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  • 1
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    Conditional Diagnosability of Burnt Pancake Networks Under the PMC Model (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-08
    Description: The $n$ -dimensional burnt pancake network, denoted by $BP_n$ , originates from the Burnt pancake problem which relates to the construction of networks of parallel processors. In the wake of rapid development of multiprocessor systems, processor fault diagnosis plays an even more important role in measuring the reliability of a multiprocessor system, and the diagnosabilities of many well-known multiprocessor systems have been investigated. The conditional diagnosability has been widely accepted as a new measure of diagnosability by assuming that any faulty set cannot contain all the neighbors of any node in a multiprocessor system. In this paper, we explore combinatorial properties of burnt pancake networks, and investigate the structural vulnerability as well as extra connectivities. Furthermore, we show that the classic diagnosability and the conditional diagnosability of $BP_n$ ( $n\geq 4$ ) under the Preparata, Metze and Chien model are $n$ and $8n-13$ , respectively.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 2
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    Transgenic poplar overexpressing the endogenous transcription factor ERF76 gene improves salinity tolerance (2016)
    Oxford University Press
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    Publication Date: 2016-08-03
    Description: The ethylene response factor (ERF) family is one of the largest plant-specific transcription factor families, playing an important role in plant development and response to stresses. The ERF76 gene is a member of the poplar ERF transcription factor gene family. First, we validated that the ERF76 gene expressed in leaf and root tissues is responsive to salinity stress. We then successfully cloned the ERF76 cDNA fragment containing an open reading frame from di-haploid Populus simonii   x   Populus nigra and proved that ERF76 protein is targeted to the nucleus. Finally, we transferred the gene into the same poplar clone by the Agrobacterium -mediated leaf disc method. Using both RNA-Seq and reverse transcription-quantitative polymerase chain reaction, we validated that expression level of ERF76 is significantly higher in transgenic plants than that in the nontransgenic control. Using RNA-Seq data, we have identified 375 genes that are differentially expressed between the transgenic plants and the control under salt treatment. Among the differentially expressed genes, 16 are transcription factor genes and 45 are stress-related genes, both of which are upregulated significantly in transgenic plants, compared with the control. Under salt stress, the transgenic plants showed significant increases in plant height, root length, fresh weight, and abscisic acid (ABA) and gibberellin (GA) concentration compared with the control, suggesting that overexpression of ERF76 in transgenic poplar upregulated the expression of stress-related genes and increased the ability of ABA and GA biosynthesis, which resulted in stronger tolerance to salt stress.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 3
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    Thermal analysis of PCM-filled glass windows in hot summer and cold winter area (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Phase change material (PCM)-filled glass window was suitable for absorbing or releasing more heat than conventional glass window. Comparisons of thermal performance between PCM-filled glass windows and insulated glass windows (double glass windows filled with dry air and surrounded by sealing strips) were presented in this paper. A 3D unsteady model was built in FLUENT to obtain the internal and external surface temperature fluctuations of these windows in 48 h. Compared with insulated glass windows, thermal performance (especially the thermal regulation effect) of double glass windows filled with Na 2 SO 4 ·10H 2 O was quite satisfactory in sunny days of summer, while double glass windows filled with CaCl 2 ·6H 2 O had a better thermal performance in overcast and rainy days of summer. Because the phase change temperature of these PCM is higher than the ambient temperature in winter, the thermal regulation effects of them were not as good as expected.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Oxford University Press
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  • 4
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    A 3-D enlarged cell technique (ECT) for elastic wave modelling of a curved free surface (2016)
    Oxford University Press
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    Publication Date: 2016-07-29
    Description: The conventional finite-difference time-domain (FDTD) method for elastic waves suffers from the staircasing error when applied to model a curved free surface because of its structured grid. In this work, an improved, stable and accurate 3-D FDTD method for elastic wave modelling on a curved free surface is developed based on the finite volume method and enlarged cell technique (ECT). To achieve a sufficiently accurate implementation, a finite volume scheme is applied to the curved free surface to remove the staircasing error; in the mean time, to achieve the same stability as the FDTD method without reducing the time step increment, the ECT is introduced to preserve the solution stability by enlarging small irregular cells into adjacent cells under the condition of conservation of force. This method is verified by several 3-D numerical examples. Results show that the method is stable at the Courant stability limit for a regular FDTD grid, and has much higher accuracy than the conventional FDTD method.
