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  • 1
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    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension (2015)
    Oxford University Press
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    Publication Date: 2015-01-13
    Description: Hypertension is a common disorder and the leading risk factor for cardiovascular disease and premature deaths worldwide. Genome-wide association studies (GWASs) in the European population have identified multiple chromosomal regions associated with blood pressure, and the identified loci altogether explain only a small fraction of the variance for blood pressure. The differences in environmental exposures and genetic background between Chinese and European populations might suggest potential different pathways of blood pressure regulation. To identify novel genetic variants affecting blood pressure variation, we conducted a meta-analysis of GWASs of blood pressure and hypertension in 11 816 subjects followed by replication studies including 69 146 additional individuals. We identified genome-wide significant ( P 〈 5.0 x 10 –8 ) associations with blood pressure, which included variants at three new loci ( CACNA1D , CYP21A2 , and MED13L ) and a newly discovered variant near SLC4A7 . We also replicated 14 previously reported loci, 8 ( CASZ1 , MOV10 , FGF5 , CYP17A1 , SOX6 , ATP2B1 , ALDH2 , and JAG1 ) at genome-wide significance, and 6 ( FIGN , ULK4 , GUCY1A3 , HFE , TBX3-TBX5 , and TBX3 ) at a suggestive level of P = 1.81 x 10 –3 to 5.16 x 10 –8 . These findings provide new mechanistic insights into the regulation of blood pressure and potential targets for treatments.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Collision and annihilation of relative equilibrium points around asteroids with a changing parameter (2015)
    Oxford University Press
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    Publication Date: 2015-08-09
    Description: In this work, we investigate the bifurcations of relative equilibria in the gravitational potential of asteroids. A theorem concerning a conserved quantity, which is about the eigenvalues and number of relative equilibria, is presented and proved. The conserved quantity can restrict the number of non-degenerate equilibria in the gravitational potential of an asteroid. It is concluded that the number of non-degenerate equilibria in the gravitational field of an asteroid varies in pairs and is an odd number. In addition, the conserved quantity can also restrict the kinds of bifurcations of relative equilibria in the gravitational potential of an asteroid when the parameter varies. Furthermore, studies have shown that there exist transcritical bifurcations, quasi-transcritical bifurcations, saddle–node bifurcations, saddle–saddle bifurcations, binary saddle–node bifurcations, supercritical pitchfork bifurcations, and subcritical pitchfork bifurcations for the relative equilibria in the gravitational potential of asteroids. It is found that for the asteroid 216 Kleopatra, when the rotation period varies as a parameter, the number of relative equilibria changes from 7 to 5 to 3 to 1, and the bifurcations for the relative equilibria are saddle–node bifurcations and saddle–saddle bifurcations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Generation of Rayleigh-wave dispersion images from multichannel seismic data using sparse signal reconstruction (2015)
    Oxford University Press
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    Publication Date: 2015-09-11
    Description: The accurate estimation of dispersion curves has been a key issue for ensuring high quality in geophysical surface wave exploration. Many studies have been carried out on the generation of a high-resolution dispersion image from array measurements. In this study, the sparse signal representation and reconstruction techniques are employed to obtain the high resolution Rayleigh-wave dispersion image from seismic wave data. First, a sparse representation of the seismic wave data is introduced, in which the signal is assumed to be sparse in terms of wave speed. Then, the sparse signal is reconstructed by optimization using l 1 -norm regularization, which gives the signal amplitude spectrum as a function of wave speed. A dispersion image in the f – v domain is generated by arranging the sparse spectra for all frequency slices in the frequency range. Finally, to show the efficiency of the proposed approach, the Surfbar-2 field test data, acquired by B. Luke and colleagues at the University of Nevada Las Vegas, are analysed. By comparing the real-field dispersion image with the results from other methods, the high mode-resolving ability of the proposed approach is demonstrated, particularly for a case with strongly coherent modes.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    Low-frequency germline variants across 6p22.2-6p21.33 are associated with non-obstructive azoospermia in Han Chinese men (2015)
    Oxford University Press
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    Publication Date: 2015-09-12
    Description: Genome-wide association studies (GWAS) have identified several common loci contributing to non-obstructive azoospermia (NOA). However, a substantial fraction of NOA heritability remains undefined, especially those low-frequency [defined here as having a minor allele frequency (MAF) between 0.5 and 5%] and rare (MAF below 0.5%) variants. Here, we performed a 3-stage exome-wide association study in Han Chinese men to evaluate the role of low-frequency or rare germline variants in NOA development. The discovery stage included 962 NOA cases and 1348 healthy male controls genotyped by exome chips and was followed by a 2-stage replication with an additional 2168 cases and 5248 controls. We identified three low-frequency variants located at 6p22.2 (rs2298090 in HIST1H1E encoding p.Lys152Arg: OR = 0.30, P = 2.40 x 10 –16 ) and 6p21.33 (rs200847762 in FKBPL encoding p.Pro137Leu: OR = 0.11, P = 3.77 x 10 –16 ; rs11754464 in MSH5 : OR = 1.78, P = 3.71 x 10 –7 ) associated with NOA risk after Bonferroni correction. In summary, we report an instance of newly identified signals for NOA risk in genes previously undetected through GWAS on 6p22.2–6p21.33 in a Chinese population and highlight the role of low-frequency variants with a large effect in the process of spermatogenesis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    One-connectivity and finiteness of Hamiltonian S1-manifolds with minimal fixed sets (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-20
    Description: Let the circle act effectively in a Hamiltonian fashion on a compact symplectic manifold $(M, \omega )$ . Assume that the fixed point set $M^{S^1}$ has exactly two components, $X$ and $Y$ , and that $\dim (X) + \dim (Y) +2 = \dim (M)$ . We first show that $X$ , $Y$ and $M$ are simply connected. Then we show that, up to $S^1$ -equivariant diffeomorphism, there are finitely many such manifolds in each dimension. Moreover, we show that in low dimensions, the manifold is unique in a certain category. We use techniques from both areas of symplectic geometry and geometric topology.
