Area-Optimized Fully-Flexible BCH Decoder for Multiple GF Dimensions

Recently, there are increasing demands for fully flexible Bose Chaudhuri Hocquenghem (BCH) decoders, which can support different dimensions of Galois fields (GF) operations. As the previous BCH decoders are mainly targeting the fixed GF operations, the conventional techniques are no longer suitable for multiple GF dimensions. For the area-optimized flexible BCH decoders, in this paper, we present several optimization schemes for reducing hardware costs of multi-dimensional GF operations. In the proposed optimizations, we first reformulate the matrix operations in syndrome calculation and Chien search for sharing more common sub-expressions between GF operations having different dimensions. The cell based multi-m GF multiplier is newly introduced for the area-efficient flexible key-equation solver. As case studies, we design several prototype flexible BCH decoders for digital video broadcasting systems and NAND flash memory controllers managing different page sizes. The implementation results show that the proposed fully-flexible BCH decoder architecture remarkably enhances the area-efficiency compared with the conventional solutions.112Ysciescopu

The Effect of Political Institutions on the Use of Citizen Participation Programs

Local governments use of citizen participation programs is influenced by external environments, especially in the form of political institutions. Local governments decide to expand or limit citizen participation in administrative decision-making processes in response to political uncertainties created by different types of political institutions. Despite the importance of institutional contexts, few studies have examined the effects of these political institutions on the use of citizen participation programs. This study empirically tested whether political institutions affect the adoption of citizen participation programs. The results suggest that the council-manager form of government increases both the adoption of citizen participation mechanisms and the use of citizen participation programs in functional areas, while nonpartisan elections are associated only with the adoption of citizen participation mechanisms. At-large elections show no statistical association with either type of citizen participation. These findings suggest that local political contexts play important roles in the adoption of bureaucratic practices such as citizen participation programs and still support the classical assertion that public dministration is closely connected to politics

The Influence of Contextual Factors on Collective Actions for Locating Facilities with Externalities: Applying the Institutional Collective Action Framework

This study applies the Institutional Collective Action Framework to two cases: proposals for the construction of Taekwondo Park and the location of a nuclear waste dump site in Booahn. While the proposed park caused excessive competition because its benefits were overestimated and its private goods were considered necessary, the proposed nuclear waste site resulted in excessive conflict because of uncertainty about its potential harms and because its public goods were considered unnecessary. The former case showed homogeneity of political power and cooperation based on trust, whereas the latter case showed heterogeneity of political power and conflict based on distrust. Both cases showed politicians active participation based on their reelection goals and a blocked network structure between central and local governments. Stakeholders in both cases showed strong internal ties with other stakeholders with similar potential political and economic benefits

Identification and analysis of in planta expressed genes of Magnaporthe oryzae

<p>Abstract</p> <p>Background</p> <p>Infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. We have employed expressed sequence tag (EST) analysis to identify rice genes involved in defense responses against infection by the blast fungus <it>Magnaporthe oryzae </it>and fungal genes involved in infectious growth within the host during a compatible interaction.</p> <p>Results</p> <p>A cDNA library was constructed with RNA from rice leaves (<it>Oryza sativa </it>cv. Hwacheong) infected with <it>M. oryzae </it>strain KJ201. To enrich for fungal genes, subtraction library using PCR-based suppression subtractive hybridization was constructed with RNA from infected rice leaves as a tester and that from uninfected rice leaves as the driver. A total of 4,148 clones from two libraries were sequenced to generate 2,302 non-redundant ESTs. Of these, 712 and 1,562 ESTs could be identified to encode fungal and rice genes, respectively. To predict gene function, Gene Ontology (GO) analysis was applied, with 31% and 32% of rice and fungal ESTs being assigned to GO terms, respectively. One hundred uniESTs were found to be specific to fungal infection EST. More than 80 full-length fungal cDNA sequences were used to validate <it>ab initio</it> annotated gene model of <it>M. oryzae</it> genome sequence.</p> <p>Conclusion</p> <p>This study shows the power of ESTs to refine genome annotation and functional characterization. Results of this work have advanced our understanding of the molecular mechanisms underpinning fungal-plant interactions and formed the basis for new hypothesis.</p

Fungal cytochrome P450 database

<p>Abstract</p> <p>Background</p> <p>Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.</p> <p>Results</p> <p>The Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.</p> <p>Conclusion</p> <p>The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site <url>http://p450.riceblast.snu.ac.kr/</url>.</p

Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

<p>Abstract</p> <p>Background</p> <p>Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).</p> <p>Description</p> <p>A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.</p> <p>Conclusions</p> <p>The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at <url>http://fsd.snu.ac.kr/</url>.</p

Silver nanoparticles inhibit VEGF-and IL-1β-induced vascular permeability via Src dependent pathway in porcine retinal endothelial cells

The aim of this study is to determine the effects of silver nanoparticles (Ag-NP) on vascular endothelial growth factor (VEGF)-and interleukin-1 beta (IL-1β)-induced vascular permeability, and to detect the underlying signaling mechanisms involved in endothelial cells. Porcine retinal endothelial cells (PRECs) were exposed to VEGF, IL-1β and Ag-NP at different combinations and endothelial cell permeability was analyzed by measuring the flux of RITC-dextran across the PRECs monolayer. We found that VEGF and IL-1β increase flux of dextran across a PRECs monolayer, and Ag-NP block solute flux induced by both VEGF and IL-1β. To explore the signalling pathway involved VEGF- and IL-1β-induced endothelial alteration, PRECs were treated with Src inhibitor PP2 prior to VEGF and IL-1β treatment, and the effects were recorded. Further, to clarify the possible involvement of the Src pathways in endothelial cell permeability, plasmid encoding dominant negative(DN) and constitutively active(CA) form of Src kinases were transfected into PRECs, 24 h prior to VEGF and IL-1β exposure and the effects were recorded. Overexpression of DN Src blocked both VEGF-and IL-1β-induced permeability, while overexpression of CA Src rescues the inhibitory action of Ag-NP in the presence or absence of VEGF and IL-1β. Further, an in vitro kinase assay was performed to identify the presence of the Src phosphorylation at Y419. We report that VEGF and IL-1β-stimulate endothelial permeability via Src dependent pathway by increasing the Src phosphorylation and Ag-NP block the VEGF-and IL-1β-induced Src phosphorylation at Y419. These results demonstrate that Ag-NP may inhibit the VEGF-and IL-1β-induced permeability through inactivation of Src kinase pathway and this pathway may represent a potential therapeutic target to inhibit the ocular diseases such as diabetic retinopathy

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

<p>Abstract</p> <p>Background</p> <p>Since the full genome sequences of <it>Saccharomyces cerevisiae</it> were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP) was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed.</p> <p>Results</p> <p>The Seoul National University Genome Browser (SNUGB) integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets) and 34 plant and animal (38 datasets) species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion.</p> <p>Conclusion</p> <p>The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site <url>http://genomebrowser.snu.ac.kr/</url>.</p