In this paper, we consider the variable selection methods in the Cox model when a large number of gene expression levels are involved with survival time. Deciding which genes are associated with survival time has been a challenging problem because of the large number of genes and relatively small sample size (n << p). Several methods for variable selection have been proposed in the Cox model. Among those, we consider least absolute shrinkage and selection operator (LASSO), threshold gradient descent regularization (TGDR), and two different clustering threshold gradient descent regularization (CTGDR)- the K-means CTGDR and the hierarchical CTGDR - and compare these four methods in an application of lung cancer data. Comparison of the four methods shows that the two CTGDR methods yield more compact gene selection than TGDR, while LASSO selects the smallest number of genes. When these methods are evaluated by the approach of Ma and Huang (2007), none of the methods shows satisfactory performance in separating the two risk groups using the log-rank statistic based on the risk scores calculated from the selected genes. However, when the risk scores are calculated from the genes that are significant in the Cox model, the performance of the log-rank statistics shows that the two risk groups are well separated. Especially, the TGDR method has the largest log-rank statistic, and the K-means CTGDR method and the LASSO method show similar performance, but the hierarchical CTGDR method has the smallest log-rank statistic.
Cluster Analysis* ; Gene Expression ; Lung Neoplasms ; Lung* ; Sample Size

BACKGROUND: Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the common malignant neoplasms of the skin. The p63 is a p53 homologue which is considered to be a reliable keratinocyte stem cell marker. Bcl-2 plays a key role in cell longevity by preventing apoptosis, whereas the bcl-6 gene functions as a transcriptional repressor. The p16-CDK4/6 complex arrests the cell cycle at G0 /G1 phase. In the present study, the expression of p63, bcl-2, bcl-6, and p16 in BCC and SCC was evaluated. METHODS: Forty-seven BCCs and 43 SCCs were selected and microarrayed in paraffin blocks. Immunohistochemical analysis was performed with specific antibodies for bcl-2, bcl-6, p16 and p63. RESULTS: p63 was found to be expressed in all BCCs and SCCs. Bcl-2 was exclusively expressed in BCCs (100%), but there was negative expression in SCCs, whereas bcl-6 was positively expressed in 18.2% of SCCs, and was negative in BCCs. In SCCs, p16 was expressed at high frequency (47.7%) than in BCCs (14.9%). The expression of p16 was correlated with the histologic grades of SCCs. CONCLUSION: The different patterns of bcl-2, bcl-6, p63 and p16 protein expression between BCCs and SCCs may represent the different histogenesis and morphologic features of two lesions.
Antibodies ; Apoptosis ; Carcinoma, Basal Cell* ; Carcinoma, Squamous Cell* ; Cell Cycle ; Keratinocytes ; Longevity ; Paraffin ; Proto-Oncogene Proteins c-bcl-6 ; Skin* ; Stem Cells

The current existing literature offers little guidance on how to decide which method to use to analyze one-channel microarray measurements when dealing with large, grouped samples. Most previous methods have focused on two-channel data;therefore they can not be easily applied to one-channel microarray data. Thus, a more reliable method is required to determine an appropriate combination of individual basic processing steps for a given dataset in order to improve the validity of onechannel expression data analysis. We address key issues in evaluating the effectiveness of basic statistical processing steps of microarray data that can affect the final outcome of gene expression analysis without focusingon the intrinsic data underlying biological interpretation.
Analysis of Variance ; Dataset ; Gene Expression ; Statistics as Topic

