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  • 1
    Publication Date: 2015-06-02
    Description: Recently, wireless sensor networks (WSNs) have been widely used in many applications, such as Smart Grid. However, it is generally known that WSNs are energy limited, which makes WSNs vulnerable to malicious attacks. Among these malicious attacks, a sinkhole attack is the most destructive one, since only one sinkhole node can attract surrounding nodes with unfaithful routing information, and it executes severe malicious attacks, e.g. the selective forwarding attack. In addition, a sinkhole node can cause a large amount of energy wastes of surrounding nodes, which results in abnormal energy hole in WSNs. Thus, it is necessary to design an effective mechanism to detect the sinkhole attack. In this paper, we propose a novel Intrusion Detection Algorithm based on neighbor information against Sinkhole Attack (IDASA). Different from traditional intrusion detection algorithms, IDASA takes full advantage of neighbor information of sensor nodes to detect sinkhole nodes. In addition, we evaluate IDASA in terms of malicious node detection accuracy, packet loss rate, energy consumption and network throughput in MATLAB. Simulation results show that the performance of IDASA is better than that of other related algorithms.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 2
    Publication Date: 2013-10-02
    Description: Accurately locating unknown nodes is a critical issue in the study of wireless sensor networks (WSNs). Many localization approaches have been proposed based on anchor nodes, which are assumed to know their locations by manual placement or additional equipments such as global positioning system. However, none of these approaches can work properly under the adversarial scenario. In this paper, we propose a novel scheme called two-step secure localization (TSSL) stand against many typical malicious attacks, e.g. wormhole attack and location spoofing attack. TSSL detects malicious nodes step by step. First, anchor nodes collaborate with each other to identify suspicious nodes by checking their coordinates, identities and time of sending information. Then, by using a modified mesh generation scheme, malicious nodes are isolated and the WSN is divided into areas with different trust grades. Finally, a novel localization algorithm based on the arrival time difference of localization information is adopted to calculate locations of unknown nodes. Simulation results show that the TSSL detects malicious nodes effectively and the localization algorithm accomplishes localization with high localization accuracy.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 3
    Publication Date: 2015-10-29
    Description: The composition of two arbitrary component automata can have deadlock states. A method is proposed to minimally reduce a component automaton such that the resulting composition with the other automaton is deadlock-free. The method is applied to deriving compositionally deadlock-free solutions of automata equations over the synchronous composition.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 4
    Publication Date: 2015-01-16
    Description: The Central Carbon Metabolic Flux Database (CeCaFDB, available at http://www.cecafdb.org ) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. It encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information gathered from hundreds of journal articles. In addition to its comprehensive literature-derived data, the CeCaFDB supports a common text search function among the data and interactive visualization of the curated flux distributions with compartmentation information based on the Cytoscape Web API, which facilitates data interpretation. The CeCaFDB offers four modules to calculate a similarity score or to perform an alignment between the flux distributions. One of the modules was built using an inter programming algorithm for flux distribution alignment that was specifically designed for this study. Based on these modules, the CeCaFDB also supports an extensive flux distribution comparison function among the curated data. The CeCaFDB is strenuously designed to address the broad demands of biochemists, metabolic engineers, systems biologists and members of the -omics community.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2012-05-23
    Description: MicroRNAs (miRNA) are a class of small RNA molecules that regulate numerous critical cellular processes and bind to partially complementary sequences resulting in down-regulation of their target genes. Due to the incomplete homology of the miRNA to its target site identification of miRNA target genes is difficult and currently based on computational algorithms predicting large numbers of potential targets for a given miRNA. To enable the identification of biologically relevant miRNA targets, we describe a novel functional assay based on a 3'-UTR-enriched library and a positive/negative selection strategy. As proof of principle we have used mir-130a and its validated target MAFB to test this strategy. Identification of MAFB and five additional targets and their subsequent confirmation as mir-130a targets by western blot analysis and knockdown experiments validates this strategy for the functional identification of miRNA targets.
