| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Chen, Kang, et al.
(författare)
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Immunoglobulin D enhances immune surveillance by activating antimicrobial, proinflammatory and B cell-stimulating programs in basophils
- 2009
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Ingår i: Nature Immunology. - : Springer Science and Business Media LLC. - 1529-2908 .- 1529-2916. ; 10:8, s. 121-889
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Tidskriftsartikel (refereegranskat)abstract
- Immunoglobulin D (IgD) is an enigmatic antibody isotype that mature B cells express together with IgM through alternative RNA splicing. Here we report active T cell-dependent and T cell-independent IgM-to-IgD class switching in B cells of the human upper respiratory mucosa. This process required activation-induced cytidine deaminase (AID) and generated local and circulating IgD-producing plasmablasts reactive to respiratory bacteria. Circulating IgD bound to basophils through a calcium-mobilizing receptor that induced antimicrobial, opsonizing, inflammatory and B cell-stimulating factors, including cathelicidin, interleukin 1 (IL-1), IL-4 and B cell-activating factor (BAFF), after IgD crosslinking. By showing dysregulation of IgD class-switched B cells and 'IgD-armed' basophils in autoinflammatory syndromes with periodic fever, our data indicate that IgD orchestrates an ancestral surveillance system at the interface between immunity and inflammation.
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| 3. |
- Liu, Bingbing, et al.
(författare)
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Effects of silver films with different nano-particle sizes on SERS of single-walled carbon nanotubes
- 2005
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Ingår i: Chemical Journal of the Chinese Universities. - 0251-0790. ; 26:10, s. 1930-1933
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Tidskriftsartikel (refereegranskat)abstract
- Surface-enhanced Raman scattering (SERS) spectra of single-walled carbon nanotubes (SWCNTs) on silver films with different nano-particle sizes from 20 to 100 nm deposited on quartz and glass substrates were studied systematically. The characteristic Raman spectral features of SWCNT G-band and D-band were analyzed. The two bands show a similar tendency with the change of nano-particle size of silver on quartz and glass substrates. The position and the intensity of the G-band are less sensitive to the films' silver particle sizes in the studied range, indicating that hexagonal carbon rings are stable and have a weak interaction with silver films. The shape of the D-band depends on the silver size. The smaller the silver particle size, the more the contribution of high frequency vibrations to the D-band, indicating that disorder carbon has a strong interaction with the active silver films.
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| 4. |
- Xu, Bing, et al.
(författare)
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Clinicopathological significance of caspase-8 and caspase-10 expression in rectal cancer
- 2008
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Ingår i: Oncology. - : S. Karger AG. - 0890-9091 .- 0030-2414 .- 1423-0232. ; 74:3-4, s. 229-236
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: To investigate the expression of caspase-8 and -10 in rectal adenoma, adenocarcinoma and the corresponding normal mucosa tissue, and to clarify the relationship between their expression and clinicopathological parameters of rectal cancer. Methods: The expression of caspase-8 and -10 was determined by real-time RT-PCR and immunohistochemistry in 36 rectal adenomas, 93 rectal cancers and 93 corresponding normal rectal mucosa samples. Results: Compared with normal mucosa, the mRNA expression of caspase-8 was higher in adenomas (p = 0.003), while that of caspase-10 was lower in adenomas (p = 0.035) and cancers (p = 0.001). Immunohistochemical results showed caspase-8 up-regulation in adenomas (p = 0.014), and caspase-10 down-regulation in adenomas (p = 0.034) and cancers (p < 0.001) compared with normal mucosa samples. Cancers with poor differentiation had lower caspase-10 mRNA and protein levels than those with better differentiation (p = 0.041 and p = 0.046, respectively). The protein expression of caspase-8 and -10 was in accordance with the mRNA expression (p = 0.043 and p = 0.018, respectively). Conclusions: Caspase-8 expression was up-regulated in rectal adenomas. Caspase-10 expression was down-regulated in both rectal adenomas and cancers, and was further related to differentiation. Caspase-8 and -10 may be involved in the pathogenesis of rectal cancer. Copyright © 2008 S. Karger AG.
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| 5. |
- Yang, Han-Xin, et al.
(författare)
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Diversity-optimized cooperation on complex networks
- 2009
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American physical society. - 1063-651X .- 1095-3787. ; 79:5, s. 056107-
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Tidskriftsartikel (refereegranskat)abstract
- We propose a strategy for achieving maximum cooperation in evolutionary games on complex networks. Each individual is assigned a weight that is proportional to the power of its degree, where the exponent α is an adjustable parameter that controls the level of diversity among individuals in the network. During the evolution, every individual chooses one of its neighbors as a reference with a probability proportional to the weight of the neighbor, and updates its strategy depending on their payoff difference. It is found that there exists an optimal value of α, for which the level of cooperation reaches maximum. This phenomenon indicates that, although high-degree individuals play a prominent role in maintaining the cooperation, too strong influences from the hubs may counterintuitively inhibit the diffusion of cooperation. Other pertinent quantities such as the payoff, the cooperator density as a function of the degree, and the payoff distribution are also investigated computationally and theoretically. Our results suggest that in order to achieve strong cooperation on a complex network, individuals should learn more frequently from neighbors with higher degrees, but only to a certain extent.
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