PURPOSE: Gallbladder cancer had poor prognosis because it is usually detected at a late stage. Some GB polyps are diagnosed as cancerous on the postoperative pathology. Because of the significance of the early detection of the cancer, the relationship between GB polyp and cancer is important. METHODS: From January 1994 to May, 2004, 94 cases of GB polypoid lesions were identified and diagnosed after cholecystectomy was performed at the Korea University Medical Center Anam hospital. The pateints' age, gender, the symptoms and signs, the diagnostic tools, the operative methods and the histopathologic findings were investigated. RESULTS: For the 94 patients, the mean age was 50.3+/-13.1 years and there were 42 males (44.7%). 92 patients were evaluated by abdominal ultrasonography, and it had a sensitivity of 72.8%. On the histopathologic results, there were 76 cases of benign polyps and 18 cases of malignant polyps. The diameter of the malignant polyps was 17.3+/-8.5 mm and the diameter of the benign polyps was 6.4+/-3.0 mm, so the malignant polyps were larger than the benign polyps. The mean age of the malignant polyp group was 62.6+/-14.2 years and the mean age of the benign polyp group was 47.1+/-11.1. The patients of the malignant polyp group were older than the patients of the benign polyp group. 19 GB polyps were greater than 10 mm in diameter and among them, there were 15 cases of malignant polyps (78.94%). CONCLUSION: The size of the polyps and the patient's age could be risk factors for malignant polyps, and the malignant potential was high for the polyps that exceeded 10 mm and for a patient age that exceeded 60 years. Surgical treatment is recommended for these patients.
Academic Medical Centers ; Cholecystectomy ; Gallbladder Neoplasms ; Gallbladder* ; Humans ; Korea ; Male ; Pathology ; Polyps* ; Prognosis ; Risk Factors ; Ultrasonography

Since the introduction of restorative dental composites, their physical properties have been significantly improved. However, polymerization shrinkage is still a major drawback. Many efforts have been made to develop a low shrinking composite, and silorane-based composites have recently been introduced into the market. In addition, many different methods have been developed to measure the polymerization shrinkage. In this study, we developed a new method to measure the linear polymerization shrinkage of composites without direct contact to a specimen using a particle tracking method with computer vision. The shrinkage kinetics of a commercial silorane-based composite (P90) and two conventional methacrylate-based composites (Z250 and Z350) were investigated and compared. The results were as follows: 1. The linear shrinkage of composites was 0.33-1.41%. Shrinkage was lowest for the silorane-based (P90) composite, and highest for the flowable Z350 composite. 2. The new instrument was able to measure the true linear shrinkage of composites in real time without sensitivity to the specimen preparation and geometry.
Kinetics ; Polymerization ; Polymers ; Silorane Resins ; Track and Field ; Vision, Ocular

OBJECTIVES: The ability to support healthcare document sharing is imperative in a health information exchange (HIE). Sharing imaging documents or images, however, can be challenging, especially when they are stored in a picture archiving and communication system (PACS) archive that does not support document sharing via standard HIE protocols. This research proposes a standard-compliant imaging gateway that enables connectivity between a legacy PACS and the entire HIE. METHODS: Investigation of the PACS solutions used at Gil Hospital was conducted. An imaging gateway application was then developed using a Java technology stack. Imaging document sharing capability enabled by the gateway was tested by integrating it into Gil Hospital's order communication system and its HIE infrastructure. RESULTS: The gateway can acquire radiology images from a PACS storage system, provide and register the images to Gil Hospital's HIE for document sharing purposes, and make the images retrievable by a cross-enterprise document sharing document viewer. CONCLUSIONS: Development of an imaging gateway that mediates communication between a PACS and an HIE can be considered a viable option when the PACS does not support the standard protocol for cross-enterprise document sharing for imaging. Furthermore, the availability of common HIE standards expedites the development and integration of the imaging gateway with an HIE.
Archives ; Delivery of Health Care ; Indonesia

In edentulous patient, not only mastication and pronunciation but also esthetics are compromised. By restoring an edentulous patient with complete dentures, masticatory function and esthetics can be rehabilitated. The advantages of the dentures using CAD/CAM are that they can be reconstructed ubiquitously with stored data, and the strength and density of CAD/CAM material are clinically acceptable. In this clinical report, interocclusal record was taken in a conventional manner and then two lab processing procedures were performed: conventional method and CAD/CAM method. Two types of processing procedures were compared and evaluated. Fair clinical results were obtained in both ways, satisfying the patient.
Denture Bases ; Denture, Complete ; Dentures ; Esthetics ; Humans ; Mastication ; Methods

