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  • 1
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    Properties of massive star-forming clumps with infall motions (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-15
    Description: In this work, we aim to characterize high-mass clumps with infall motions. We selected 327 clumps from the Millimetre Astronomy Legacy Team 90-GHz survey, and identified 100 infall candidates. Combined with the results of He et al., we obtained a sample of 732 high-mass clumps, including 231 massive infall candidates and 501 clumps where infall is not detected. Objects in our sample were classified as pre-stellar, proto-stellar, H ii or photodissociation region (PDR). The detection rates of the infall candidates in the pre-stellar, proto-stellar, H ii and PDR stages are 41.2 per cent, 36.6 per cent, 30.6 per cent and 12.7 per cent, respectively. The infall candidates have a higher H 2 column density and volume density compared with the clumps where infall is not detected at every stage. For the infall candidates, the median values of the infall rates at the pre-stellar, proto-stellar, H ii and PDR stages are 2.6 x 10 –3 , 7.0 x 10 –3 , 6.5 x 10 –3 and 5.5 x 10 –3 M  yr –1 , respectively. These values indicate that infall candidates at later evolutionary stages are still accumulating material efficiently. It is interesting to find that both infall candidates and clumps where infall is not detected show a clear trend of increasing mass from the pre-stellar to proto-stellar, and to the H ii stages. The power indices of the clump mass function are 2.04 ± 0.16 and 2.17 ± 0.31 for the infall candidates and clumps where infall is not detected, respectively, which agree well with the power index of the stellar initial mass function (2.35) and the cold Planck cores (2.0).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Infall motions in massive star-forming regions: results from years 1 and 2 of the MALT90 survey (2015)
    Oxford University Press
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    Publication Date: 2015-05-01
    Description: Massive star-forming regions with observed infall motions are good sites for studying the birth of massive stars. In this paper, 405 compact sources have been extracted from the APEX Telescope Large Area Survey of the Galaxy (ATLASGAL) compact sources that also have been observed in the Millimetre Astronomy Legacy Team 90-GHz (MALT90) survey during years 1 and 2. These observations are complemented with Spitzer GLIMPSE/MIPSGAL mid-IR survey data to help classify the elected star-forming clumps into three evolutionary stages: pre-stellar, proto-stellar and UCHII regions. The results suggest that 0.05 g cm –2 is a reliable empirical lower bound for the clump surface densities required for massive-star formation to occur. The optically thick HCO + (1-0) and HNC(1-0) lines, as well as the optically thin N 2 H + (1-0) line were used to search for infall motions towards these sources. By analysing the asymmetries of the optically thick HCO + (1-0) and HNC(1-0) lines and the mapping observations of HCO + (1-0), a total of 131 reliable infall candidates have been identified. The HCO + (1-0) line shows the highest occurrence of obvious asymmetric features, suggesting that it may be a better infall motion tracer than other lines such as HNC(1-0). The detection rates of infall candidates towards pre-stellar, proto-stellar and UCHII clumps are 0.3452, 0.3861 and 0.2152, respectively. The relatively high detection rate of infall candidates towards UCHII clumps indicates that many UCHII regions are still accreting matter. The peak column densities and masses of the infall candidates, in general, display an increasing trend with progressing evolutionary stages. However, the rough estimates of the mass infall rate show no obvious variation with evolutionary stage.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry (2014)
    Oxford University Press
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    Publication Date: 2014-07-04
    Description: 5-Hydroxymethylcytosine (5hmC) is present in T-even phage and mammalian DNA as well as some nucleoside antibiotics, including mildiomycin and bacimethrin, during whose synthesis 5hmC is produced by the hydrolysis of 5-hydroxymethyl cytidine 5'-monophosphate (hmCMP) by an N -glycosidase MilB. Recently, the MilB–CMP complex structure revealed its substrate specificity for CMP over dCMP. However, hmCMP instead of CMP is the preferred substrate for MilB as supported by that its K M for CMP is ~27-fold higher than that for hmCMP. Here, we determined the crystal structures of MilB and its catalytically inactive E103A mutant in complex with hmCMP. In the structure of the complex, Phe22 and Arg23 are positioned in a cage-like active site resembling the binding pocket for the flipped 5-methylcytosine (5mC) in eukaryotic 5mC-binding proteins. Van der Waals interaction between the benzene ring of Phe22 and the pyrimidine ring of hmCMP stabilizes its binding. Remarkably, upon hmCMP binding, the guanidinium group of Arg23 was bent ~65° toward hmCMP to recognize its 5-hydroxymethyl group, inducing semi-closure of the cage-like pocket. Mutagenesis studies of Arg23 and bioinformatics analysis demonstrate that the positively charged Arg/Lys at this site is critical for the specific recognition of the 5-hydroxymethyl group of hmCMP.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    RiceWiki: a wiki-based database for community curation of rice genes (2013)
