Pattern finding is one of the important tasks in a protein or DNA sequence analysis. Alignment is the widely used technique for finding patterns in sequence analysis. BLAST (Basic Local Alignment Search Tool) is one of the most popularly used tools in bio-informatics to explore available DNA or protein sequence databases. BLAST may generate a huge output for a large sequence data that contains various sequence patterns. However, BLAST does not provide a tool to summarize and analyze the patterns or matched alignments in the BLAST output file. BLAST lacks of general and robust parsing tools to extract the essential information out from its output. This paper presents a pattern summary system which is a powerful and comprehensive tool for discovering pattern structures in huge amount of sequence data in the BLAST. The pattern summary system can identify clusters of patterns, extract the cluster pattern sequences from the subject database of BLAST, and display the clusters graphically to show the distribution of clusters in the subject database.
Computational Biology ; Databases, Protein ; DNA ; Sequence Analysis* ; Sequence Analysis, DNA

OBJECTIVES: To reexamine the association between air pollution and daily mortality in Seoul, Korea using a method of meta-analysis with the data filed for 1991 through 1995. METHODS: A separate Poisson regression analysis on each district within the metropolitan area of Seoul was conducted to regress daily death counts on levels of each ambient air pollutant, such as total suspended particulates (TSP), sulfur dioxide (SO2), and ozone (O3), controlling for variability in the weather condition. We calculated a weighted mean as a meta-analysis summary of the estimates and its standard error. RESULTS: We found that the p value from each pollutant model to test the homogeneity assumption was small (p<0.01) because of the large disparity among district-specific estimates. Therefore, all results reported here were estimated from the random effect model. Using the weighted mean that we calculated, the mortality at a 100 microgram/m3 increment in a 3-day moving average of TSP levels was 1.034 (95% CI 1.009-1.059). The mortality was estimated to increase 6% (95% CI 3-10%) and 3% (95% CI 0-6%) with each 50 ppb increase for 3-day moving average of SO2 and 1-hr maximum O3, respectively. CONCLUSIONS: Like most of air pollution epidemiologic studies, this meta-analysis cannot avoid fleeing from measurement misclassification since no personal measurement was taken. However, we can expect that a measurement bias be reduced in a district-specific estimate since a monitoring station is better representative of air quality of the matched district. The similar results to those from the previous studies indicated existence of health effect of air pollution at current levels in many industrialized countries, including Korea.
Air Pollution* ; Bias (Epidemiology) ; Developed Countries ; Epidemiologic Methods ; Epidemiologic Studies ; Humans ; Korea ; Mortality* ; Ozone ; Seoul* ; Sulfur Dioxide ; Weather ; Information Storage and Retrieval

BACKGROUND/AIMS: We aimed to verify the prognostic factors of stage II rectal cancer and the effect of radiation therapy on the survival and local recurrence rate. METHODS: This study was undertaken in 202 patients who underwent curative resection of rectal cancer and confirmed to be stage II between July 1989 and December 1996. Univariate and multivariate (Cox's model) analyses of survival were employed to identify prognostic factors. Statistical significance was assigned by p value of <0.05. RESULTS: Overall recurrence occurred in 32 patients. Four patterns of recurrence were observed: hematogenous recurrence in 17 patients, local recurrence in 11, peritoneal seeding in two and simultaneous hematogenous and local recurrence in two cases. Overall 5-year survival rate was 85.6% and 5 year disease free survival rate was 82.8%. There was no significant difference in local recurrence rate and survival according to radiation therapy or location of cancer. In multivariate analysis, the number of harvested lymph node was only a prognostic factor. CONCLUSIONS: The number of harvested lymph nodes has prognostic value in stage II rectal cancer. Postoperative radiation therapy should be considered for stage II rectal cancer with poor prognostic factors although radiation did not decrease local recurrence rate in present study.
Adolescent ; Adult ; Aged ; Child ; English Abstract ; Female ; Humans ; Male ; Middle Aged ; Neoplasm Metastasis ; Neoplasm Recurrence, Local ; Prognosis ; Rectal Neoplasms/pathology/*surgery

BACKGROUND AND OBJECTIVES: The number of permanent pacemakers (PPMs) implanted in patients in Japan and Korea differs significantly. We aimed to investigate the differences in decision making processes of implanting a PPM. MATERIALS AND METHODS: Our survey included 15 clinical case scenarios based on the 2008 AHA/ACC/HRS guidelines for device-based therapy of cardiac rhythm abnormalities (class unspecified). Members of the Korean and Japanese Societies of Cardiology were asked to rate each scenario according to a 5-point scale and to indicate their decisions for or against implantation. RESULTS: Eighty-nine Korean physicians and 192 Japanese physicians replied to the questionnaire. For the case scenarios in which there was a class I indication for PPM implantation, the decision to implant a PPM did not differ significantly between the two physician groups. However, the Japanese physicians were significantly more likely than the Korean physicians to choose implantation in class IIa scenarios (48% vs. 37%, p<0.001), class IIb scenarios (40% vs. 19%, p<0.001), and class III scenarios (36% vs. 18%, p<0.001). These results did not change when the cases were categorized based on disease entity, such as sinus node dysfunction and conduction abnormality. CONCLUSION: Korean physicians are less likely than Japanese physicians to favor a PPM implantation when considering a variety of clinical case scenarios, which probably contributes to the relatively small number of PPMs implanted in patients in Korea as compared with those in Japan.
Asian Continental Ancestry Group ; Atrioventricular Block ; Cardiology ; Decision Making* ; Humans ; Japan* ; Korea* ; Pacemaker, Artificial ; Sick Sinus Syndrome

