• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.11-16
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• 2011

In this study, we report the generation and analysis of a total of 1,211 expressed sequence tags (ESTs) from Pinus koraiensis. A cDNA library was generated from the young leaf tissue and a total of 1,211 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. In all, 857 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 50 nucleotides. A total of 411 unigene, consisting of 89 contigs and 322 singletons, was identified after assembling. Also, we identified 77 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 63.1% of ESTs were homologous with known function and 22.2% of ESTs were matched with putative or unknown function. The remaining 14.6% of ESTs showed no significant similarity to any protein sequences found in the public database. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Pinus and provided for the useful tools as a genetic resource.

• Korean Journal of Agricultural Science
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• v.43 no.1
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• pp.33-39
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• 2016

Brassicaceae consists of important species that have significant amounts of metabolites, and many studies have been carried out in order to understand the mechanism that improves the content of these metabolites. In Brassicacea, Cardamine manshurica Nakai is one of the important edible plants and is rich in oil, fiber, and various nutrients. In this study, we constructed cDNA library using leaves from 4 week-old plants and analyzed the ESTs of C. manshurica Nakai. One thousand thirty-nine ESTs were discovered which assembled to form 468 unigenes. The latter contained 116 contigs and 352 singletons. Similarity search of these ESTs with BLASTX revealed similarities with Arabidopsis thaliana 285 (31.9%), Arabidopsis lyrata 172 (19.3%), Capsella rubella 162 (18.1%), and Eutrema salsugineum 137 (15.3%). ESTs were functionally categorized into molecular function, biological process, and cellular component, and each category took 10.6%, 58.5%, and 30.9%, respectively. The functional analysis also found that 94.9% of ESTs showed at least one GO ID. Microsatellite analysis of 468 unigene sequences revealed 225 structures of which Di-, Tri-, Tetra-, Penta-repeats were 35.6% (80/225), 63.1% (142/225), 0.9% (2/225), and 0.4% (1/225), respectively. The results from our study can be a valuable resource for Cardamine research.

• The Journal of Advanced Prosthodontics
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• v.10 no.1
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• pp.8-17
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• 2018

PURPOSE. The study aimed to identify the accuracy and reproducibility of preparations made by gypsum materials of various colors using quantitative and semi-quantitative three-dimensional (3D) approach. MATERIALS AND METHODS. A titanium maxillary first molar preparation was created as reference dataset (REF). Silicone impressions were duplicated from REF and randomized into 6 groups (n=8). Gypsum preparations were formed and grouped according to the color of gypsum materials, and light-scanned to obtain prepared datasets (PRE). Then, in terms of accuracy, PRE were superimposed on REF using the best-fit-algorithm and PRE underwent intragroup pairwise best-fit alignment for assessing reproducibility. Root mean square deviation (RMSD) and degrees of similarity (DS) were computed and analyzed with SPSS 20.0 statistical software (${\alpha}=.05$). RESULTS. In terms of accuracy, PREs in 3D directions were increased in the 6 color groups (from 19.38 to $20.88{\mu}m$), of which the marginal and internal variations ranged $51.36-58.26{\mu}m$ and $18.33-20.04{\mu}m$, respectively. On the other hand, RMSD value and DS-scores did not show significant differences among groups. Regarding reproducibility, both RMSD and DS-scores showed statistically significant differences among groups, while RMSD values of the 6 color groups were less than $5{\mu}m$, of which blue color group was the smallest ($3.27{\pm}0.24{\mu}m$) and white color group was the largest ($4.24{\pm}0.36{\mu}m$). These results were consistent with the DS data. CONCLUSION. The 3D volume of the PREs was predisposed towards an increase during digitalization, which was unaffected by gypsum color. Furthermore, the reproducibility of digitalizing scanning differed negligibly among different gypsum colors, especially in comparison to clinically observed discrepancies.

• The Journal of Advanced Prosthodontics
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• v.8 no.3
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• pp.194-200
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• 2016

