• Nuclear Medicine and Molecular Imaging
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• 제41권4호
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• pp.299-308
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• 2007

Purpose: The aim of this study was to develop a bioinformatics software and to test it in serum samples of papillary thyroid cancer using mass spectrometry (SELDI-TOF-MS). Materials and Methods: Development of 'Protein analysis' software performing decision tree analysis was done by customizing C4.5. Sixty-one serum samples from 27 papillary thyroid cancer, 17 autoimmune thyroiditis, 17 controls were applied to 2 types of protein chips, CM10 (weak cation exchange) and IMAC3 (metal binding - Cu). Mass spectrometry was performed to reveal the protein expression profiles. Decision trees were generated using 'Protein analysis' software, and automatically detected biomarker candidates. Validation analysis was performed for CM10 chip by random sampling. Results: Decision tree software, which can perform training and validation from profiling data, was developed. For CM10 and IMAC3 chips, 23 of 113 and 8 of 41 protein peaks were significantly different among 3 groups (p<0.05), respectively. Decision tree correctly classified 3 groups with an error rate of 3.3% for CM10 and 2.0% for IMAC3, and 4 and 7 biomarker candidates were detected respectively. In 2 group comparisons, all cancer samples were correctly discriminated from non-cancer samples (error rate = 0%) for CM10 by single node and for IMAC3 by multiple nodes. Validation results from 5 test sets revealed SELDI-TOF-MS and decision tree correctly differentiated cancers from non-cancers (54/55, 98%), while predictability was moderate in 3 group classification (36/55, 65%). Conclusion: Our in-house software was able to successfully build decision trees and detect biomarker candidates, therefore it could be useful for biomarker discovery and clinical follow up of papillary thyroid cancer.

• Progress in Medical Physics
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• 제23권2호
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• pp.91-98
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• 2012

Verification of internal organ motion during treatment and its feedback is essential to accurate dose delivery to the moving target. We developed an offline based internal organ motion verification system (IMVS) using cine EPID images and evaluated its accuracy and availability through phantom study. For verification of organ motion using live cine EPID images, a pattern matching algorithm using an internal surrogate, which is very distinguishable and represents organ motion in the treatment field, like diaphragm, was employed in the self-developed analysis software. For the system performance test, we developed a linear motion phantom, which consists of a human body shaped phantom with a fake tumor in the lung, linear motion cart, and control software. The phantom was operated with a motion of 2 cm at 4 sec per cycle and cine EPID images were obtained at a rate of 3.3 and 6.6 frames per sec (2 MU/frame) with $1,024{\times}768$ pixel counts in a linear accelerator (10 MVX). Organ motion of the target was tracked using self-developed analysis software. Results were compared with planned data of the motion phantom and data from the video image based tracking system (RPM, Varian, USA) using an external surrogate in order to evaluate its accuracy. For quantitative analysis, we analyzed correlation between two data sets in terms of average cycle (peak to peak), amplitude, and pattern (RMS, root mean square) of motion. Averages for the cycle of motion from IMVS and RPM system were $3.98{\pm}0.11$ (IMVS 3.3 fps), $4.005{\pm}0.001$ (IMVS 6.6 fps), and $3.95{\pm}0.02$ (RPM), respectively, and showed good agreement on real value (4 sec/cycle). Average of the amplitude of motion tracked by our system showed $1.85{\pm}0.02$ cm (3.3 fps) and $1.94{\pm}0.02$ cm (6.6 fps) as showed a slightly different value, 0.15 (7.5% error) and 0.06 (3% error) cm, respectively, compared with the actual value (2 cm), due to time resolution for image acquisition. In analysis of pattern of motion, the value of the RMS from the cine EPID image in 3.3 fps (0.1044) grew slightly compared with data from 6.6 fps (0.0480). The organ motion verification system using sequential cine EPID images with an internal surrogate showed good representation of its motion within 3% error in a preliminary phantom study. The system can be implemented for clinical purposes, which include organ motion verification during treatment, compared with 4D treatment planning data, and its feedback for accurate dose delivery to the moving target.

