| 1. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 3. |
- Du, Lin, et al.
(author)
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Review of user parameter-free robust adaptive beamforming algorithms
- 2009
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In: Digital signal processing (Print). - : Elsevier BV. - 1051-2004 .- 1095-4333. ; 19:4, s. 567-582
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Research review (peer-reviewed)abstract
- This paper provides a comprehensive review of user parameter-free robust adaptive beamforming algorithms. We present the ridge regression Capon beamformers (RRCBs), the mid-way (MW) algorithm, and the convex combination (CC) as well as the general linear combination (GLC) approaches. The purpose of these methods is to mitigate the effect of small sample size and steering vector errors on the standard Capon beamformer (SCB). We also present sparsity based iterative beamforming algorithms, namely the iterative adaptive approach (IAA), maximum likelihood based IAA (referred to as IAA-ML) and M-SBL (multi-snapshot sparse Bayesian learning), which exploit sparsity to estimate the signal parameters. We provide a thorough evaluation of these beamforming methods in terms of power and spatial spectrum estimation accuracies. output signal-to-interference-plusnoise ratio (SINR) and resolution under various scenarios including coherent, non-coherent and distributed sources, steering vector mismatches, snapshot limitations and low signal-to-noise ratio (SNR) levels. Furthermore, we discuss the computational complexities of the algorithms and provide insights into which algorithm is the best choice under which circumstances.
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| 7. |
- Garrison, Sean P, et al.
(author)
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Selection against PUMA gene expression in Myc-driven B-cell lymphomagenesis.
- 2008
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In: Molecular and cellular biology. - 1098-5549. ; 28:17, s. 5391-402
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Journal article (peer-reviewed)abstract
- The p53 tumor suppressor pathway limits oncogenesis by inducing cell cycle arrest or apoptosis. A key p53 target gene is PUMA, which encodes a BH3-only proapoptotic protein. Here we demonstrate that Puma deletion in the Emu-Myc mouse model of Burkitt lymphoma accelerates lymphomagenesis and that approximately 75% of Emu-Myc lymphomas naturally select against Puma protein expression. Furthermore, approximately 40% of primary human Burkitt lymphomas fail to express detectable levels of PUMA and in some tumors this is associated with DNA methylation. Burkitt lymphoma cell lines phenocopy the primary tumors with respect to DNA methylation and diminished PUMA expression, which can be reactivated following inhibition of DNA methyltransferases. These findings establish that PUMA is silenced in human malignancies, and they suggest PUMA as a target for the development of novel chemotherapeutics.
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| 8. |
- Leng, Jian-Cai, et al.
(author)
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Orientation of Decanethiol Molecules in Self-Assembled Monolayers Determined by Inelastic Electron Tunneling Spectroscopy
- 2009
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:42, s. 18353-18357
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Journal article (peer-reviewed)abstract
- We present first-principles calculations for the inelastic electron tunneling spectroscopy (IETS) of decanethiolate molecules sandwiched between Au(111) surface and scanning tunneling microscope (STM) reported by Hallback et at, (Nano Left. 2004, 4, 2393). It is demonstrated here that the IET spectra are very sensitive to the molecule-metal contact structure, orientation of the molecule adsorbed on the surface, and the distance between the carbon of the terminal methyl group and the STM tip. With correct assignation of the experimental spectral features, the orientation of the molecule and then the probable configuration of the molecular junction are
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| 10. |
- Lin, Li-Li, et al.
(author)
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Effect of Aromatic Coupling on Electronic Transport in Bimolecular Junctions
- 2009
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:32, s. 14474-14477
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Journal article (peer-reviewed)abstract
- We have performed a systematic first-principles study on conductance-voltage characteristics of bioligo(phenylene ethynylene)-monothiol molecular junctions as recently reported by Wu et al.[Nalure Nanotech. 2008, 3, 569]. It is found that the molecular conductance is very sensitive to the vertical distance between two molecules as well as the titled angle between two molecular planes. By comparing with experimental results, key structure parameters for bimolecular junction are determined, indicating that in the experimental devices, the vertical distance between two molecules is around 0.30 mn, the two planar molecules have a cofacial arrangement, and the length of the molecular bridge is about 2.88 nm. The underlying mechanism for electron transport in these aromatically coupled bimolecular junctions has also been discussed.
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