• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2004.11a
• /
• pp.272-278
• /
• 2004

Recently, Pepe et al. (2003) employed the receiver operating characteristic (ROC) approach to rank candidate genes from a microarray experiment that can be used for the biomarker development with the ultimate purpose of the population screening of a cancer, In the cancer microarray experiment based on n patients the researcher often wants to compare the tumor tissue with the normal tissue within the same individual using a common reference RNA. This design is referred to as a reference design or an indirect design. Ideally, this experiment produces n pairs of microarray data, where each pair consists of two sets of microarray data resulting from reference versus normal tissue and reference versus tumor tissue hybridizations. However, for certain individuals either normal tissue or tumor tissue is not large enough for the experimenter to extract enough RNA for conducting the microarray experiment, hence there are missing values either in the normal or tumor tissue data. Practically, we have $n_1$ pairs of complete observations, $n_2$ 'normal only' and $n_3$ 'tumor only' data for the microarray experiment with n patients, where n=$n_1$+$n_2$+$n_3$. We refer to this data set as a mixed data set, as it contains a mix of fully observed and partially observed pair data. This mixed data set was actually observed in the microarray experiment based on human tissues, where human tissues were obtained during the surgical operations of cancer patients. Pepe et al. (2003) provide the rationale of using ROC approach based on two independent samples for ranking candidate gene instead of using t or Mann -Whitney statistics. We first modify ROC approach of ranking genes to a paired data set and further extend it to a mixed data set by taking a weighted average of two ROC values obtained by the paired data set and two independent data sets.

• Journal of the korean academy of Pediatric Dentistry
• /
• v.8 no.1
• /
• pp.55-63
• /
• 1981

The purpose of this study is to observe the effect of formocresol and glutaraldehyde to tooth germs and periapical tissues after perforation of interradicular portion of pulpal floor and application of physiological saline solution in control groups, formocresol and glutaraldehyde in experimental groups. The following results were obtained 1. In control groups, normal healing processes were seen, and, on the sixteenth day, the epithelization of injured areas was completed. Inflammatory reactions were limited to the injured surface, and the underlying alveolar bone were normal and successive tooth germs were normal. 2. In both formocresol groups and glutaraldehyde groups, tissue reactions were identical. Inflammatory reactions were slightly compared with control groups, but the surface epithelizations were delayed compared with control group. 3. In both formocresol and glutaraldehyde groups, necrosis was seen in superficial tissue of bone marrow, and, at 24th day, center area of bone marrow on the successive tooth germs were losed and replaced with connective tissue, and superficial soft tissue of the injured area was connected with soft tissue on the successive tooth germ. In remaining alveolar bone, osteoclastic reaction was remarkable. 4. In both formocresol and glutaraldehyde groups, there is no injury to the successive tooth germs. 5. In both formocresol and glutaraldehyde groups, periodontal membrane was normal, but the partial resorption of cementum and dentin near the injured area were seen.

• Molecular & Cellular Toxicology
• /
• v.3 no.4
• /
• pp.320-325
• /
• 2007

Promoter hypermethylation of the $p16^{INK4a}$ gene was investigated in 52 sets of samples of tumor tissue and adjacent normal tissue from Korean patients with colorectal cancer, using the proposed modified the Real-time PCR/SYBR Green detection method presented in this study. In normal tissue, 29 of 52 patients (56%) were methylated and in tumor tissue, 23 of 52 patients (44%) were methylated. The 34 cases (65.4%) showed a concordant DNA methylation pattern in both normal tissue and tumor tissue. Analyzing the association between the clinicopathologic features and DNA methylation status of the $p16^{INK4a}$ gene, the DNA methylation status according to by Duke's stage was different while other clinicopathological characteristics, including the age, sex, tumor stage, and histologic type of the patient were not found to be correlated with $p16^{INK4a}$ methylation. With multivariate logistic regression, it was observed that the DNA methylation status of $p16^{INK4a}$ gene in normal tissue was correlated with the DNA methylation status of the $p16^{INK4a}$ gene in tumor tissue (P=0.026). According to a Kaplan-Meier survival analysis, a difference in the survival rate by DNA methylation status was found, but it was not significant.

• BMB Reports
• /
• v.50 no.6
• /
• pp.285-298
• /
• 2017

The cancer stem cell (CSC) hypothesis has captured the attention of many scientists. It is believed that elimination of CSCs could possibly eradicate the whole cancer. CSC surface markers provide molecular targeted therapies for various cancers, using therapeutic antibodies specific for the CSC surface markers. Various CSC surface markers have been identified and published. Interestingly, most of the markers used to identify CSCs are derived from surface markers present on human embryonic stem cells (hESCs) or adult stem cells. In this review, we classify the currently known 40 CSC surface markers into 3 different categories, in terms of their expression in hESCs, adult stem cells, and normal tissue cells. Approximately 73% of current CSC surface markers appear to be present on embryonic or adult stem cells, and they are rarely expressed on normal tissue cells. The remaining CSC surface markers are considerably expressed even in normal tissue cells, and some of them have been extensively validated as CSC surface markers by various research groups. We discuss the significance of the categorized CSC surface markers, and provide insight into why surface markers on hESCs are an attractive source to find novel surface markers on CSCs.