• Development and Reproduction
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• 제5권2호
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• pp.167-173
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• 2001

To characterize the difference in glycoconjugates of mouse epididymis, lectin labeling of the tissue section was conducted using Ulex europaeus agglutinin I(UEA I), succinylated wheat germ agglutinin(sWGA), and Griffonia simplicifolia lectin-I(GSL-I). UEA I which binds to outer $\alpha$-L-fucose residue that is a terminal sugar of the side chain branched from oligosaccharide chain gave the labeling in the proximal caput epithelia exclusively. Lumen was commonly labeled in all of the organ. It suggested that the glycoconjugates bearing outer $\alpha$ -L-fucose residue were largely expressed in the initial segments ot epididymis and subjected to secretion. GSL-I which binds to terminal $\alpha$ -D-galactosyl residue of glycoconjugates gave the labeling in the cytoplasm of clear cells and basal cells, and cilia in corpus and cauda regions but not in the caput region. There was no vast difference in labeling pattern by sWGA which binds to N-acetyl-glucosamine residue among the epididymal regions. Clear cells in corpus and cauda epithelia showed more intense labeling by sWGA compared to principal cells, suggesting the functional specialization of this type of cells. The labeling intensities of luminal content by UEA I and sWGA decreased in cauda region compared to corpus region suggesting the presence of enzymatic activities responsible for processing the $\alpha$-L-fucose and N-acetyl-glucosamine residues from secreted glycoconjugates. In summary, the difference in glycoconjugates bearing the $\alpha$-L-fucose, $\alpha$-D-galactose, and N-acetyl-glucosamine residues according to the type of epithelial cells and epididymal segments suggests functional specialization and different roles of each segment in the processing of sperm surface antigens during the epididymal transit.

• Journal of Korean Society of Forest Science
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• 제90권2호
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• pp.169-175
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• 2001

Genomic DNAs were extracted from the leaves of 182 ginkgo trees (Ginkgo biloba L.) planted in 6 regions and subjected to the analysis of both I-SSR and RAPD markers. A total of 227 amplicon variants were generated by PCR using 15 I-SSR primers and 67 amplicons by PCR with 5 RAPD primers. Levels of genetic diversity within 6 populations were turned out to be similar (Shannon's Index, I-SSR : 0.35~0.40; mean of 0.38, RAPD : 0.31~0.38; mean of 0.35, combined : 0.35~0.40; mean of 0.37). Ranks of the level of genetic diversity estimated from I-SSR, RAPD, and combined data were not coincided each other. Majority of genetic diversity was allocated among individuals within populations (I-SSR : 94.31%, RAPD : 93.62%, combined : 93.57%), which resulted in pretty low level of population differentiation. Genetic differentiation between male and female groups was turned out to be quite low (I-SSR : 0.03, RAPD : 0.091, combined : 0.043), which slightly fluctuated when analysis was restricted to the data obtained from 3 regions where both male and female trees were sampled (I-SSR : 0.038, RAPD : 0.084, combined : 0.047). Genetic relationships among the populations, reconstructed by UPGMA, were not coincided with geographic affinity, which might be resulted from sharing of seed sources in some regions. Whereas independent cluster analyses with I-SSR data and RAPD data, respectively, reclassified by sexes revealed two sexual groups in which all the male and the female populations were clustered together, cluster analysis with combined data did not show clear sexual grouping.

• Radiation Oncology Journal
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• 제25권1호
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• pp.43-53
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• 2007

[ $\underline{Purpose}$ ]: To evaluate the relationship between the expression of EGFR, p53, Cox-2, Bcl-2 and the clinical parameters of NPC (nasopharyngeal carcinoma) patients treated with radiotherapy with/without chemotherapy, and to determine if these could be used as a biologic marker. $\underline{Materials\;and\;Methods}$: This study retrospectively examined 75 NPC patients who were pathologically diagnosed at St. Mary's Hospital and Kangnam St Mary's Hospital from March 1988 to August 2002 and treated with radiotherapy with/without chemotherapy. The levels of EGFR, p53, Cox-2, and Bcl-2 expression were determined immunohistochemically. The relationship between the levels of EGFR, p53, Cox-2 and Bcl-2 expression and the H- E staining findings including the WHO classification, TNM stage, tumor response to chemotherapy and radiotherapy, disease free survival (DFS), and overall survival (OS) was analyzed. $\underline{Results}$: At a median follow up of 50.8 months (range: $5.5{\sim}201$ months), the 3 years OS rate and PFS rate were 68.7% and 68.2%, respectively. The five year OS rate and PFS rate were 53.5% and 51.1%, respectively. The median OS duration and PFS duration were 85.5 months and 61.1 months, respectively. The WHO classification correlated with the complete response rate, lymph node metastasis and distant metastasis. The expression of p53 was associated with increased mitosis and poor overall survival. The expression of Bcl-2 correlated with the DFS and WHO classification. The expression of Cox-2 correlated with a poor overall survival and response rate in the lymph node. However, EGFR was not correlated with any factors. $\underline{Conclusion}$: These results suggest that the expression of p53, Cox-2, Bcl-2 plays role in predicting prognostic factors for NPC treated with radiotherapy with/without chemotherapy. However, further study on a larger number of patients will be needed to identify more useful biomarkers of NPC.