PURPOSE. The prospective follow-up aimed to assess the performance of lithium disilicate crowns and clinical reasons of adverse events compromising survival and quality. MATERIALS AND METHODS. 58 patients were treated with 375 heat-pressed monolithic crowns, which were bonded with resin cement. Annual recalls up to five years included a complete dental examination as well as quality assessment using CDA-criteria. Any need for clinical intervention led to higher complication rate and any failure compromised the survival rate. Kaplan-Meier-method was applied to all crowns and a dataset containing one randomly selected crown from each patient. RESULTS. Due to drop-outs, 45 patients (31 females, 14 males) with the average age of 43 years (range = 17-73) who had 327 crowns (176 anterior, 151 posterior; 203 upper jaw, 124 lower jaw) were observed and evaluated for between 4 and 51 months (median = 28). Observation revealed 4 chippings, 3 losses of retention, 3 fractures, 3 secondary caries, 1 endodontic problem, and 1 tooth fracture. Four crowns had to be removed. Survival and complication rate was estimated 98.2% and 5.4% at 24 months, and 96.8% and 7.1% at 48 months. The complication rate was significantly higher for root canal treated teeth (12%, P<.01) at 24 months. At the last observation, over 90% of all crowns showed excellent ratings (CDA-rating Alfa) for color, marginal fit, and caries. CONCLUSION. Heat pressed lithium disilicate crowns showed an excellent performance. Besides a careful luting, dentists should be aware of patients' biological prerequisites (grade of caries, oral hygiene) to reach full success with these crowns.

• Journal of KIISE:Databases
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• v.34 no.1
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• pp.46-58
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• 2007

Since microarray data acquire tens of thousands of gene expression values simultaneously, they could be very useful in identifying the phenotypes of diseases. However, the results of analyzing several microarray datasets which were independently carried out with the same biological objectives, could turn out to be different. One of the main reasons is attributable to the limited number of samples involved in one microarry experiment. In order to increase the classification accuracy, it is desirable to augment the sample size by integrating and maximizing the use of independently-conducted microarray datasets. In this paper, we propose a novel two-stage approach which firstly integrates individual microarray datasets to overcome the problem caused by limited number of samples, and identifies informative genes, secondly builds a classifier using only the informative genes. The classifier from large samples by integrating independent microarray datasets achieves high accuracy up to 24.19% increase as against other comparison methods, sensitivity, and specificity on independent test sample dataset.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.372-377
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• 2007

For more than 2,500 years, surgical teaching has been based on the so called "see one, do one, teach one" paradigm, in which the surgical trainee learns by operating on patients under close supervision of peers and superiors. However, higher demands on the quality of patient care and rising malpractice costs have made it increasingly risky to train on patients. Minimally invasive surgery, in particular, has made it more difficult for an instructor to demonstrate the required manual skills. It has been recognized that, similar to flight simulators for pilots, virtual reality (VR) based surgical simulators promise a safer and more comprehensive way to train manual skills of medical personnel in general and surgeons in particular. One of the major challenges in the development of VR-based surgical trainers is the real-time and realistic simulation of interactions between surgical instruments and biological tissues. It involves multi-disciplinary research areas including soft tissue mechanical behavior, tool-tissue contact mechanics, computer haptics, computer graphics and robotics integrated into VR-based training systems. The research described in this paper addresses the problem of characterizing soft tissue properties for medical virtual environments. A system to measure in vivo mechanical properties of soft tissues was designed, and eleven sets of animal experiments were performed to measure in vivo and in vitro biomechanical properties of porcine intra-abdominal organs. Viscoelastic tissue parameters were then extracted by matching finite element model predictions with the empirical data. Finally, the tissue parameters were combined with geometric organ models segmented from the Visible Human Dataset and integrated into a minimally invasive surgical simulation system consisting of haptic interface devices and a graphic display.

• Journal of Korean Society on Water Environment
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• v.25 no.5
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• pp.735-741
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• 2009

In order to support the basic information for planning and performing the environment management such as Total Maximum Daily Loads (TMDLs), it is highly recommended to understand the spatial distribution of water quality and runoff data in the unit watersheds. Therefore, in the present study, we applied Self-Organizing Map (SOM) to detect the characteristics of spatial distribution of Biological Oxygen Demand (BOD) concentration and runoff data which have been measured in the Yeongsan, Seomjin, and Tamjin River basins. For the purpose, the input dataset for SOM was constructed with the mean, standard deviation, skewness, and kurtosis values of the respective data measured from the stations of 22-subbasins in the rivers. The results showed that the $4{\times}4$ array structure of SOM was selected by the trial and error method and the best performance was revealed when it classified the stations into three clusters according to the basic statistics. The cluster-1 and 2 were classified primarily by the skewness and kurtosis of runoff data and the cluster-3 including the basic statistics of YB_B, YB_C, and YB_D stations was clearly decomposed by the mean value of BOD concentration showing the worst condition of water quality among the three clusters. Consequently, the methodology based on the SOM proposed in the present study can be considered that it is highly applicable to detect the spatial distribution of BOD concentration and runoff data and it can be used effectively for the further utilization using different water quality items as a data analysis tool.

