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Some Properties of Generalized Self-reciprocal Polynomials over Finite Fields
Ryul Kim,Ok-Hyon Song,Hyon-Chol Ri
Mathematics , 2013,
Abstract: Numerous results on self-reciprocal polynomials over finite fields have been studied. In this paper we generalize some of these to a-self reciprocal polynomials defined in [4]. We consider some properties of the divisibility of a-reciprocal polynomials and characterize the parity of the number of irreducible factors for a-self reciprocal polynomials over finite fields of odd characteristic.
Upper Bound of Code-word Number of Some Separating Codes
Ryul Kim,Myong-son Sihn,Ok-hyon Song
Journal of Theoretical Physics and Cryptography , 2013,
Abstract: In this paper, We study upper bounds for separating codes. First, some new upper bound for restricted separating codes is proposed. Finally, we illustrate that the Upper Bound Conjecture for separating Reed-Solomon codes inherited from Silverberg’s question holds true for almost all Reed-Solomon codes.
Upper Bounds on the Number of Codewords of Some Separating Codes
Ryul Kim,Myong-Son Sin,Ok-Hyon Song
Mathematics , 2012,
Abstract: Separating codes have their applications in collusion-secure fingerprinting for generic digital data, while they are also related to the other structures including hash family, intersection code and group testing. In this paper we study upper bounds for separating codes. First, some new upper bound for restricted separating codes is proposed. Then we illustrate that the Upper Bound Conjecture for separating Reed-Solomon codes inherited from Silverberg's question holds true for almost all Reed-Solomon codes.
On the Divisibility of Trinomials by Maximum Weight Polynomials over F2
Ryul Kim,Ok-Hyon Song,Myong-Hui Ri
Mathematics , 2013,
Abstract: Divisibility of trinomials by given polynomials over finite fields has been studied and used to construct orthogonal arrays in recent literature. Dewar et al.\ (Des.\ Codes Cryptogr.\ 45:1-17, 2007) studied the division of trinomials by a given pentanomial over $\F_2$ to obtain the orthogonal arrays of strength at least 3, and finalized their paper with some open questions. One of these questions is concerned with generalizations to the polynomials with more than five terms. In this paper, we consider the divisibility of trinomials by a given maximum weight polynomial over $\F_2$ and apply the result to the construction of the orthogonal arrays of strength at least 3.
Visualization of Retrieved Documents using a Presentation Server
Sa-Kwang Song,Sung Hyon Myaeng
Computer Science , 1999,
Abstract: In any search-based digital library (DL) systems dealing with a non-trivial number of documents, users are often required to go through a long list of short document descriptions in order to identify what they are looking for. To tackle the problem, a variety of document organization algorithms and/or visualization techniques have been used to guide users in selecting relevant documents. Since these techniques require heavy computations, however, we developed a presentation server designed to serve as an intermediary between retrieval servers and clients equipped with a visualization interface. In addition, we designed our own visual interface by which users can view a set of documents from different perspectives through layers of document maps. We finally ran experiments to show that the visual interface, in conjunction with the presentation server, indeed helps users in selecting relevant documents from the retrieval results.
Modeling and Analysis of the Molecular Basis of Pain in Sensory Neurons
Sang Ok Song, Jeffrey Varner
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006758
Abstract: Intracellular calcium dynamics are critical to cellular functions like pain transmission. Extracellular ATP plays an important role in modulating intracellular calcium levels by interacting with the P2 family of surface receptors. In this study, we developed a mechanistic mathematical model of ATP-induced P2 mediated calcium signaling in archetype sensory neurons. The model architecture, which described 90 species connected by 162 interactions, was formulated by aggregating disparate molecular modules from literature. Unlike previous models, only mass action kinetics were used to describe the rate of molecular interactions. Thus, the majority of the 252 unknown model parameters were either association, dissociation or catalytic rate constants. Model parameters were estimated from nine independent data sets taken from multiple laboratories. The training data consisted of both dynamic and steady-state measurements. However, because of the complexity of the calcium network, we were unable to estimate unique model parameters. Instead, we estimated a family or ensemble of probable parameter sets using a multi-objective thermal ensemble method. Each member of the ensemble met an error criterion and was located along or near the optimal trade-off surface between the individual training data sets. The model quantitatively reproduced experimental measurements from dorsal root ganglion neurons as a function of extracellular ATP forcing. Hypothesized architecture linking phosphoinositide regulation with P2X receptor activity explained the inhibition of P2X-mediated current flow by activated metabotropic P2Y receptors. Sensitivity analysis using individual and the whole system outputs suggested which molecular subsystems were most important following P2 activation. Taken together, modeling and analysis of ATP-induced P2 mediated calcium signaling generated qualitative insight into the critical interactions controlling ATP induced calcium dynamics. Understanding these critical interactions may prove useful for the design of the next generation of molecular pain management strategies.