    Oxford University Press
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    Publication Date: 2013-12-29
    Description: Rice is the most important staple food for a large part of the world’s human population and also a key model organism for biological studies of crops as well as other related plants. Here we present RiceWiki ( http://ricewiki.big.ac.cn ), a wiki-based, publicly editable and open-content platform for community curation of rice genes. Most existing related biological databases are based on expert curation; with the exponentially exploding volume of rice knowledge and other relevant data, however, expert curation becomes increasingly laborious and time-consuming to keep knowledge up-to-date, accurate and comprehensive, struggling with the flood of data and requiring a large number of people getting involved in rice knowledge curation. Unlike extant relevant databases, RiceWiki features harnessing collective intelligence in community curation of rice genes, quantifying users' contributions in each curated gene and providing explicit authorship for each contributor in any given gene, with the aim to exploit the full potential of the scientific community for rice knowledge curation. Based on community curation, RiceWiki bears the potential to make it possible to build a rice encyclopedia by and for the scientific community that harnesses community intelligence for collaborative knowledge curation, covers all aspects of biological knowledge and keeps evolving with novel knowledge.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    On the origin of the soft photons of the high-synchrotron-peaked blazar PKS 1424+240 (2016)
    Oxford University Press
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    Publication Date: 2016-07-09
    Description: PKS 1424+240 is a distant very-high-energy gamma-ray BL Lac object with redshift z  = 0.601. It has been found that models utilizing pure synchrotron self-Compton (SSC) processes normally need extreme input parameters (e.g. a very low magnetic field intensity and an extraordinarily high Doppler factor) to explain this particular object spectral energy distributions (SEDs). In order to avoid these extreme model parameters, various other models have been proposed (e.g. the two-zone SSC model or lepto-hadronic model). In this work, we employ the traditional one-zone leptonic model after including a weak external Compton component in order to explore the simultaneous multiwavelength SEDs of PKS 1424+240 in both the high (2009) and the low (2013) state. We find that the input parameters of the magnetic field and Doppler factor are roughly consistent with those of other BL Lacs if a weak external photon field from either the broad line region (BLR) or the dust torus is assumed. However, the required energy density of seed photons from the BLR or torus is about three orders of magnitude lower than that the energy density estimated from the observations in luminous quasars (e.g. flat-spectrum radio quasars, FSRQs). This result suggests that the BLR/torus in BL Lacs is much weaker than that of luminous FSRQs (but has not fully disappeared), and that the inverse-Compton process of external photons from the BLR/torus may still play a role even in high-synchrotron-peaked blazars.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    PASPA: a web server for mRNA poly(A) site predictions in plants and algae (2015)
    Oxford University Press
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    Publication Date: 2015-05-12
    Description: Motivation: Polyadenylation is an essential process during eukaryotic gene expression. Prediction of poly(A) sites helps to define the 3' end of genes, which is important for gene annotation and elucidating gene regulation mechanisms. However, due to limited knowledge of poly(A) signals, it is still challenging to predict poly(A) sites in plants and algae. PASPA is a web server for p oly( A ) s ite prediction in p lants and a lgae, which integrates many in-house tools as add-ons to facilitate poly(A) site prediction, visualization and mining. This server can predict poly(A) sites for ten species, including seven previously poly(A) signal non-characterized species, with sensitivity and specificity in a range between 0.80 and 0.95. Availability and implementation: http://bmi.xmu.edu.cn/paspa Contact : xhuister@xmu.edu.cn 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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  • 7