BACKGROUND: Microsatellite instability (MSI) analysis is becoming increasingly important in many types of tumor including colorectal cancer (CRC). The commonly used MSI tests are either time-consuming or labor-intensive. A fully automated MSI test, the Idylla MSI assay, has recently been introduced. However, its diagnostic performance has not been extensively validated in clinical CRC samples.METHODS: We evaluated 133 samples whose MSI status had been rigorously validated by standard polymerase chain reaction (PCR), clinical next-generation sequencing (NGS) cancer panel test, or both. We evaluated the diagnostic performance of the Idylla MSI assay in terms of sensitivity, specificity, and positive and negative predictive values, as well as various sample requirements, such as minimum tumor purity and the quality of paraffin blocks.RESULTS: Compared with the gold standard results confirmed through both PCR MSI test and NGS, the Idylla MSI assay showed 99.05% accuracy (104/105), 100% sensitivity (11/11), 98.94% specificity (93/94), 91.67% positive predictive value (11/12), and 100% negative predictive value (93/93). In addition, the Idylla MSI assay did not require macro-dissection in most samples and reliably detected MSI-high in samples with approximately 10% tumor purity. The total turnaround time was about 150 minutes and the hands-on time was less than 2 minutes.CONCLUSIONS: The Idylla MSI assay shows good diagnostic performance that is sufficient for its implementation in the clinic to determine the MSI status of at least the CRC samples. In addition, the fully automated procedure requires only a few slices of formalin-fixed paraffin-embedded tissue and might greatly save time and labor.
Colorectal Neoplasms ; Microsatellite Instability ; Microsatellite Repeats ; Paraffin ; Polymerase Chain Reaction ; Sensitivity and Specificity

The trial of external quality assessment for inborn error of metabolism was performed in 2003. A total 10 specimens for neonatal screening tests were distributed to 43 laboratories with a response rate of 83%. All the control materials were sent as a filter paper form. Each laboratory replied the test result as the screening items they were doing as a rountine test at the reception of the specimen among PKU screening, neonatal TSH, neonatal T4(total/free), galactosemia screen, homocytinuria screen and histidinemia screen. The mean, SD, and CV were analyzed.
Galactosemias ; Infant, Newborn ; Korea* ; Mass Screening ; Metabolism* ; Neonatal Screening

Prognostic value of p53 and bcl-2 expression on treatment outcome in breast cancer patients has been extensively evaluated, but the results were inconclusive. We evaluated the prognostic significance of these molecular markers in patients treated with breast conserving surgery and radiotherapy. One hundred patients whose immunostaining of p53 and bcl-2 expression was available among 125 patients who underwent radiotherapy after breast conserving surgery and axillary lymph node dissection were enrolled into this study. Eighty-seven patients also received adjuvant chemotherapy and/or hormonal therapy. Conventional clinicopathologic variables and treatment-related factors were also considered. The 5-yr loco-regional relapse-free and distant metastasis-free survival rates were 91.7% and 90.9%, respectively. On univariate analysis, age, T stage and the absence of bcl-2 & estrogen receptor (ER) expression were associated with loco-regional relapse-free survival. When incorporating these variables into Cox proportional hazard model, only bcl-2(-)/ER(-) phenotype was an adverse prognostic factor (P=0.018). As for the distant metastasis-free survival, age, T stage, and p53 expression were significant on univariate analysis. However, p53 expression was the only prognosticator on multivariate analysis (P=0.009). A bcl-2(-)/ER(-) phenotype and p53 expression are useful molecular markers predicting loco-regional relapse-free and distant metastasis-free survival, respectively, in patients treated with breast conserving surgery and radiotherapy.
Adult ; Aged ; Breast Neoplasms/metabolism/radiotherapy/*surgery ; Combined Modality Therapy ; Disease-Free Survival ; Female ; Humans ; *Mastectomy, Segmental ; Middle Aged ; Multivariate Analysis ; Phenotype ; Prognosis ; Proto-Oncogene Proteins c-bcl-2/genetics/*metabolism ; Receptors, Estrogen/metabolism ; Tumor Suppressor Protein p53/genetics/*metabolism