• The Journal of the Korea Contents Association
• /
• v.15 no.8
• /
• pp.416-423
• /
• 2015

The study was conducted targeting 25 patients who underwent the respiratory gated radiation therapy in the abdominal region at Radiation Oncology of a University Hospital from December 2013 to June 2014 and types of cancer included liver(64%), CBD(8%), gastric(8%), GB(8%), pancreas(8%), SMA(4%). The means of ITV and PTV volume are 471.44 cm3 and 425.48 cm3, showing an increase in volume. Normal tissue volume was also found to have increased due to the increase of the section selected from PTV section to ITV section. Right kidney showed a significant increase in differences between increase in normal tissue volume, increase in target volume and increase in therapy irradiation area and difference between the means of dose applied to normal tissue. There was no significant difference in the mean dose applied to normal tissue according to the respiratory average. Both kidneys showed a significant difference in the difference between mean doses of target moving and normal tissue. In this study, both therapy methods through PTV section and ITV section volume setting were appropriate for protection doses of normal tissue and distributed over 95% of the prescribed dose and therefore, it is considered to be okay to be optionally used depending on the patient's therapeutic purpose. But in order to minimize the unexpected side effect, the plan of PTV section and ITV section should be established and used by evaluating normal tissue protection dose.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.1
• /
• pp.233-237
• /
• 2015

Background: Lung cancer is the leading cause of cancer death in Brunei Darussalam, accounting for almost 20% of the total. The epidermal growth factor receptor (EGFR) is a member of the erbB family of tyrosine kinase receptor proteins, which includes c-erbb2(HER2/neu), erb-B3, and erb-B4. EGFR overexpression is found in a third of all epithelial cancers, often associated with a poor prognosis. Materials and Methods: Protein expression of EGFR in 27 cases of lung cancer tissue samples and 9 cases of normal lung tissue samples was evaluated using an immunohistochemical approach. Results: The results demonstrated significant increase and overexpression of EGFR in Bruneian lung cancer tissue samples in comparison to normal lung tissue. However, there was no significant relationship between clinicopathologic variables (age and sex) of patients and EGFR protein expression. Conclusions: EGFR is overexpressed in Bruneian lung cancer patient tissue samples in comparison to normal lung tissue samples. This may indicate that EGFR protein over expression plays an important role in the genesis of this type of cancer in Brunei Darussalam.

• Restorative Dentistry and Endodontics
• /
• v.2 no.1
• /
• pp.20-26
• /
• 1976

Cellulose acetate electrophoresis was used for differential diagnosis of radicular cysts and granulomas. Sixteen periapical lesions were excised from sixteen teeth with radiographic evidence of periapical pathosis, and two normal periodontal tissues were surgically removed from two wisdom teeth. The tissue samples were separated into two parts. Half was prepared for cellulose acetate electrophoresis, and the electrophoretic patterns were scanned with Helena densitometer. The other half was examined histologically, and the histologic diagnoses were then compared with the electrophoretic patterns and with the x-ray findings. The results were the following: 1. The histopathologic results showed the presence of 13 granulomas (81.8%) and 3 cysts (18.3%). 2. An albumin pattern, alpha-globulin pattern, beta-globulin pattern, fibrinogen pattern and gamma-globulin pattern were found in all eighteen cases. 3. All eighteen cases were divided into normal periodontal tissue group, dental granuloma group, and radicular cyst group by the histopathologic diagnosis. The electrophoretic pattern of dental granuloma group and that of normal periodontal tissue group resembled each other. The two groups showed the highest percentage in beta-globulin fraction, and the beta-globulin of dental granuloma group(47.17%) was higher than that of normal periodontal tissue group (40.54%) by 6.63%. On the contrary, beta-globulin fraction of radicular cyst group (28.00%) was much lower than those of the granuloma group (47.17%) and normal periodontal tissue group (40.54%), and alpha-globulin of radicular cyst group (34.16%) was much higher than those of the granuloma group (20.04%) and normal group (19.58%). 4. Five cases (31.3%) of the sixteen periodontal lesions showed different results between histopathologic diagnoses and radiographic findings.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.9
• /
• pp.4405-4408
• /
• 2016