• Journal of Chest Surgery
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• 제36권10호
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• pp.711-720
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• 2003

Bakground : Complete resection by the surgery has been selected as the treatment of choice in lung cancer patients, but in cases of recurrence after excision or inoperable cases, the importance of anticancer chemotherapy has been emphasized. If one can select a set of the sensitive chemotherapeutic agents before anticancer chemotherapy, it will give more favourable results. Subrenal capsular assay has been recognized as a useful in-vivo chemosensitivity test of thoracic and abdominal tumors and it can be done in a short time for a rapid interpretation of tumor responsiveness to anticancer chemotherapeutic drugs. It has been reported that various kinds of cancer cells can be implantable to the kidney, but so far there is no comparative study of xenogeneic cell implantation on liver, spleen and kidney. The author implanted the human lung cancer cells under the capsule of S.D rat's liver, spleen and kidney respectively and compared the pattern of growth and histology. Material and Method: After incubation of human lung cancer cell line (SW-900 G IV) in RPMI 1640 (Leibovitz L-15 medium) culture media, 3${\times}$3${\times}$3 mm size fibrin clots which contain 108 cancer cells were made. Thereafter the fibrin clots were implanted at subcapsule area of liver, spleen and kidney of S.D. female rat. For immune suppression, cyclosporin-A (80 mg/Kg) was injected subcutaneously daily from post-implantation first day to sixth day. The body weight was measured at pre and post implantation periods. The growth pattern and the size of tumor mass were observed and the pathologic examination and serum tumor marker tests were performed. Result: Body weight increased in both of control and experimental groups. Serum Cyfra 21-1 was not detected. Serum levels of CEA and NSE revealed no significant change. The SCC-Ag increased significantly in implanted group. The growth rate of human lung cancer cells which was implanted on spleen was higher than on liver or kidney. The surface area, thickness, and volume of tumor mass were predominant at spleen. The success rates of implantation were 80% on kidney, 76.7% on spleen and 43.3% on liver. Pathologic examination of implanted tumors showed characteristic findings according to different organs. Tumors that were implanted on kidney grew in a round shape, small and regular pattern. In the spleen, tumors grew well and microscopic neovascularization and tumor thrombi were also found, but the growth pattern was irregular representing frequent daughter mass. Human lung cancer cells that were implanted in the liver, invaded to the liver parenchyme, and had low success rate of implantation. Microscopically, coagulation necrosis and myxoid fibrous lesion were observed. Conclusion: The success rate of implantation was highest in the kidney. And the mass revealed regular growth that could be measured easily. The SCC-Ag was presented earlier than CEA or Cyfra21-1. The Cyfra21-1 was not detected at early time after implantation. The best model for tumor implantation experiment for chemosensitivity test was subrenal capsular analysis than liver and spleen and the useful serum tumor marker in early period of implantation was the SCC-Ag.

• Journal of Korean Society of Forest Science
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• 제95권4호
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• pp.483-494
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• 2006

We conducted QTL mapping for 6-year growths of open-pollinated half-sib progenies from a selected clone 7-1037 in Pinus taeda. With an AFLP marker analysis on haploid DNA samples from the megagametophytes of the open-pollinated seeds, we constructed 20 framework maps spanning a total of 1,869 cM in total length and 18.5 cM in an average interval length between markers. Composite interval mapping reveals that one QTL explains 5.9% of the total phenotypic variation of height, and three QTLs account for 3.9~5.6% of the variation of diameter at breast height (DBH). There are no correlations between the QTLs. The genetic effects of the QTLs are 39.6 cm in height and 7.20~9.41 mm in DBH, respectively, The average effects of gene substitution of the markers closely linked with the QTLs are 44.3 cm in height and 8.38~11.81 m in DBH. Under an assumption that the within-family heritability for the growth traits of loblolly pine is less than 0.2, the QTLs account for 26.8% of the additive genetic variance of the progenies. In terms of relative selection efficiency, the individual selection based on QTL markers could be 5 times as high as phenotypic selection. The results in this study indicate that the QTL mapping method with open-pollinated half-sib family could be more practical and applicable to the conventional seed orchard-based selection work than other mapping methods with a single full-sib family, in particular from the viewpoint that it can provide crucial information for within-family individual selection such as breeding value.

