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- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 2. |
- Badelek, B, et al.
(författare)
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The photon collider at TESLA
- 2004
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Ingår i: International Journal of Modern Physics A. - 0217-751X. ; 19:30, s. 5097-5186
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Forskningsöversikt (refereegranskat)abstract
- High energy photon colliders (gammagamma,gammae) are based on e(-)e(-) linear colliders where high energy photons are produced using Compton scattering of laser light on high energy electrons just before the interaction point. This paper is a part of the Technical Design Report of the linear collider TESLA.(1) Physics program, possible parameters and some technical aspects of the photon collider at TESLA are discussed.
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| 7. |
- Han, W. G., et al.
(författare)
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A theoretical study of the UV/visible absorption and emission solvatochromic properties of solvent-sensitive dyes
- 2003
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Ingår i: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 4:10, s. 1084-1094
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Tidskriftsartikel (refereegranskat)abstract
- Using the density-functional vertical self-consistent reaction field (VSCRF) solvation model, incorporated with the conductor-like screening model (COSMO) and the self-consistent reaction field (SCRF) methods, we have studied the solvatochromic shifts of both the absorption and emission bands of four solvent sensitive dyes in different solutions. The dye molecules studies here are: S-TBA merocyanine, Abdel-Halim's merocyanine, the rigidified amino-coumarin C153, and Nile red. These dyes were selected because they exemplify different structural features likely to impact the solvent-sensitive fluorescence of push-pull, or merocyanine, fluorophores. All trends of the blue or red shifts were correctly predicted, comparing with the experimental observations. Explicit h-bonding interactions were also considered in several protic solutions like H2O, methanol and ethanol, showing that including explicit H-bonding solvent molecule(s) in the calculations is important to obtain the correct order of the excitation and emission energies. The geometries, electronic structures, dipole moments, and intra- and intermolecular charge transfers of the dyes in different solvents are also discussed.
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| 8. |
- Holme, Petter, et al.
(författare)
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Attack vulnerability of complex networks
- 2002
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 65:5, s. 056109-
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Tidskriftsartikel (refereegranskat)abstract
- We study the response of complex networks subject to attacks on vertices and edges. Several existing complex network models as well as real-world networks of scientific collaborations and Internet traffic are numerically investigated, and the network performance is quantitatively measured by the average inverse geodesic length and the size of the largest connected subgraph. For each case of attacks on vertices and edges, four different attacking strategies are used: removals by the descending order of the degree and the betweenness centrality, calculated for either the initial network or the current network during the removal procedure. It is found that the removals by the recalculated degrees and betweenness centralities are often more harmful than the attack strategies based on the initial network, suggesting that the network structure changes as important vertices or edges are removed. Furthermore, the correlation between the betweenness centrality and the degree in complex networks is studied.
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| 10. |
- Liu, T. Q., et al.
(författare)
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Density functional vertical self-consistent reaction field theory for solvatochromism - Studies of solvent-sensitive dyes
- 2004
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 108:16, s. 3545-3555
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Tidskriftsartikel (refereegranskat)abstract
- On the basis of the Franck-Condon principle, a density functional vertical self-consistent reaction field (VSCRF) solvation model for vertical excitation and emission processes is established. The principles and implementation of the VSCRF model are presented. The predicted blue shifts of the vertical excitation energies of diazines in different solvents from n-heptane to water solutions are compared with the corresponding time dependent density functional calculations and are in very good agreement with experiment. We have also applied this method to predict the blue shifts and the vertical excitation and emission energies of Brooker's merocyanine dye with increasing solvent polarities from CHCI3 to H2O solutions. Overall, our calculations predicted the relative excitation and emission energy orderings for Brooker's merocyanine in different solvents with different polarities. Also, the calculated Stokes shift is fairly well represented for different solvents, and the calculations correctly show that the absorption energies have a much stronger solvent dependence than the emission energies. The importance of both relaxation of the molecular structures and consideration of explicit H-bonding H2O and CH3OH molecules in water and methanol solvents in predicting the solvatochromic shifts is also discussed.
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