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  • Institute of Physics  (1,176)
  • Oxford University Press  (664)
  • American Association for the Advancement of Science (AAAS)  (309)
  • 11
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    A Trust Routing for Multimedia Social Networks (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-27
    Description: Due to the disconnected and store-and-forward architecture in multimedia social networks (MSNs), routing becomes a great challenge with the frequent path disruptions. Moreover, some nodes in MSNs tend to be selfish or malicious, e.g. they sometimes will not forward packets for other nodes or will launch passive and active attacks in order to save their limited resources such as bandwidth, battery or storage. In order to address this issue, we propose a fuzzy-based trust management technique for context-based routing in MSNs. We incorporate social trust metrics and quality of service metrics into our trust model. By adopting fuzzy sets, every node can evaluate the credibility of other nodes based on the direct and indirect relationship. By ranking all its neighbors according to the trust values, each node can purge untrustworthy nodes. Since only trusted nodes’ packets will be forwarded, the selfish or malicious nodes have the incentive to behave well again in order to be able to send packets. Additionally, we perform extensive security and performance evaluation with the opportunistic network environment simulator. The simulation results show that our trust model can dynamically update the trust value in real time, effectively measure the trust relationship and correctly identify malicious or selfish nodes. Furthermore, the proposed trust routing is a lightweight protocol balancing the message overhead and delivery ratio.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 12
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    Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Lnc2Cancer ( http://www.bio-bigdata.net/lnc2cancer ) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 13
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    Single-cell multiomics sequencing and analyses of human colorectal cancer (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018
    Description: 〈p〉Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multiomics sequencing together with multiregional sampling of the primary tumor and lymphatic and distant metastases, we developed insights beyond intratumoral heterogeneity. Genome-wide DNA methylation levels were relatively consistent within a single genetic sublineage. The genome-wide DNA demethylation patterns of cancer cells were consistent in all 10 patients whose DNA we sequenced. The cancer cells’ DNA demethylation degrees clearly correlated with the densities of the heterochromatin-associated histone modification H3K9me3 of normal tissue and those of repetitive element long interspersed nuclear element 1. Our work demonstrates the feasibility of reconstructing genetic lineages and tracing their epigenomic and transcriptomic dynamics with single-cell multiomics sequencing.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 14
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    Structural basis for the Smad5 MH1 domain to recognize different DNA sequences (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-15
    Description: Smad proteins are important intracellular mediators of TGF-β signalling, which transmit signals directly from cell surface receptors to the nucleus. The MH1 domain of Smad plays a key role in DNA recognition. Two types of DNA sequence were identified as Smad binding motifs: the Smad binding element (SBE) and the GC-rich sequence. Here we report the first crystal structure of the Smad5 MH1 domain in complex with the GC-rich sequence. Compared with the Smad5-MH1/SBE complex structure, the Smad5 MH1 domain contacts the GC-rich site with the same β-hairpin, but the detailed interaction modes are different. Conserved β-hairpin residues make base specific contacts with the minimal GC-rich site, 5'-GGC-3'. The assembly of Smad5-MH1 on the GC-rich DNA also results in distinct DNA conformational changes. Moreover, the crystal structure of Smad5-MH1 in complex with a composite DNA sequence demonstrates that the MH1 domain is targeted to each binding site (GC-rich or SBE) with modular binding modes, and the length of the DNA spacer affects the MH1 assembly. In conclusion, our work provides the structural basis for the recognition and binding specificity of the Smad MH1 domain with the DNA targets.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 15
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    The deepest X-ray view of high-redshift galaxies: constraints on low-rate black hole accretion (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-10
    Description: We exploit the 7 Ms Chandra observations in the Chandra  Deep Field-South (CDF-S), the deepest X-ray survey to date, coupled with CANDELS/GOODS-S data, to measure the total X-ray emission arising from 2076 galaxies at 3.5 ≤ z 〈 6.5. This aim is achieved by stacking the Chandra data at the positions of optically selected galaxies, reaching effective exposure times of ≥10 9 s. We detect significant (〉3.7) X-ray emission from massive galaxies at z 4. We also report the detection of massive galaxies at z 5 at a 99.7 per cent confidence level (2.7), the highest significance ever obtained for X-ray emission from galaxies at such high redshifts. No significant signal is detected from galaxies at even higher redshifts. The stacking results place constraints on the BHAD associated with the known high-redshift galaxy samples, as well as on the SFRD at high redshift, assuming a range of prescriptions for X-ray emission due to X- ray binaries. We find that the X-ray emission from our sample is likely dominated by processes related to star formation. Our results show that low-rate mass accretion on to SMBHs in individually X-ray-undetected galaxies is negligible, compared with the BHAD measured for samples of X-ray detected AGN, for cosmic SMBH mass assembly at high redshift. We also place, for the first time, constraints on the faint-end of the AGN X-ray luminosity function (logL X ~ 42) at z 〉 4, with evidence for fairly flat slopes. The implications of all of these findings are discussed in the context of the evolution of the AGN population at high redshift.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 16
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    Predicting regulatory variants with composite statistic (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-12
