| 1. |
- Reinius, Björn, et al.
(författare)
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Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:1, s. 614-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sexual dimorphism in brain gene expression has been recognized in several animal species.However, the relevant regulatory mechanisms remain poorly understood. To investigatewhether sex-biased gene expression in mammalian brain is globally regulated or locallyregulated in diverse brain structures, and to study the genomic organisation of brain-expressedsex-biased genes, we performed a large scale gene expression analysis of distinct brainregions in adult male and female mice. Results: This study revealed spatial specificity in sex-biased transcription in the mouse brain, andidentified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampusand 31 in the eye. Genes located on sex chromosomes were consistently over-represented inall brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealedY-encoded male-biased transcripts and X-encoded female-biased transcripts known to escapeX-inactivation. In addition, we identified novel coding and non-coding X-linked genes withfemale-biased expression in multiple tissues. Interestingly, the chromosomal positions of allof the female-biased non-coding genes are in close proximity to protein-coding genes thatescape X-inactivation. This defines X-chromosome domains each of which contains a codingand a non-coding female-biased gene. Lack of repressive chromatin marks in non-codingtranscribed loci supports the possibility that they escape X-inactivation. Moreover, RNADNAcombined FISH experiments confirmed the biallelic expression of one such noveldomain. Conclusion: This study demonstrated that the amount of genes with sex-biased expression variesbetween individual brain regions in mouse. The sex-biased genes identified are localized onmany chromosomes. At the same time, sexually dimorphic gene expression that is common toseveral parts of the brain is mostly restricted to the sex chromosomes. Moreover, the studyuncovered multiple female-biased non-coding genes that are non-randomly co-localized onthe X-chromosome with protein-coding genes that escape X-inactivation. This raises thepossibility that expression of long non-coding RNAs may play a role in modulating geneexpression in domains that escape X-inactivation in mouse.
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| 2. |
- Chen, Yancang, et al.
(författare)
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A Trace-driven Hardware-level Simulator for Design and Verification of Network-on-Chips
- 2010
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Ingår i: 2011 INTERNATIONAL CONFERENCE ON COMPUTERS, COMMUNICATIONS, CONTROL AND AUTOMATION (CCCA 2011), VOL II. - : IEEE. ; , s. 32-35
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Konferensbidrag (refereegranskat)abstract
- Traditional communications of general-purpose multi-core processor and application-specific System-on-Chip face challenges in terms of scalability and complexity. Network-on-Chip (NoC) has been the most promising solution for the communications of multi-core and many-core chips. In this paper, we present a trace-driven hardware-level simulator (noted HS) based on SystemVerilog for the design and verification of NoCs. Different from the state-of-the-art NoC simulators, the HS owns three important characteristics in addition to the capability of creating simulation and synthesizable NoC descriptions: 1) hardware-level simulation can be done, which means more implementation details of hardware than flit-level simulation; 2) router debugging and verification can be done at RTL by inserting assertions and coverage; 3) trace-based application simulations can be done besides synthetic workloads. A 4 X 4 2D mesh NoC with output virtual-channel routers verifies the capability of our HS.
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| 3. |
- Lango Allen, Hana, et al.
(författare)
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Hundreds of variants clustered in genomic loci and biological pathways affect human height.
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
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Tidskriftsartikel (refereegranskat)abstract
- Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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| 4. |
- Lu, Jun, et al.
(författare)
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On Epitaxy of Ultrathin Ni1-xPtx Silicide Films on Si(001)
- 2010
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Ingår i: Electrochemical and solid-state letters. - : The Electrochemical Society. - 1099-0062 .- 1944-8775. ; 13:10, s. H360-H362
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Tidskriftsartikel (refereegranskat)abstract
- Epitaxial Ni(Pt)Si2-y (y < 1) films readily grow upon thermal treatment of 2 nm thick Ni and Ni0.96Pt0.04 films deposited on Si(001). For annealing at 500 degrees C, the films are 5.4-5.6 nm thick with 61-70 mu cm in resistivity. At 750 degrees C, the epitaxial Ni(Pt)Si2-y films become 6.1-6.2 nm thick with a resistivity of 42-44 mu cm. Structural analysis reveals twins, facet wedges, and thickness inhomogeneities in the films grown at 500 degrees C. For higher temperature, an almost defect-free NiSi2-y film with a flat and sharp interface is formed. The presence of Pt makes the aforementioned imperfections more persistent.
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| 5. |
- Luo, Jun, et al.
(författare)
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Surface-energy triggered phase formation and epitaxy in nanometer-thick Ni1-xPtx silicide films
- 2010
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 96:3
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Tidskriftsartikel (refereegranskat)abstract
- The formation of ultrathin silicide films of Ni1-xPtx at 450-850 degrees C is reported. Without Pt (x=0) and for t(Ni)< 4 nm, epitaxially aligned NiSi2-y films readily grow and exhibit extraordinary morphological stability up to 800 degrees C. For t(Ni)>= 4 nm, polycrystalline NiSi films form and agglomerate at lower temperatures for thinner films. Without Ni (x=1) and for t(Pt)=1-20 nm, the annealing behavior of the resulting PtSi films follows that for the NiSi films. The results for Ni1-xPtx of other compositions support the above observations. Surface energy is discussed as the cause responsible for the distinct behavior in phase formation and morphological stability.
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| 6. |
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| 7. |
- Siegbahn, Per E. M., et al.
(författare)
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Significant van der Weals Effects in Transition Metal Complexes
- 2010
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:7, s. 2040-2044
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Tidskriftsartikel (refereegranskat)abstract
- There is, in general, very good experience using hybrid DFT to study mechanisms of enzyme reactions containing transition metals. For redox reactions, the B3LYP* functional, which has 15% exact exchange, has been shown to be particularly accurate. Still, there are some cases which have turned out to be quite difficult with large errors. In the present study, the effects of van der Waals interaction have been investigated for these cases, using the empirical formula of Grimme. The results are encouraging.
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| 8. |
- Speliotes, Elizabeth K., et al.
(författare)
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Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:11, s. 937-948
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ~2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10−8), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.
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| 9. |
- Zhou, Jingmin, et al.
(författare)
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Rationale and design of the beta-blocker in heart failure with normal left ventricular ejection fraction (beta-PRESERVE) study.
- 2010
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Ingår i: European journal of heart failure : journal of the Working Group on Heart Failure of the European Society of Cardiology. - : Wiley. - 1879-0844. ; 12:2, s. 181-5
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Tidskriftsartikel (refereegranskat)abstract
- Chronic heart failure with normal left ventricular ejection fraction (HFNEF) is not only common, but also carries a high risk of substantial morbidity and mortality. However, few studies have been conducted in this population and no proven treatment is available. Although beta-blockers are evidence-based first-line therapy in systolic heart failure, they have not been well studied in HFNEF.
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