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    A genome-wide association study identifies susceptibility loci of silica-related pneumoconiosis in Han Chinese (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Pneumoconiosis is the most serious occupational disease in China and its leading cause is occupational silica exposure. Pneumoconiosis takes several years to develop depending on the exposure level of silica. However, individual variation in the susceptibility to pneumoconiosis has been observed among the subjects with similar exposure. We conducted a genome-wide screening with 710 999 single nucleotide polymorphisms (SNPs) in a cohort of 400 coal workers (202 cases and 198 exposed controls) for pneumoconiosis susceptible loci. Seven promising variants were evaluated in an independent cohort of 568 coal workers (323 cases and 245 exposed controls), followed by a second replication on 463 iron ore workers (167 cases and 296 exposed controls). By pooling all of the genome-wide association studies and replication stages together, we found a genome-wide significant ( P 〈 5.0 x 10 –8 ) association for rs73329476 ( P = 1.74 x 10 –8 , OR = 2.17, 95% CI = 1.66–2.85) and two additional replicated associations for rs4320486 ( P 〈 0.05) and rs117626015 ( P 〈 0.05) with combined P -values of 4.29 x 10 –6 and 5.05 x 10 –6 , respectively. In addition, the risk allele T of rs73329476 was significantly associated with lower mRNA expression levels of carboxypeptidase M ( CPM ) in total cellular RNA from whole blood of 156 healthy individuals ( P = 0.0252). The identified pneumoconiosis susceptibility loci may provide new insights into the pathogenesis of pneumoconiosis, and may also have some clinical utility for risk prediction for pneumoconiosis and high-risk population screening for workers with occupational silica exposure.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-02
    Description: Motivation: How chromatin folds in three-dimensional (3D) space is closely related to transcription regulation. As powerful tools to study such 3D chromatin conformation, the recently developed Hi-C technologies enable a genome-wide measurement of pair-wise chromatin interaction. However, methods for the detection of biologically meaningful chromatin interactions, i.e. peak calling, from Hi-C data, are still under development. In our previous work, we have developed a novel hidden Markov random field (HMRF) based Bayesian method, which through explicitly modeling the non-negligible spatial dependency among adjacent pairs of loci manifesting in high resolution Hi-C data, achieves substantially improved robustness and enhanced statistical power in peak calling. Superior to peak callers that ignore spatial dependency both methodologically and in performance, our previous Bayesian framework suffers from heavy computational costs due to intensive computation incurred by modeling the correlated peak status of neighboring loci pairs and the inference of hidden dependency structure. Results: In this work, we have developed FastHiC, a novel approach based on simulated field approximation, which approximates the joint distribution of the hidden peak status by a set of independent random variables, leading to more tractable computation. Performance comparisons in real data analysis showed that FastHiC not only speeds up our original Bayesian method by more than five times, bus also achieves higher peak calling accuracy. Availability and Implementation: FastHiC is freely accessible at: http://www.unc.edu/~yunmli/FastHiC/ Contacts : yunli@med.unc.edu or ming.hu@nyumc.org 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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  • 9
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    Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-14
    Description: The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative "parasitism genes." Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus , a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Image and Video Encryption based on Dual Space-Filling Curves (2012)
    Oxford University Press
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    Publication Date: 2012-05-31
    Description: In this paper, a new encryption scheme with three different modes of operations is proposed based on dual space-filling curves (SFSs) and a fractional wavelet transform (FrWT). This scheme is initially proposed for images and then extended to videos. The core idea behind the proposed schemes is to decompose an image/video first by the FrWT followed by the shuffling of each sub-band coefficients by means of a dual SFC. At last, an inverse FrWT is performed to get the encrypted image/video. A reliable decryption process is also proposed to construct the original image from the encrypted image. The experimental results, security and comparative analysis demonstrate the efficiency and robustness of the proposed scheme. Further, this paper also proposes an efficient implementation of an FrWT based on chaotic maps.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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