-8 than we will achieve over the entire 10,000 deg(2). We provide flux densities, source sizes, and spectral indices for the 425 sources detected in the image. We identify similar to 100 new flat-spectrum radio sources; we project that when completed PiGSS will identify 10(4) flat-spectrum sources. We identify one source that is a possible transient radio source. This survey provides new limits on faint radio transients and variables with characteristic durations of months.
|
|
| 3. |
- Croft, S., et al.
(författare)
-
THE ALLEN TELESCOPE ARRAY TWENTY-CENTIMETER SURVEY-A 690 DEG(2), 12 EPOCH RADIO DATA SET. I. CATALOG AND LONG-DURATION TRANSIENT STATISTICS
- 2010
-
Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 719:1, s. 45-58
-
Tidskriftsartikel (refereegranskat)abstract
- We present the Allen Telescope Array Twenty-centimeter Survey (ATATS), a multi-epoch (12 visits), 690 deg(2) radio image and catalog at 1.4 GHz. The survey is designed to detect rare, very bright transients as well as to verify the capabilities of the ATA to form large mosaics. The combined image using data from all 12 ATATS epochs has rms noise sigma = 3.94 mJy beam(-1) and dynamic range 180, with a circular beam of 150 '' FWHM. It contains 4408 sources to a limiting sensitivity of 5 sigma = 20 mJy beam(-1). We compare the catalog generated from this 12 epoch combined image to the NRAO VLA Sky Survey (NVSS), a legacy survey at the same frequency, and find that we can measure source positions to better than similar to 20 ''. For sources above the ATATS completeness limit, the median flux density is 97% of the median value for matched NVSS sources, indicative of an accurate overall flux calibration. We examine the effects of source confusion due to the effects of differing resolution between ATATS and NVSS on our ability to compare flux densities. We detect no transients at flux densities greater than 40 mJy in comparison with NVSS and place a 2 sigma upper limit of 0.004 deg(-2) on the transient rate for such sources. These results suggest that the greater than or similar to 1 Jy transients reported by Matsumara et al. may not be true transients, but rather variable sources at their flux density threshold.
|
|
| 4. |
|
|
| 5. |
- Leszczynska, M., et al.
(författare)
-
Thermal Variation of Structure and Electrical Conductivity in Bi4YbO7.5
- 2013
-
Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 1520-5002 .- 0897-4756. ; 25:3, s. 326-336
-
Tidskriftsartikel (refereegranskat)abstract
- The thermal behavior of the oxide ion-conducting solid electrolyte Bi4YbO7.5 was investigated using a combination of variable temperature X-ray and neutron powder diffraction, thermal analysis (DTA and TGA), and ac impedance spectroscopy. The title compound shows a fluorite-type structure throughout the measured temperature range (20-850 degrees C), with a phase separation at ca. 600 degrees C into a cubic delta-type phase and an orthorhombic phase of assumed stoichiometry Bi17Yb7O36. This type of transition is a relatively common feature in bismuth oxide-based systems and can limit their practical application. Here, the transition was carefully studied using isothermal measurements, which showed that it is accompanied by changes in oxide-ion stoichiometry, as well as significant disorder in the oxide ion sublattice in the delta-type phase. These results correlate with the observed electrical behavior. Analysis of the total neutron scattering through reverse Monte Carlo (RMC) modeling reveals details of the coordination environments for both cations. The oxide-ion vacancy distribution seems to be consistent with a favoring of vacancy pairs, although vacancy pairs exhibit the highest frequency as they have the maximum likelihood. A vacancy ordering model based on three vacancies per cell is presented.
|
|
| 6. |
- Terenius, Olle, et al.
(författare)
-
RNA interference in Lepidoptera : An overview of successful and unsuccessful studies and implications for experimental design
- 2011
-
Ingår i: Journal of insect physiology. - : Elsevier BV. - 0022-1910 .- 1879-1611. ; 57:2, s. 231-245
-
Tidskriftsartikel (refereegranskat)abstract
- Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive experiments have not been collected in such a way that they are possible to analyze. In this review, we have collected detailed data from more than 150 experiments including all to date published and many unpublished experiments. Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity. On the contrary, gene expression in epidermal tissues seems to be most difficult to silence. In addition, gene silencing by feeding dsRNA requires high concentrations for success. Possible causes for the variability of success in RNAi experiments in Lepidoptera are discussed. The review also points to a need to further investigate the mechanism of RNAi in lepidopteran insects and its possible connection to the innate immune response. Our general understanding of RNAi in Lepidoptera will be further aided in the future as our public database at http://insectacentral.org/RNAi will continue to gather information on RNAi experiments.
|
|
| 7. |
|
|
| 8. |
- Leszczynska, M., et al.
(författare)
-
Oxide ion distribution, vacancy ordering and electrical behaviour in the Bi3NbO7-Bi3YbO6 pseudo-binary system
- 2014
-
Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 2:43, s. 18624-18634
-
Tidskriftsartikel (refereegranskat)abstract
- Oxide ion distribution, vacancy ordering and electrical conductivity has been examined in the Nb/Yb double substituted bismuth oxide based system Bi3Nb1-xYbxO7-x, using X-ray and neutron powder diffraction, reverse Monte Carlo modelling of total neutron scattering data and a. c. impedance spectroscopy. Transference number measurements confirm the system to be predominantly ionically conducting above ca. 450 degrees C. Niobium rich compositions show incommensurate ordering of the fluorite subcell, while increasing ytterbium content results in a commensurate fluorite, with fully disordered cation and anion sublattices. Oxide ion distribution shows both compositional and thermal dependencies. The latter is discussed with respect to its effect on the thermal variation of cubic lattice parameter. Substitution of bismuth by niobium and ytterbium in the cation sublattice of bismuth oxide leads to the creation of Frenkel interstitial oxide ions, which increase the tetrahedral vacancy concentration. The high vacancy concentration is confirmed in both Rietveld and RMC analyses of neutron data. Examination of vacancy ordering, in the x - 0.6 composition, indicates a favouring of vacancy pair alignment.
|
|
| 9. |
- Leszczynska, M., et al.
(författare)
-
Total scattering analysis of cation coordination and vacancy pair distribution in Yb substituted delta-Bi2O3
- 2013
-
Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 25:45
-
Tidskriftsartikel (refereegranskat)abstract
- Reverse Monte Carlo (RMC) modelling of neutron total scattering data, combined with conventional Rietveld analysis of x-ray and neutron data, has been used to describe the cation coordination environments and vacancy pair distribution in the oxide ion conducting electrolyte Bi3YbO6. The thermal variation of the cubic fluorite unit cell volume, monitored by variable temperature x-ray and neutron experiments, reveals significant curvature, which is explained by changes in the oxide ion distribution. There is a significant increase in tetrahedral oxide ion vacancy concentration relative to delta-Bi2O3, due to the creation of Frenkel defects associated with the Yb3+ cation. The tetrahedral oxide ion vacancy concentration increases from room temperature to 800 degrees C, but little change is observed in the vacancy pair distribution with temperature. The vacancy pair distributions at both temperatures are consistent with a favouring of vacancy pairs.
|
|
| 10. |
- von der Lieth, Claus-Wilhelm, et al.
(författare)
-
EUROCarbDB : an open-access platform for glycoinformatics
- 2011
-
Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 21:4, s. 493-502
-
Tidskriftsartikel (refereegranskat)abstract
- The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.
|
|