    Keywords: Targeted inhibition of gene function
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2012-02-28
    Description: Both kinetochore function and sister chromatid cohesion can depend upon pericentromere chromatin structure, and factors associated with heterochromatin have been proposed to have general, conserved roles in distinguishing centromeres and pericentromeres and in conferring pericentromere-intrinsic functions. We applied genome-wide sequencing approaches to quantify RNA expression, DNA methylation and histone modification distributions in maize ( Zea mays ), focusing on two maize chromosomes with nearly fully sequenced centromeres and pericentromeres. Aside from the presence of the Histone H3 variant common to all centromeres, Centromeric Histone H3 (CENH3), we found no RNA expression or chromatin modifications that clearly differentiate pericentromeres from either centromeres or from chromosome arms, nor did we identify an epigenetic signature that accurately predicts CENH3 location. RNA expression and chromatin modification frequencies were broadly associated with distance from centromeres, gradually peaking or dipping toward arms. When interpreted in the context of experimental data from other systems, our results suggest that centromeres may confer essential functions (such as cohesion retention) to flanking sequence regardless of the local heterochromatin profile.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2013-10-08
    Description: Ubiquitylation plays key roles in DNA damage signal transduction. The current model envisions that lysine63-linked ubiquitin chains, via the concerted action of E3 ubiquitin ligases RNF8-RNF168, are built at DNA double-strand breaks (DSBs) to effectively assemble DNA damage-repair factors for proper checkpoint control and DNA repair. We found that RNF168 is a short-lived protein that is stabilized by the deubiquitylating enzyme USP34 in response to DNA damage. In the absence of USP34, RNF168 is rapidly degraded, resulting in attenuated DSB-associated ubiquitylation, defective recruitment of BRCA1 and 53BP1 and compromised cell survival after ionizing radiation. We propose that USP34 promotes a feed-forward loop to enforce ubiquitin signaling at DSBs and highlight critical roles of ubiquitin dynamics in genome stability maintenance.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2014-04-03
    Description: Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine () modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with () and without (UUU) modifications. Comparison of the two structures shows that H69 has the following unique features: (i) the loop region is closed by a Watson–Crick base pair between 1911 and A1919, which is potentially reinforced by interactions involving 1911N1H and (ii) modifications at loop residues 1915 and 1917 promote base stacking from 1915 to A1918. In contrast, the H69 UUU loop region, which lacks modifications, is less organized. Structure modulation by leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2014-11-27
    Description: The brain–blood barrier (BBB) tightly limits immune cell migration into the central nervous system (CNS), avoiding unwanted inflammation under the normal state. However, immune cells can traverse the BBB when inflammation occurs within the CNS, suggesting a certain signal that creates a gateway that bypasses the BBB might exist. We revealed the inflammation amplifier as a mechanism of this signal, and identified dorsal vessels of the fifth lumber (L5) spinal cord as the gateway. The inflammation amplifier is driven by a simultaneous activation of NF-B and STATs in non-immune cells, causing the production of a large amount of inflammatory chemokines to open the gateway at L5 vessels. It was found that the activation of the amplifier can be modulated by neural activation and artificially operated by electric pulses followed by establishment of new gateways, Gateway Reflex, at least in mice. Furthermore, genes required for the inflammation amplifier have been identified and are highly associated with various inflammatory diseases and disorders in the CNS. Thus, physical and/or pharmacological manipulation of the inflammation amplifier holds therapeutic value to control neuro-inflammation.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 10
    Publication Date: 2014-08-20
    Description: Vector time series data are widely met in practice. In this paper we propose a multivariate functional-coefficient regression model with heteroscedasticity for modelling such data. A local linear smoother is employed to estimate the unknown coefficient matrices. Asymptotic normality of the proposed estimators is established, and bandwidth selection is considered. To deal with the co-integration commonly observed in financial markets, we propose an error-corrected multivariate functional-coefficient model. Simulations show that our proposed estimation procedures capture nonlinear structures of coefficients well. Analysis of United States interest rates illustrates the proposed methods.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
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