• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8741-8747
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• 2014

Purpose: We aimed to investigate the associations between polymorphisms of interleukin-1A (IL-1A), IL-1B, and IL-1 receptor antagonist (IL-1RN) and prostate cancer (PCa) risk. Materials and Methods: A comprehensive search for articles of MEDLINE and EMBASE databases and bibliographies of retrieved articles published up to August 3, 2014 was performed. Methodological quality assessment of the trials was based on a standard quality scoring system. The meta-analysis was performed using STATA 12.0. Results: We included 9 studies (1 study for IL-1A, 5 studies for IL-1B, and 3 studies for IL-1RN), and significant association was found between polymorphisms of IL-1B-511 (rs16944) as well as IL-1B-31 (rs1143627) and PCa risk. IL-1B-511 (rs16944) polymorphism was significantly associated with PCa risk in homozygote and recessive models, as well as allele contrast (TT vs CC: OR, 0.74; 95%CI, 0.58-0.94; P=0.012; TT vs TC+CC; OR, 0.79; 95%CI, 0.63-0.98; P=0.033; T vs C: OR, 0.86; 95%CI, 0.77-0.96; P=0.008). The association between IL-1B-31 (rs1143627) polymorphism and PCa risk was weakly significant under a heterozygote model (OR, 1.35; 95%CI, 1.00-1.80; P=0.047). Conclusions: Sequence variants in IL-1B-511 (rs16944) and IL-1B-31 (rs1143627) are significantly associated with PCa risk, which provides additional novel evidence that proinflammatory cytokines and inflammation play an important role in the etiology of PCa.

• Proceedings of the Korea Water Resources Association Conference
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• 2011.05a
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• pp.58-58
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• 2011

The Texas Commission on Environmental Quality(TCEQ) WAM(Water Availability Modeling) System consists of the generalized Water Rights Analysis Package(WRAP) river/reservoir system water management simulation model, 22 sets of WRAP hydrology and water rights input files for the 23 river basins of Texas, geographic information system tools, and other supporting databases. The WRAP/WAM modeling system, as routinely applied since the late 1990s, has not included consideration of water quality. Recently developed WRAP-SALT(Water Rights Analysis Package) is designed primarily for computing concentration frequency statistics and supply reliability indices at locations of interest in a river system for alternative water development and management scenarios. Though motivated primarily by natural salt pollution, WRAP-SALT water quality modeling features are applicable to essentially any conservative water quality constituent. The Brazos River studies discussed in this paper focus on total dissolved solids, though the available observed data also includes chloride and sulfate which can be modeled as individual constituents. The WRAP-SALT salinity input file contains loads or concentrations of salinity inflows during each month of the hydrologic period-of-analysis and reservoir storage at the beginning of the simulation. The WRAP-SALT model computes salt loads and concentrations for each control point of a river/reservoir system for inflows and outflows during the month and end-of-month reservoir storage for each month of the hydrologic period-of-analysis, for given loads entering the system. River reaches connect control points. The mass balance algorithms proceed from upstream to downstream, with outflow from one river reach contributing to inflow to the next downstream reach. In a given month, for each control point in sequence, the inflow loads are first computed. Loads and concentrations of outflows and reservoir storage at the control point are then determined. Complete mixing during the month is assumed at locations without reservoir storage.

• Journal of KIISE:Databases
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• v.32 no.3
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• pp.254-262
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• 2005

This paper presents a new sequential indexing method called segment-page indexing (SP-indexing) for multidimensional range queries. The design objectives of SP-indexing are twofold:(1) improving the range query performance of multidimensional indexing methods (MIMs) and (2) providing a compromise between optimal index clustering and the full index reorganization overhead. Although more than ten years of database research has resulted in a great variety of MIMs, most efforts have focused on data-level clustering and there has been less attempt to cluster indexes. As a result, most relevant index nodes are widely scattered on a disk and many random disk accesses are required during the search. SP-indexing avoids such scattering by storing the relevant nodes contiguously in a segment that contains a sequence of contiguous disk pages and improves performance by offering sequential access within a segment. Experimental results demonstrate that SP-indexing improves query performance up to several times compared with traditional MIMs using small disk pages with respect to total elapsed time and it reduces waste of disk bandwidth due to the use of simple large pages.

• Journal of KIISE:Databases
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• v.35 no.4
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• pp.368-378
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• 2008

In recent years, publish-subscribe (pub-sub) systems based on XML document filtering have received much attention. In a typical pub-sub system, subscribed users specify their interest in profiles expressed in the XPath language, and each new content is matched against the user profiles so that the content is delivered to only the interested subscribers. As the number of subscribed users and their profiles can grow very large, the scalability of the system is critical to the success of pub-sub services. In this paper, we propose a fast and scalable XML filtering system called SFiST which is an extension of the FiST system. Sharable segments are extracted from twig patterns and stored into the hash-based Segment Table in SFiST system. Segments are used to represent user profiles as Terse Sequences and stored in the Compact Segment Index during filtering. Our experimental study shows that SFiST system has better performance than FiST system in terms of filtering time and memory usage.