Background: To investigate the characteristics of allelic distribution of IGF2 and H19 gene polymorphisms in molar tissues compared to normal placentas. Materials and Methods: Forty-nine specimens of molar tissues as well as 100 control normal placental tissues, delivered on the same days, were collected. Polymerase chain reaction (PCR) with restriction fragment length polymorphism (RFLP) on 2% agarose gel electrophoresis was conducted to determine the allelic distribution. The ApaI polymorphism within exon 9 of IGF2 and the RsaI polymorphism within exon 5 of H19 were employed to identify the allelic distribution of the IGF2 and H19 genes, respectively. Then the data for these genes in the molar and normal placenta tissues were compared. Results: The allelic distribution of IGF2 genes found in molar tissue were 21 (42.9%) aa (undigested), 10 (20.4%) ab (heterozygous) and 18 (36.7%) bb (digested), while in normal placenta tissue the values were 22 (22%) aa, 51 (51%) ab, and 27 (27%) bb. The allelic distribution of H19 in molar tissues was 8 (16.2%) aa (undigested), 8 (16.3%) ab (heterozygous) and 33 (67.4%) bb (digested) and in normal placental tissue was 16 (16%) aa, 36 (36%) ab and 48 (48%) bb in normal placenta tissue. These results were significantly different with P values of 0.001 and 0.037 for the allelic distribution of IGF2 and H19, respectively. Conclusions: Molar tissues showed significant differences of allelic distribution of IGF2 and H19 from normal placenta tissues.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.1
• /
• pp.271-274
• /
• 2015

Background: To explore vascular endothelial growth factor C (VEGF-C) and VEGF-D expression and its correlation with lymph node metastasis in esophageal squamous cell cancer (ESCC) tissue. Materials and Methods: Immunohistochemical methods were applied to detect the levels of VEGF-C and VEGF-D expression in 64 surgicall removal ESCC tissues, tissues adjacent to cancer and normal tissues, and the relationship between VEGF-C and VEGF-D expression and lymph node metastasis was analyzed. Results: Both VEGF-C and VEGF-D were expressed by varying degrees in esophageal cancer tissue, the tissue adjacent to cancer and normal tissue, and the positive expression rate went down successively. The positive expression rates of VEGF-C (59.4%) and VEGF-D (43.8%) in esophageal cancer tissue were significantly higher than in the tissue adjacent to cancer (34.4%, 15.6%) and normal tissue (20.3%, 12.5%), respectively, in which significant differences were manifested (p<0.01). Positive expression rates of VEGF-C and VEGF-D in esophageal cancers with lymph node metastasis were markedly higher than without such metastasis (p<0.01), while those in the tissue with TNM staging I~II were markedly lower than that with TNM staging III~IV (p<0.01). Conclusions: Both VEGF-C and VEGF-D are highly expressed in ESCC tissue, which may be related to the lymph node metastasis of cancer cells. Hence, VEGF-C and VEGF-D can be clinically considered as important reference indexes of lymph node metastasis in esophageal cancer.

• Journal of Veterinary Clinics
• /
• v.20 no.4
• /
• pp.443-448
• /
• 2003

To determine whether localization of tartrate-resistant acid phosphatase (TRAP) and cathepsin K was associated with rupture of the cranial cruciate ligament (CCL) in dogs. Tissue specimens were obtained from 30 dogs with CCL rupture during surgical treatment, 8 aged normal dogs, and 9 young normal dogs that were necropsied for reasons unrelated to this study and unrelated to musculoskeletal disease. The cranial cruciate ligament was examined histologically. $TRAP^+$ cells and cathepsin $K^+$ cells were identified by histochemical staining and immunohistochemical staining respectively. TRAP and cathepsin $K^+$ were co-localized within the same cells principally located within the epiligamentous region and to a lesser extent in the core region of ruptured CCL. Localization of $TRAP^+$ cells (P < 0.05) and cathepsin $K^+$ cells (P =0.05) within CCL tissue was significantly increased in dogs with CCL rupture, compared with aged-normal dogs, and young normal dogs (P < 0.05 - TRAP, P < 0.001 - cathepsin K). Localization of $TRAP^+$ cells and cathepsin $K^+$ cells within the CCL tissue of aged-normal dogs was also increased compared with young normal dogs (P < 0.05). Small numbers of $TRAP^+$ cells and cathepsin $K^+$ cells were seen in the intact ligaments of aged-normal dogs, which were associated with ligament fasicles in which there was chondroid transformation of ligament fibroblasts and disruption of the organized hierarchical structure of the extracellular matrix. $TRAP^+$ cells and cathepsin $K^+$ cells were not seen in CCL tissue from young-normal dogs. Localization of the proteinases $TRAP^+$ and cathepsin $K^+$ in CCL tissue was significantly associated with CCL rupture. Small numbers of proteinase positive cells were also localized in the CCL of agednormal dogs without CCL rupture, but were not detected in CCL from young-normal dogs. Taken together, these findings suggest that the cell signaling pathways that regulate expression of these proteinases in CCL tissue may form part of the mechanism that leads to upregulation of collagenolytic ligament remodeling and progressive structural failure of the CCL over time.