    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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  • 5
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    Network-based analysis of genotype-phenotype correlations between different inheritance modes (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: Recent studies on human disease have revealed that aberrant interaction between proteins probably underlies a substantial number of human genetic diseases. This suggests a need to investigate disease inheritance mode using interaction, and based on which to refresh our conceptual understanding of a series of properties regarding inheritance mode of human disease. Results: We observed a strong correlation between the number of protein interactions and the likelihood of a gene causing any dominant diseases or multiple dominant diseases, whereas no correlation was observed between protein interaction and the likelihood of a gene causing recessive diseases. We found that dominant diseases are more likely to be associated with disruption of important interactions. These suggest inheritance mode should be understood using protein interaction. We therefore reviewed the previous studies and refined an interaction model of inheritance mode, and then confirmed that this model is largely reasonable using new evidences. With these findings, we found that the inheritance mode of human genetic diseases can be predicted using protein interaction. By integrating the systems biology perspectives with the classical disease genetics paradigm, our study provides some new insights into genotype–phenotype correlations. Contact: haodapeng@ems.hrbmu.edu.cn or biofomeng@hotmail.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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  • 6
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    Enrichment of Cdk1-cyclins at DNA double-strand breaks stimulates Fun30 phosphorylation and DNA end resection (2016)
    Oxford University Press
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    Publication Date: 2016-04-08
    Description: DNA double-strand breaks (DSBs) are one of the most cytotoxic types of DNA lesion challenging genome integrity. The activity of cyclin-dependent kinase Cdk1 is essential for DSB repair by homologous recombination and for DNA damage signaling. Here we identify the Fun30 chromatin remodeler as a new target of Cdk1. Fun30 is phosphorylated by Cdk1 on Serine 28 to stimulate its functions in DNA damage response including resection of DSB ends. Importantly, Cdk1-dependent phosphorylation of Fun30-S28 increases upon DNA damage and requires the recruitment of Fun30 to DSBs, suggesting that phosphorylation increases in situ at the DNA damage. Consistently, we find that Cdk1 and multiple cyclins become highly enriched at DSBs and that the recruitment of Cdk1 and cyclins Clb2 and Clb5 ensures optimal Fun30 phosphorylation and checkpoint activation. We propose that the enrichment of Cdk1-cyclin complexes at DSBs serves as a mechanism for enhanced targeting and modulating of the activity of DNA damage response proteins.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    More evidence for the red-shift dependence of colour from the Joint Light-curve Analysis supernova sample using red-shift tomography (2016)
    Oxford University Press
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    Publication Date: 2016-06-17
    Description: In this work, by applying the red-shift tomography method to the Joint Light-curve Analysis (JLA) supernova sample, we explore the possible red-shift dependence of the stretch luminosity α and the colour luminosity β. The basic idea is to divide the JLA sample into different red-shift bins, assuming that α and β are piecewise constants. Then, by constraining the CDM model, we check the consistency of the cosmology-fitting results given by the supernova sample of each red-shift bin. We also adopt the same technique to explore the possible evolution of β in various subsamples of JLA. Using the full JLA data, we find that α is always consistent with a constant value. In contrast, at high red shift, β has a significant trend of decreasing, at ~3.5 confidence level (CL). Moreover, we find that the low- z subsample favours a constant β; in contrast, the Sloan Digital Sky Survey and Supernova Legacy Survey subsamples favour a decreasing β at 2 and 3.3 CL, respectively. Besides, by using a binned parametrization of β, we study the impact of the evolution of β on parameter estimation. We find that compared with a constant β, a varying β yields a larger best-fitting value of fractional matter density m 0 , which slightly deviates from the best-fitting result given by other cosmological observations. However, for both the varying β and the constant β cases, the 1 regions of m 0 are still consistent with the result given by other observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Resistivity inversion in 2-D anisotropic media: numerical experiments (2015)
    Oxford University Press
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    Publication Date: 2015-02-19