• Pediatric Infection and Vaccine
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• 제11권1호
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• pp.73-80
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• 2004

Purpose : The serial clinical findings, biochemical results, and serological hepatitis B virus(HBV) markers in Korean children with chronic HBV infection were analyzed to determine the relationships among these factors. Methods : Ninety children have been chosen from those who have visited to the Department of Pediatrics at St. Vincent's Hospital in The Catholic University of Korea from July 1st, 1995 to June 30th, 2000. The sample patients were followed up for over six months. HBV markers and liver function tests were all performed. Results : All children were asymptomatic at presentation. Eighty-three percent of the children had a history of chronic HBV infection in their families. Eighty-one percent were HBeAg positive, 16% were anti-HBe positive, while 3% were all HBeAg and anti-HBe negative. The prevalence of HBeAg among three age groups : 0~5; 6~10; and 11~15 year-old was 90%, 96% and 61% respectively. The prevalence of HBeAg in less than 10 year-old group was significantly higher than 11~15 year-old group(P=0.001). Serum ALT levels were within 40 IU/L in 64% children, 41~80 IU/L in 17%, 81~200 IU/L in 10%, and beyond 201 IU/L in 9%. The percentage of abnormality of ALT levels in HBeAg positive patients was significantly higher than that of HBeAg negative(P=0.036). Eleven of the 73 HBeAg positive children lost their HBeAg and seroconverted to anti-HBe. In these cases, all had transient elevations in ALT levels before HBeAg seroconversions. The annual rates of spontaneous seroconversion of HBeAg and HBsAg were 9.7% and 0.6%, respectively. Conclusion : Recognition of the dynamics of these changes in viral markers and biochemical findings is needed in the selection and evaluation of therapeutic regimens, establishment of treatment, and calling for controlled trials with adequate follow-up. The hepatitis B carrier state may be asymptomatic in children however, continued surveillance of carriers is important to determine the individual adverse prognostic factors of chronic HBV infections.

• Horticultural Science & Technology
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• 제32권1호
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• pp.84-90
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• 2014

Berchemia racemosa var. magna is only found in Anmyeon Island of South Korea. Genetic diversity and the spatial genetic structure of B. racemosa var. magna in Anmyeon Island were studied by I-SSR marker system. Fifty I-SSR amplicons were produced from 8 selected primers. We used 13 polymorphic markers to analyze the genetic structure. Distribution of 39 individuals in the study plot($90m{\times}70m$) showed aggregate pattern (aggregation index = 0.706). Total 21 genets were observed from 39 individuals through I-SSR genotyping. Proportion of distinguishable genotype (G/N), genotype diversity (D) and genotype evenness (E) were 53.8%, 0.966 and 0.946, respectively. In spite of the small number and the narrow distribution, Shannon's diversity index (I = 0.598) was relatively high as compared with those of the other plant species. For ex situ genetic conservation of B. racemosa var. magna, the sampling strategy based on spatial autocorrelation using Tanimoto distance is efficient at choosing the conserved individuals with a 6 meter interval between individual trees.

• Journal of Korean Society of Forest Science
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• 제102권4호
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• pp.560-565
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• 2013

Population genetic structure and diversity of Ulmus davidiana var. japonica in South Korea were studied using ISSR markers. A total of 45 polymorphic ISSR amplicons were cropped from 7 ISSR primers and 171 individuals of 7 populations. The average of effective alleles and the proportion of polymorphic loci were 1.5 and 89% respectively. The Shannon's diversity index (I) was 0.435 and the expected heterozygosity from the frequentist's method ($H_e$) and the Bayesian inference (hs) were 0.289 and 0.323 respectively. From AMOVA, 4.2% of total genetic variation in the elm populations was explained with the difference among populations (${\Phi}_{ST}=0.042$) and the other 95.8% was distributed within populations. The ${\theta}^{II}$ value by Bayesian method which was comparable to the FST was 0.043. So the level of genetic diversity in the elm populations was similar to that in Genus Ulmus and the level of genetic differentiation was lower than that of others. No population showed a significant difference in the population-specific fixation indices (average of $PS-F_{IS}=0.822$) or the population-specific genetic differentiations (average of $PS-F_{ST}=0.101$). Seven populations were allocated into 3 groups in the UPGMA and the PCA, but the grouping patterns were different. Also, we could not confirm any geographic trend from Bayesian clustering.