• 농업과학연구
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• 제38권1호
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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.

• 농업과학연구
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• 제43권1호
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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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• 제10권1호
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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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• 제8권3호
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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.

• 한국정보과학회논문지:데이타베이스
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• 제34권1호
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• pp.46-58
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• 2007

마이크로어레이 데이타는 동시에 수 만개 유전자의 발현 값을 포함하고 있기 때문에 질병의 발현 형질 분류에 매우 유용하게 쓰인다. 그러나 동일한 생물학적 주제라 할지라도 여러 독립된 연구 집단에서 생성된 마이크로어레이의 분석결과는 서로 다르게 나타날 수 있다. 이에 대한 주된 이유는 하나의 마이크로어레이 실험에 참여한 샘플의 수가 제한적이기 때문이다. 따라서 개별적으로 수행된 마이크로어레이 데이타를 통합하여 샘플의 수를 늘리는 것은, 보다 정확한 분석을 하는데 있어 매우 중요하다. 본 연구에서는 이에 대한 해결 방안으로 두 단계 접근방법을 제안한다. 제 1 단계에서는 개별적으로 생성된 동일주제의 마이크로어레이 데이타를 통합한 후 인포머티브(Informative) 유전자를 추출하고 제 2 단계에서는 인포머티브 유전자만을 이용하여 클래스 분류(Classification) 과정 후 분류자를 추출한다. 이 분류자를 다른 테스트 샘플 데이타에 적용한 실험결과를 보면 마이크로어레이 데이타를 통합하여 샘플의 수를 증가시킬수록, 비교 방법에 비해 정확도가 최대 24.19% 높은 분류자를 만들어 내는 것을 알 수 있다.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2007년도 춘계학술대회A
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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.

• 한국물환경학회지
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• 제25권5호
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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.

• 전자공학회논문지CI
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• 제45권4호
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• pp.19-26
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• 2008

Gene set enrichment analysis (GSEA)는 두 개의 클래스를 가지는 마이크로어레이 실험 데이터 분석을 위해 생물학적 특징을 기반으로 구성된 다양한 유전자-집합 중에서 두 클래스의 발현값들이 통계적으로 중요한 차이를 나타내는 유의한 유전자-집합을 추출하기 위한 분석 방법이다. 특히, 유전자에 대한 다양한 생물학적인 정보를 지닌 유전자 주석 데이터베이스(Cytogenetic Band, KEGG pathway, Gene Ontology 등)를 이용하여 마이크로어레이 실험에 사용된 전체 유전자 중 특정 기능을 가지는 유전자들을 그룹화하여 다양한 유전자-집합을 발굴하고, 각 유전자-집합 내에서 두 클래스간에 발현값의 차이를 참조하여 유의한 유전자들을 결정하여, 이를 기반으로 통계적으로 유의한 유전자-집합들을 최종 검출하는 방법이다. 본 논문에서는 GSEA 분석 과정에서 현재 주로 사용되고 있는 signal-to-noise ratio 기반 유전자 서열화(gene ranking) 방법 대신에, Fisher criterion을 이용한 유전자 서열화 방법을 적용함으로써 기존의 GSEA 방법에서 추출하지 못한 생물학적으로 의미 있는 새로운 유의 유전자-집합을 추출하는 방법을 제안하고자 한다. 또한, 제안한 방법의 성능을 고찰하기 위하여 공개된 Leukemia 관련 마이크로어레이 실험 데이터 분석에 적용하였으며, 기존의 알려진 결과와 비교 분석함으로써 제안한 방법의 유용성을 검증하고자 하였다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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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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• 제40권2호
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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.