    Description: Many rocks and layered/fractured sequences have a clearly expressed electrical anisotropy although it is rare in practice to incorporate anisotropy into resistivity inversion. In this contribution, we present a series of 2.5-D synthetic inversion experiments for various electrode configurations and 2-D anisotropic models. We examine and compare the image reconstructions obtained using the correct anisotropic inversion code with those obtained using the false but widely used isotropic assumption. Superior reconstruction in terms of reduced data misfit, true anomaly shape and position, and anisotropic background parameters were obtained when the correct anisotropic assumption was employed for medium to high coefficients of anisotropy. However, for low coefficient values the isotropic assumption produced better-quality results. When an erroneous isotropic inversion is performed on medium to high level anisotropic data, the images are dominated by patterns of banded artefacts and high data misfits. Various pole–pole, pole–dipole and dipole–dipole data sets were investigated and evaluated for the accuracy of the inversion result. The eigenvalue spectra of the pseudo-Hessian matrix and the formal resolution matrix were also computed to determine the information content and goodness of the results. We also present a data selection strategy based on high sensitivity measurements which drastically reduces the number of data to be inverted but still produces comparable results to that of the comprehensive data set. Inversion was carried out using transversely isotropic model parameters described in two different co-ordinate frames for the conductivity tensor, namely Cartesian versus natural or eigenframe. The Cartesian frame provided a more stable inversion product. This can be simply explained from inspection of the eigenspectra of the pseudo-Hessian matrix for the two model descriptions.
    Keywords: Marine Geosciences and Applied Geophysics
    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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  • 9
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    A deep learning framework for modeling structural features of RNA-binding protein targets (2016)
    Oxford University Press
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    Publication Date: 2016-03-01
    Description: RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been developed for modeling RBP binding preferences, discovering a complete structural representation of the RBP targets by integrating their available structural features in all three dimensions is still a challenging task. In this paper, we develop a general and flexible deep learning framework for modeling structural binding preferences and predicting binding sites of RBPs, which takes (predicted) RNA tertiary structural information into account for the first time . Our framework constructs a unified representation that characterizes the structural specificities of RBP targets in all three dimensions, which can be further used to predict novel candidate binding sites and discover potential binding motifs. Through testing on the real CLIP-seq datasets, we have demonstrated that our deep learning framework can automatically extract effective hidden structural features from the encoded raw sequence and structural profiles, and predict accurate RBP binding sites. In addition, we have conducted the first study to show that integrating the additional RNA tertiary structural features can improve the model performance in predicting RBP binding sites, especially for the polypyrimidine tract-binding protein (PTB), which also provides a new evidence to support the view that RBPs may own specific tertiary structural binding preferences. In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https://github.com/thucombio/deepnet-rbp .
    Keywords: Nucleic acid structure, Protein-nucleic acid interaction, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Multiscale modeling of macromolecular biosystems (2012)
    Oxford University Press
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    Publication Date: 2012-07-26
    Description: In this article, we review the recent progress in multiresolution modeling of structure and dynamics of protein, RNA and their complexes. Many approaches using both physics-based and knowledge-based potentials have been developed at multiple granularities to model both protein and RNA. Coarse graining can be achieved not only in the length, but also in the time domain using discrete time and discrete state kinetic network models. Models with different resolutions can be combined either in a sequential or parallel fashion. Similarly, the modeling of assemblies is also often achieved using multiple granularities. The progress shows that a multiresolution approach has considerable potential to continue extending the length and time scales of macromolecular modeling.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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