    Print ISSN: 0024-6107
    Electronic ISSN: 1469-7750
    Topics: Mathematics
    Published by Oxford University Press
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  • 6
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    Parallel Domestication of the Heading Date 1 Gene in Cereals (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-22
    Description: Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 ( HD1 ), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Deduplication-Based Energy Efficient Storage System in Cloud Environment (2015)
    Oxford University Press
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    Publication Date: 2015-06-02
    Description: In cloud computing, companies usually use high-end storage systems to guarantee the I/O performance of virtual machines (VM). These storage systems cost a lot of energy for their high performance. In this paper, we propose an EEVS, a deduplication-based energy efficiency storage system for VM storage. We firstly investigate some VM image files with general operating systems. With the analysis result, we find there are many redundant data blocks that bring extra energy cost VM storage. Therefore, in the EEVS, we design an online-deduplication mechanism to reduce these redundant data without service interruption, while traditional deduplication technology is used for offline backup. Based on the system design, we implement an EEVS with the existing cloud platform. Since this mechanism needs considerable computing resources, we design a deduplication selection algorithm such that the storage energy consumption is minimized for a given set of VMs with limited resources for deduplication. Experiment results in a para-virtualization environments of the EEVS show that energy consumption is reduced by even up to 66% with negligible performance degradation.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 8
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    Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-09
    Description: Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10–15%. Complex and computationally intensive pipelines are required to assemble such reads. Results: We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools. Availability and implementation: https://github.com/lh3/minimap and https://github.com/lh3/miniasm Contact: hengli@broadinstitute.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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    A new molecular signature method for prediction of driver cancer pathways from transcriptional data (2016)
    Oxford University Press
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    Publication Date: 2016-06-21
    Description: Assigning cancer patients to the most effective treatments requires an understanding of the molecular basis of their disease. While DNA-based molecular profiling approaches have flourished over the past several years to transform our understanding of driver pathways across a broad range of tumors, a systematic characterization of key driver pathways based on RNA data has not been undertaken. Here we introduce a new approach for predicting the status of driver cancer pathways based on signature functions derived from RNA sequencing data. To identify the driver cancer pathways of interest, we mined DNA variant data from TCGA and nominated driver alterations in seven major cancer pathways in breast, ovarian and colon cancer tumors. The activation status of these driver pathways were then characterized using RNA sequencing data by constructing classification signature functions in training datasets and then testing the accuracy of the signatures in test datasets. The signature functions differentiate well tumors with nominated pathway activation from tumors with no signs of activation: average AUC equals to 0.83. Our results confirm that driver genomic alterations are distinctively displayed at the transcriptional level and that the transcriptional signatures can generally provide an alternative to DNA sequencing methods in detecting specific driver pathways.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Mutations of charged amino acids at the cytoplasmic end of transmembrane helix 2 affect transport activity of the budding yeast multidrug resistance protein Pdr5p (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-11
    Description: Pdr5p is a major ATP-binding cassette (ABC) transporter in Saccharomyces cerevisiae. It displays a sequence and functional homology to the pathogenic Candida albicans multidrug resistance protein Cdr1p. The transmembrane helices of Pdr5p act in substrate recognition, binding, translocation and eventual removal of toxic substances out of the plasma membrane via the formation of a binding pocket. In this study, we identify two novel Pdr5 mutants (E574K and E580K), which exhibit impaired substrate efflux functions. Both mutants remained hypersensitive to all tested Pdr5p substrates without affecting their protein expression levels, localization or ATPase activities. As E574 and E580 are both located adjacent to the predicted cytoplasmic end of transmembrane helix 2, this implies that such charged residues are functionally essential for Pdr5p. Molecular docking studies suggest the possibility that oppositely charged substitution at residue E574 may disturb the interaction between the substrates and Pdr5p, resulting in impaired transport activity. Our results present new evidence, suggesting that transmembrane helix 2 plays an important role for the efflux function of Pdr5p.
    Print ISSN: 1567-1356
    Electronic ISSN: 1567-1364
    Topics: Biology
    Published by Oxford University Press
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