BACKGROUND: Neurodegenerative diseases are associated with oxidative stress. Antioxidants including 15-deoxy- Delta (12,14) prostaglandin J2 (15d-PGJ2) have been tried as potential therapeutic regimens of the experimental model of neurodegenerative disease. In this study, we investigated the neuroprotective role of 15d-PGJ2 on cytochrome c mediated apoptotic signals in oxidative stress injured neuronally-differentiated PC12 cells (nPC12 cells) by exposing them to H2O2. METHODS: Following 100 micor M H2O2 exposure, the viability of nPC12 cells (pretreated with 15d-PGJ2 vs. not pretreated) was evaluated by using MTT assay. Immunoreactivity (IR) of cytochrome c, caspase-3, and poly (ADP-ribose) polymerase (PARP) was examined by using a Western blot. RESULTS: In this study, 15d-PGJ2 pretreated nPC12 cells showed an increase in cell viability until the concentrations of 15d-PGJ2 reached up to 4 micor M, but there was no increment of cell viability in higher concentrations. The inhibition of cytochrome c release, activation of caspase-3, and cleavage of PARP were demonstrated by the pretreatment of 15d-PGJ2 up to 4 micor M. However, these were not observed in the pretreatment with 8 micor M 15d-PGJ2. CONCLUSIONS: These data show that 15d-PGJ2 affects the apoptotic pathway through downstream signals including cytochrome c and caspase-3 pathway. Therefore, these results suggest that 15d-PGJ2 could be a new potential therapeutic candidate for the oxidative stress-injury model of neurodegenerative diseases.
Animals ; Antioxidants ; Apoptosis ; Blotting, Western ; Caspase 3 ; Cell Survival ; Cytochromes c ; Models, Theoretical ; Neurodegenerative Diseases ; Oxidative Stress ; PC12 Cells*

BACKGROUND AND OBJECTIVES: This study examined the expressions of p16 and the programmed cell death 1 ligand (PD-L1) in patients with oropharyngeal cancer (OPC) treated with radiotherapy (RT) to identify the correlation between p16 and PD-L1 expression, and to examine the prognostic significance of these markers for OPC patients receiving RT.SUBJECTS AND METHOD: Forty-eight OPC patients diagnosed and treated at a tertiary referral hospital were enrolled in this retrospective analysis. Patients were initially treated with RT or chemoradiotherapy (CRT) with curative intent and completed the planned schedule. Expression of p16 and PD-L1 by primary tumors was evaluated by immunohistochemistry, and results were interpreted separately and dichotomized according to outcome analyses. RESULTS: Of the 48 patients, 25 (52.1%) expressed p16 and 15 (31.3%) expressed PD-L1. Expression of these markers showed a mutual positive correlation (p=0.046). Positive PD-L1 expression was associated with poor complete remission (CR) rates after RT (p=0.040). Positive p16 expression was associated with better recurrence-free survival (RFS) (p=0.004) but not overall survival (OS) (p=0.192). PD-L1 expression showed no independent association with survival (p>0.05); however, PD-L1 expression tended toward poorer RFS, even in p16-positive individuals. CONCLUSION There was a positive correlation between the expression of p16 and PD-L1 in OPCs. PD-L1 expression was associated with poorer CR rates after RT or CRT. PD-L1 alone did not show an association with RFS or OS, but when combined with p16, it tended toward poorer RFS, even in p16-positive cases.

The objective of this study was to compare dentin shear bond strength (DSBS) of dentin bonding agents (DBAs) cured with a plasma arc (PAC) light curing unit (LCU) and those cured with a light emitting diode (LED) LCU. Optical properties were also analyzed for Elipar freelight 2 (3M ESPE); LED LCU, Apollo 95E (DMT Systems); PAC LCU and VIP Junior (Bisco); Halogen LCU. The DBAs used for DSBS test were Scotchbond Multipurpose (3M ESPE), Singlebond 2 (3M ESPE) and Clearfil SE Bond (Kuraray). After DSBS testing, fractured specimens were analyzed for failure modes with SEM. The total irradiance and irradiance between 450 nm and 490 nm of the LCUs were different. LED LCU showed narrow spectral distribution around its peak at 462 nm whereas PAC and Halogen LCU showed a broad spectrum. There were no significant differences in mean shear bond strength among different LCUs (P > 0.05) but were significant differences among different DBAs (P < 0.001).
Dentin ; Dentin-Bonding Agents ; Enzyme Multiplied Immunoassay Technique ; Light ; Plasma ; Resin Cements