• Ocean and Polar Research
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• v.39 no.2
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• pp.149-158
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• 2017

The opsin family of light sensitive proteins family makes up are the universal photoreceptor molecules of all visual systems in the vertebrates including teleosts. They can change their conformation from a resting state to a signaling state upon light absorption, which activates the G-protein coupled receptor, thereby resulting in a signaling cascade that produces physiological responses. However, this species is poorly characterized at molecular level due to little sequence information available in public databases. We have investigated the opsin family of nocturnal cutlass fish using the whole transcriptome sequencing method. The opsin genes were cloned and its expression in the tissues and organs were examined by qPCR. We cloned 6 opsin genes (RRH, Opn4, Rh1, Rh2, VA-opsin, and Opn3) in retina and brain tissue. It contained the seven presumed transmembrane domains that are characteristic of the G-protein-coupled receptor family. However, short wavelength sensitive pigment (SWS) and long wavelength sensitive pigment (LWS) were not detected in this study. The mRNA expression of the 6 photoreceptor genes were detected in retina and peripheral tissue. Our studies will lead to further investigation of the photic entrainment mechanism at molecular and cellular levels in cutlass fish and can be used in comparative studies of other fishes.

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.144-152
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• 2010

As the International Rice Genome Sequencing Project (IRGSP) was completed in 2005 and opened to the public, many countries are making a lot of investments in researches on the utilization of sequence information along with system development. Also, the necessity of the functional genomics researches using microarray is increased currently to secure unique genes related with major agricultural traits and analyze metabolic pathways. Microrarray enables efficient analysis of large scale gene expression and related transcription regulation. This review aims to introduce available microarrays made based on rice genome information and current status of gene expression analysis using these microarrays integrated with the databases available to the public. Also, we introduce the researches on the large scale functional analysis of genes related with useful traits and genetic networks. Understanding of the mechanism related with mutual interaction between proteins with co-expression among rice genes can be utilized in the researches for improving major agricultural traits. The direct and indirect interactions of various genes would provide new functionality of rice. The recent results of the various expression profiling analysis in rice will promote functional genomic researches in plants including rice and provide the scientists involved in applications researches with wide variety of expression informations.

• Journal of Plant Biotechnology
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• v.44 no.3
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• pp.287-295
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• 2017

Water temperature is one of the major factors that impacts the growth and life cycle of Pyropia tenera, one of the most valuable and cultivated marine red algae belonging to Bangiales (Rhodophytes). We analyzed transcriptome from gametophyte of P. tenera under normal and high temperature conditions, and identified four small heat shock proteins (sHSPs). They have no significant amino acid sequence homology with known proteins in public databases except PhsHSP22 from Pyropia haitanensis. PtsHSP19.3 gene responded to high temperature but slightly or not to desiccation, freezing or high salt condition. When the PtsHSP19.3 gene was overexpressed in Chlamydomonas reinhardtii, transformed Chlamydomonas lines revealed much higher growth rate than that of control cells under heat stress condition. Transformed cells also grew well in those of the control cell onto the medium containing high salt or $H_2O_2$. When the PtsHSP19.3 was fused to GFP and introduced into tobacco protoplast, fluorescence was detected at several spots. Results indicate that PtsHSP19.3 may form super-molecular assembles and be involved in tolerance to heat stress.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• Journal of KIISE:Databases
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• v.31 no.2
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• pp.183-194
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• 2004

As XML is a do facto standard for a data exchange language, there have been several researches on efficient processing XML queries. The most important thing to consider when processing XML queries is how efficiently we can process path expressions in queries. Some previous works make results by performing a sequence of join operations on all records corresponding to labels in the path expression. Others works check the existence of paths in the query using an RDBMS's string comparison operator and make results by extracting the records corresponding to the paths. In this paper we suggested a new query planning algorithm based on path containment relationships and two join operators supporting the planning algorithm. The join operators use only the records related to the paths in a query as input data, scan them only once, and generate result data using a pipelining mechanism. By analysis and experiments, we confirmed that our techniques(a new query planning algorithm and two join operators) achieved significantly higher performance than other previous works.

• Journal of KIISE:Databases
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• v.33 no.4
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• pp.423-436
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• 2006

In recent years, publish-subscribe (pub-sub) systems based on XML document filtering have received much attention. In a typical pub-sub system, subscribing users specify their interest in profiles expressed in the XPath language, and each new content is matched against the user profiles so that the content is delivered only to the interested subscribers. As the number of subscribed users and their profiles can grow very large, the scalability of the system is critical to the success of pub-sub services. In this paper, we propose a novel scalable filtering system called FiST(Filtering by Sequencing Twigs) that transforms twig patterns expressed in XPath and XML documents into sequences using Prufer's method. As a consequence, instead of matching linear paths of twig patterns individually and merging the matches during post-processing, FiST performs holistic matching of twig patterns with incoming documents. FiST organizes the sequences into a dynamic hash based index for efficient filtering. We demonstrate that our holistic matching approach yields lower filtering cost and good scalability under various situations.