Streptococcus pyogenes c-di-AMP Phosphodiesterase, GdpP, Influences SpeB Processing and Virulence
Kyu Hong Cho, Song Ok Kang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069425
Abstract: Small cyclic nucleotide derivatives are employed as second messengers by both prokaryotes and eukaryotes to regulate diverse cellular processes responding to various signals. In bacteria, c-di-AMP has been discovered most recently, and some Gram-positive pathogens including S. pyogenes use this cyclic nucleotide derivative as a second messenger instead of c-di-GMP, a well-studied important bacterial second messenger. GdpP, c-di-AMP phosphodiesterase, is responsible for degrading c-di-AMP inside cells, and the cellular role of GdpP in S. pyogenes has not been examined yet. To test the cellular role of GdpP, we created a strain with a nonpolar inframe deletion of the gdpP gene, and examined the properties of the strain including virulence. From this study, we demonstrated that GdpP influences the biogenesis of SpeB, the major secreted cysteine protease, at a post-translational level, susceptibility to the beta lactam antibiotic ampicillin, and is necessary for full virulence in a murine subcutaneous infection model.
Identification of active Plasmodium falciparum calpain to establish screening system for Pf-calpain-based drug development
Soh Byoung,Song Hyun-Ok,Lee Yoonji,Lee Junghyun
Malaria Journal , 2013, DOI: 10.1186/1475-2875-12-47
Abstract: Background With the increasing resistance of malaria parasites to available drugs, there is an urgent demand to develop new anti-malarial drugs. Calpain inhibitor, ALLN, is proposed to inhibit parasite proliferation by suppressing haemoglobin degradation. This provides Plasmodium calpain as a potential target for drug development. Pf-calpain, a cysteine protease of Plasmodium falciparum, belongs to calpain-7 family, which is an atypical calpain not harboring Ca2+-binding regulatory motifs. In this present study, in order to establish the screening system for Pf-calpain specific inhibitors, the active form of Pf-calpain was first identified. Methods Recombinant Pf-calpain including catalytic subdomain IIa (rPfcal-IIa) was heterologously expressed and purified. Enzymatic activity was determined by both fluorogenic substrate assay and gelatin zymography. Molecular homology modeling was carried out to address the activation mode of Pf-calpain in the aspect of structural moiety. Results Based on the measurement of enzymatic activity and protease inhibitor assay, it was found that the active form of Pf-calpain only contains the catalytic subdomain IIa, suggesting that Pf-calpain may function as a monomeric form. The sequence prediction indicates that the catalytic subdomain IIa contains all amino acid residues necessary for catalytic triad (Cys-His-Asn) formation. Molecular modeling suggests that the Pf-calpain subdomain IIa makes an active site, holding the catalytic triad residues in their appropriate orientation for catalysis. The mutation analysis further supports that those amino acid residues are functional and have enzymatic activity. Conclusion The identified active form of Pf-calpain could be utilized to establish high-throughput screening system for Pf-calpain inhibitors. Due to its unique monomeric structural property, Pf-calpain could be served as a novel anti-malarial drug target, which has a high specificity for malaria parasite. In addition, the monomeric form of enzyme may contribute to relatively simple synthesis of selective inhibitors.
Statistical immersions between statistical manifolds of constant curvature
Chol Rim Min,Song Ok Choe,Yun Ho An
Mathematics , 2014,
Abstract: The condition for the curvature of a statistical manifold to admit a kind of standard hypersurface is given. We study the statistical hypersurfces of some types of the statistical manifolds $(M, \nabla, g )$, which enable $(M, \nabla^{(\alpha)}, g ), \forall\alpha\in\mathbf{R}$ to admit the structure of a constant curvature.
First-principles study on electron field emission from nanostructures
Hyon-Chol Choe,Nam-Hyok Kim,Hyok Kim,Song-Jin Im
Physics , 2014,
Abstract: A first-principles approach is introduced to calculate electron field emission characteristics of nanostructures, based on the nonequilibrium Green function technique combined with the density functional theory. The method employs atomic-like basis orbitals with large confinement radii and lithium anode to describe the electron density in the vacuum between the nanostructure tip and the anode, so takes the presence of emitted current into account. The simulation results on a capped single-walled carbon nanotube reproduce the experimental trend closely, in particular, the current saturation and the deviation from the Fowler-Nordheim behavior.
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