    Description: Motivation: Prediction and prioritization of human non-coding regulatory variants is critical for understanding the regulatory mechanisms of disease pathogenesis and promoting personalized medicine. Existing tools utilize functional genomics data and evolutionary information to evaluate the pathogenicity or regulatory functions of non-coding variants. However, different algorithms lead to inconsistent and even conflicting predictions. Combining multiple methods may increase accuracy in regulatory variant prediction. Results: Here, we compiled an integrative resource for predictions from eight different tools on functional annotation of non-coding variants. We further developed a composite strategy to integrate multiple predictions and computed the composite likelihood of a given variant being regulatory variant. Benchmarked by multiple independent causal variants datasets, we demonstrated that our composite model significantly improves the prediction performance. Availability and Implementation: We implemented our model and scoring procedure as a tool, named PRVCS, which is freely available to academic and non-profit usage at http://jjwanglab.org/PRVCS . Contact: wang.junwen@mayo.edu , jliu@stat.harvard.edu , or limx54@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 17
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    Gas-phase metallicity profiles of the Bluedisk galaxies: Is metallicity in a local star formation regulated equilibrium? (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-29
    Description: As part of the Bluedisk survey, we analyse the radial gas-phase metallicity profiles of 50 late-type galaxies. We compare the metallicity profiles of a sample of H i -rich galaxies against a control sample of H i -‘normal’ galaxies. We find the metallicity gradient of a galaxy to be strongly correlated with its H i mass fraction ( $\textrm {M(H\,\small {I})} / \textrm {M}_{\ast }$ ). We note that some galaxies exhibit a steeper metallicity profile in the outer disc than in the inner disc. These galaxies are found in both the H i -rich and control samples. This contradicts a previous indication that these outer drops are exclusive to H i -rich galaxies. These effects are not driven by bars, although we do find some indication that barred galaxies have flatter metallicity profiles. By applying a simple analytical model, we are able to account for the variety of metallicity profiles that the two samples present. The success of this model implies that the metallicity in these isolated galaxies may be in a local equilibrium, regulated by star formation. This insight could provide an explanation of the observed local mass–metallicity relation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 18
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    Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-24
    Description: Arginine methylation is a posttranslational modification that impacts wide-ranging cellular functions, including transcription, mRNA splicing and translation. RNA binding proteins (RBPs) represent one of the largest classes of arginine methylated proteins in both mammals and the early diverging parasitic protozoan, Trypanosoma brucei . Here, we report the effects of arginine methylation on the functions of the essential and previously uncharacterized T. brucei RBP, DRBD18. RNAseq analysis shows that DRBD18 depletion causes extensive rearrangement of the T. brucei transcriptome, with increases and decreases in hundreds of mRNAs. DRBD18 contains three methylated arginines, and we used complementation of DRBD18 knockdown cells with methylmimic or hypomethylated DRBD18 to assess the functions of these methylmarks. Methylmimic and hypomethylated DRBD18 associate with different ribonucleoprotein complexes. These altered macromolecular interactions translate into differential impacts on the T. brucei transcriptome. Methylmimic DRBD18 preferentially stabilizes target RNAs, while hypomethylated DRBD18 is more efficient at destabilizing RNA. The protein arginine methyltransferase, TbPRMT1, interacts with DRBD18 and knockdown of TbPRMT1 recapitulates the effects of hypomethylated DRBD18 on mRNA levels. Together, these data support a model in which arginine methylation acts as a switch that regulates T. brucei gene expression.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 19
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    Gas-phase metallicity profiles of the Bluedisk galaxies: Is metallicity in a local star formation regulated equilibrium? (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-12
    Description: As part of the Bluedisk survey, we analyse the radial gas-phase metallicity profiles of 50 late-type galaxies. We compare the metallicity profiles of a sample of H i -rich galaxies against a control sample of H i -‘normal’ galaxies. We find the metallicity gradient of a galaxy to be strongly correlated with its H i mass fraction ( $\textrm {M(H\,\small {I})} / \textrm {M}_{\ast }$ ). We note that some galaxies exhibit a steeper metallicity profile in the outer disc than in the inner disc. These galaxies are found in both the H i -rich and control samples. This contradicts a previous indication that these outer drops are exclusive to H i -rich galaxies. These effects are not driven by bars, although we do find some indication that barred galaxies have flatter metallicity profiles. By applying a simple analytical model, we are able to account for the variety of metallicity profiles that the two samples present. The success of this model implies that the metallicity in these isolated galaxies may be in a local equilibrium, regulated by star formation. This insight could provide an explanation of the observed local mass–metallicity relation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 20
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    Planet Hunters IX. KIC 8462852 - where's the flux? (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-02
    Description: Over the duration of the Kepler mission, KIC 8462852 was observed to undergo irregularly shaped, aperiodic dips in flux of up to ~20 per cent. The dipping activity can last for between 5 and 80 d. We characterize the object with high-resolution spectroscopy, spectral energy distribution fitting, radial velocity measurements, high-resolution imaging, and Fourier analyses of the Kepler light curve. We determine that KIC 8462852 is a typical main-sequence F3 V star that exhibits no significant IR excess, and has no very close interacting companions. In this paper, we describe various scenarios to explain the dipping events observed in the Kepler light curve. We confirm that the dipping signals in the data are not caused by any instrumental or data processing artefact, and thus are astrophysical in origin. We construct scenario-independent constraints on the size and location of a body in the system that are needed to reproduce the observations. We deliberate over several assorted stellar and circumstellar astrophysical scenarios, most of which have problems explaining the data in hand. By considering the observational constraints on dust clumps in orbit around a normal main-sequence star, we conclude that the scenario most consistent with the data in hand is the passage of a family of exocomet or planetesimal fragments, all of which are associated with a single previous break-up event, possibly caused by tidal disruption or thermal processing. The minimum total mass associated with these fragments likely exceeds 10 –6 M , corresponding to an original rocky body of 〉100 km in diameter. We discuss the necessity of future observations to help interpret the system.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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