BACKGROUND AND OBJECTIVES: The inner ear is an organ used for hearing and balance. For its normal function, the inner ear fluid homeostasis is required. There has been controversy over the regulatory mechanisms of maintaining inner ear fluid balance, and they have not yet been clearly defined. TonEBP is the protein that binds tonicity-responsive enhancer elements in the osmoprotective gene, which elevates the compatible osmolytes, which in turn induces cell survival in hypertonic condition. The aim of this study was to elucidate if there is an osmoregulatory mechanism in cochlea. Material and Method: The localization of TonEBP in the cochlea of male Sprague-Dawley rats was studied by immunohistochemistry with an anti rabbit polyclonal anti-rat TonEBP antibody. RESULTS: TonEBP was expressed at outer hair cells, Deiter cells, spiral ligaments, sprial limbus connective tissues, and epithelial lining of basilar membrane facing scala tympani. CONCLUSION: TonEBP in cochlea is one of the proteins involved in elucidating cell survival in changed tonicity during inner ear homeostasis.
Animals ; Basilar Membrane ; Carrier Proteins* ; Cell Survival ; Cochlea* ; Connective Tissue ; Ear, Inner ; Enhancer Elements, Genetic ; Hair ; Hearing ; Homeostasis ; Humans ; Immunohistochemistry ; Male ; Rats* ; Rats, Sprague-Dawley ; Scala Tympani ; Spiral Ligament of Cochlea ; Water-Electrolyte Balance

BACKGROUND AND OBJECTIVES: It has been shown that the coronary flow reserve (CFR) of an infarct related artery can predict left ventricular functional recovery following acute myocardial infarction (AMI). However, the prognostic value of CFR on the long-term clinical outcome of patients with an AMI has not been studied. SUBJECTS AND METHODS: Using a Doppler guide wire, we measured the CFR in 130 patients with an AMI following successful intervention (6+/-3 days after onset of the AMI). Two-year follow-up was conducted with regard to end points, including : cardiac death, non-fatal AMI, and severe congestive heart failure (CHF; > or = NYHA III). RESULTS: During the follow-ups, cardiac events occurred in 17 patients (5 deaths, 3 non-fatal AMIs and 9 severe CHFs). After analysis of the receiver operating characteristic curves, the best cut-off value for CFR in predicting cardiac events was 1.4 (sensitivity 76.5%, specificity 73.5%, accuracy 82.0%). With cardiac events as an end point, a 2-year Kaplan-Meier event survival analysis revealed that the patients with a CFR < or = 1.4 had a worse prognosis than those with a CFR >1.4 (Event free survival rates were 69.8% vs. 95.4%, respectively, p<0.001). Using Cox proportional hazard analyses, as an independent predictor, age, heart rate, CFR and left ventricular end systolic volume index, were also found to be significantly associated with cardiac events (hazard ratios 1.1224, 1.0404, 0.1887, and 1.0588, respectively). CONCLUSION: The coronary flow reserve, of infarct related arteries, measured during the early recovery phase can be used as an independent predictor for the prognosis of patients with an acute myocardial infarction following successful intervention.
Arteries ; Coronary Circulation ; Death ; Follow-Up Studies ; Heart Failure ; Heart Rate ; Humans ; Myocardial Infarction* ; Prognosis ; ROC Curve ; Sensitivity and Specificity ; Stroke Volume ; Survival Rate

The purpose of this study was to evaluate treatment patterns, outcome and prognosticators for patients with leptomeningeal metastases from solid tumor. Medical records of 80 patients from January 1, 2004 to May 31, 2011 were retrospectively reviewed. Most frequent site of origin was the lung (59%) followed by the breast (25%). Most patients were treated with intrathecal chemotherapy (90%) and/or whole brain radiotherapy (67.5%). Systemic therapy was offered to 27 patients (33.8%). Percentage of patients treated with single, dual, and triple modality were 32.5%, 43.8%, and 23.8%, respectively. Median survival was 2.7 months and 1 yr survival rate was 11.3%. Multivariate analysis showed that negative cerebrospinal fluid cytology, fewer chemotherapy regimen prior to leptomeningeal metastases, whole brain radiotherapy, systemic therapy, and combined modality treatment (median survival; single 1.4 vs. dual 2.8 vs. triple 8.3 months, P<0.001) had statistical significance on survival. Subgroup analysis of non-small cell lung cancer (NSCLC) patients showed that targeted therapy had significant independent impact on survival (median survival; 10.5 vs. 3.0 months, P=0.008). Unlike previous reports, survival of patients with NSCLC primary was comparable to breast primary. Furthermore, combined modality treatment for all patients and additionally targeted therapy for NSCLC patients should be considered in the treatment of leptomeningeal metastases from solid tumor.
Adult ; Aged ; Chemoradiotherapy/methods/*mortality/*statistics & numerical data ; Disease-Free Survival ; Female ; Humans ; Male ; Meningeal Neoplasms/mortality/*secondary/*therapy ; Middle Aged ; Neoplasm Recurrence, Local/*mortality/*prevention & control ; Prevalence ; Republic of Korea/epidemiology ; Retrospective Studies ; Risk Factors ; Survival Rate ; Treatment Outcome