• Journal of the Institute of Electronics Engineers of Korea CI
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• v.45 no.4
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• pp.19-26
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• 2008

Gene set enrichment analysis (GSEA) is a computational method to identify statistically significant gene sets showing significant differences between two groups of microarray expression profiles and simultaneously uncover their biological meanings in an elegant way by employing gene annotation databases, such as Cytogenetic Band, KEGG pathways, gene ontology, and etc. For the gone set enrichment analysis, all the genes in a given dataset are first ordered by the signal-to-noise ratio between the groups and then further analyses are proceeded. Despite of its impressive results in several previous studies, however, gene ranking by the signal-to-noise ratio makes it difficult to consider highly up-regulated genes and highly down-regulated genes at the same time as the candidates of significant genes, which possibly reflect certain situations incurred in metabolic and signaling pathways. To deal with this problem, in this article, we investigate the gene set enrichment analysis method with Fisher criterion for gene ranking and also evaluate its effects in Leukemia related pathway analyses.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.126-126
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• 2017

Mitochondria are important in wheat, as in all crops, as the main source of ATP for cell maintenance and growth including vitamin synthesis, amino acid metabolism and photorespiration. To investigate the mitochondrial proteome of the roots of wheat seedlings, a systematic and targeted analysis were carried out on the mitochondrial proteome from 15 day-old wheat seedling root material. Mitochondria were isolated by Percoll gradient centrifugation; and extracted proteins were separated and analyzed by Tricine SDS-PAGE along with LTQ-FTICR mass spectrometry. From the isolated the sample, 184 proteins were identified which is composed of 140 proteins as mitochondria and 44 proteins as other subcellular proteins that are predicted by the freeware subcellular predictor. The identified proteins in mitochondria were functionally classified into 12 classes using the ProtFun 2.2 server based on biological processes. Proteins were shown to be involved in amino acid biosynthesis (17.1%), biosynthesis of cofactors (6.4%), cell envelope (11.4%), central intermediary metabolism (10%), energy metabolism (20%), fatty acid metabolism (0.7%), purines and pyrimidines (5.7%), regulatory functions (0.7%), replication and transcription (1.4%), translation (22.1%), transport and binding (1.4%), and unknown (2.8%). These results indicate that many of the protein components present and functions of identifying proteins are common to other profiles of mitochondrial proteins performed to date. This dataset provides the first extensive picture, to our knowledge, of mitochondrial proteins from wheat roots. Future research is required on quantitative analysis of the wheat mitochondrial proteomes at the spatial and developmental level.

• Ocean Science Journal
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• v.40 no.2
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• pp.67-78
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• 2005

Complex physical, chemical and biological interactions off the Korean coast created several striking patterns in the phytoplankton blooms, which became conspicuous during the measurements of ocean color from space. This study concentrated on analyzing the spatial and temporal aspects of phytoplankton chlorophyll variability in these areas using an integrated dataset from a Sea-viewing Wide Field-of-view Sensor (SeaWiFS), Advanced Very High Resolution (AVHRR) sensor, and Conductivity Temperature Depth (CTD) sensor. The results showed that chlorophyll concentrations were elevated in coastal and open ocean regions, with strong summer and fall blooms, which appeared to spread out in most of the enclosed bays and neighboring waters due to certain oceanographic processes. The chlorophyll concentration was observed to range between 3 and $54\;mg\;m^{-3}$ inside Jin-hae Bay and adjacent coastal bays and 0.5 and $8\;mg\;m^{-3}$ in the southeast sea offshore waters, this gradual decrease towards oceanic waters suggested physical transports of phytoplankton blooms from the shallow shelves to slope waters through the influence of the Tsushima Warm Current (TWC) along the Tsushima Strait. Horizontal distribution of potential temperature $(\theta)$ and salinity (S) of water off the southeastern coast exhibited cold and low saline surface water $(\theta and warm and high saline subsurface water $({\theta}>12^{\circ}C; S>34.4)$ at 75dBar, corroborating TWC intrusion along the Tsushima Strait. An eastward branch of this current was called the East Korean Warm Current (EKWC), tracked with the help of CTD data and satellite-derived sea surface temperature, which often influenced the dynamics of mesoscale anticyclonic eddy fields off the Korean east coast during the summer season. The process of such mesoscale anticyclonic eddy features might have produced interior upwelling that could have shoaled and steepened the nutricline, enhancing phytoplankton population by advection or diffusion of nutrients in the vicinity of Ulleungdo in the East Sea.