Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs) that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740) has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait.
Blood Glucose ; Classification ; Diagnosis ; Fasting* ; Glucose Tolerance Test* ; Glucose* ; Methods ; Phenotype ; Polymorphism, Single Nucleotide ; World Health Organization

A survival prediction model has recently been developed to evaluate the prognosis of resected nonmetastatic pancreatic ductal adenocarcinoma based on a Cox model using two nationwide databases: Surveillance, Epidemiology and End Results (SEER) and Korea Tumor Registry System-Biliary Pancreas (KOTUS-BP). In this study, we applied two machine learning methods—random survival forests (RSF) and support vector machines (SVM)—for survival analysis and compared their prediction performance using the SEER and KOTUS-BP datasets. Three schemes were used for model development and evaluation. First, we utilized data from SEER for model development and used data from KOTUS-BP for external evaluation. Second, these two datasets were swapped by taking data from KOTUS-BP for model development and data from SEER for external evaluation. Finally, we mixed these two datasets half and half and utilized the mixed datasets for model development and validation. We used 9,624 patients from SEER and 3,281 patients from KOTUS-BP to construct a prediction model with seven covariates: age, sex, histologic differentiation, adjuvant treatment, resection margin status, and the American Joint Committee on Cancer 8th edition T-stage and N-stage. Comparing the three schemes, the performance of the Cox model, RSF, and SVM was better when using the mixed datasets than when using the unmixed datasets. When using the mixed datasets, the C-index, 1-year, 2-year, and 3-year time-dependent areas under the curve for the Cox model were 0.644, 0.698, 0.680, and 0.687, respectively. The Cox model performed slightly better than RSF and SVM.

To identify miRNA-mRNA interaction pairs associated with binary phenotypes, we propose a hierarchical structural component model for miRNA-mRNA integration (HisCoM-mimi). Information on known mRNA targets provided by TargetScan is used to perform HisCoM-mimi. However, multiple databases can be used to find miRNA-mRNA signatures with known biological information through different algorithms. To take these additional databases into account, we present our advanced application software for HisCoM-mimi for binary phenotypes. The proposed HisCoM-mimi supports both TargetScan and miRTarBase, which provides manually-verified information initially gathered by text-mining the literature. By integrating information from miRTarBase into HisCoM-mimi, a broad range of target information derived from the research literature can be analyzed. Another improvement of the new HisCoM-mimi approach is the inclusion of updated algorithms to provide the lasso and elastic-net penalties for users who want to fit a model with a smaller number of selected miRNAs and mRNAs. We expect that our HisCoM-mimi software will make advanced methods accessible to researchers who want to identify miRNA-mRNA interaction pairs related with binary phenotypes.
MicroRNAs ; Phenotype ; RNA, Messenger

Background: This study aimed to investigate the capability of an automated immunohistochemical (IHC) evaluation of hormonal receptor status in breast cancer patients compared to a well-validated quantitative reverse transcription–polymerase chain reaction (RT-qPCR) method. Methods: This study included 93 invasive breast carcinoma cases that had both standard IHC assay and Oncotype Dx assay results. The same paraffin blocks on which Oncotype Dx assay had been performed were selected. Estrogen receptor (ER) and progesterone receptor (PR) receptor status were evaluated through IHC stains using SP1 monoclonal antibody for ER, and 1E2 monoclonal antibody for PR. All ER and PR immunostained slides were scanned, and invasive tumor areas were marked. Using the QuantCenter image analyzer provided by 3DHISTECH, IHC staining of hormone receptors was measured and converted to histochemical scores (H scores). Pearson correlation coefficients were calculated between Oncotype Dx hormone receptor scores and H scores, and between Oncotype Dx scores and Allred scores. Results: H scores measured by an automated imaging system showed high concordance with RT-qPCR scores. ER concordance was 98.9% (92/93), and PR concordance was 91.4% (85/93). The correlation magnitude between automated H scores and RT-qPCR scores was high and comparable to those of Allred scores (for ER, 0.51 vs. 0.37 [p=.121], for PR, 0.70 vs. 0.72 [p=.39]). Conclusions Automated H scores showed a high concordance with quantitative mRNA expression levels measured by RT-qPCR.

Sleep-disordered breathing (SDB) induces dysfunction of the orofacial muscles, leading to morphologic alteration of the face and dental malalignment. Early diagnosis and treatment of SDB is required in pediatric patients to ensure normal facial growth. Myofunctional therapy (MFT) is a modality for the treatment of SDB and prefabricated appliances can be used. Herein 2 cases of malocclusion with SDB, in which MFT with a prefabricated appliance was used for orthodontic treatment, have been described. SDB was diagnosed based on clinical symptoms taken by interview and home respiratory polygraphy. In both cases, SDB was improved using prefabricated appliance for MFT. However, resolution of crowding depended on the degree of crowding.
Child ; Crowding ; Early Diagnosis ; Humans ; Malocclusion ; Muscles ; Myofunctional Therapy ; Sleep Apnea Syndromes

This study was aimed to evaluate orofacial morphologies on the cases of developmental disorders of maxillary first molars.Panoramic radiographs, lateral cephalographs, and clinical photos of 2983 children who attended the Pediatric Dental Clinic of Pusan National University Dental Hospital from 2006 to August 2017 were assessed retrospectively. 34 patients were selected whose maxillary first molars were missed or developmentally delayed unilaterally or bilaterally. Demirjian' s method was used for estimating dental age, then which was compared to chronologic age of children. Parameters expressing skeletal and dentoalveolar disharmony were checked and compared with control. Additionally, occlusion relationship was evaluated.Maxillary dental age was significantly delayed compared to chronologic age. Several parameters which show skeletal open-bite tendency and skeletal class III malocclusion with maxillary retrusion were statistically significant. Anterior crossbite and edge-bite were expected in most of these cases, but compensation by occlusion and soft tissue was also verified which might mask skeletal class III tendency.Congenital missed or developmentally delayed maxillary first molars might be related with declined growth of maxilla. If developmental disorders of maxillary first molars were verified during clinical examination, careful monitoring of orofacial growth was necessary during puberty and timed orthopedic and orthodontic intervention were considered.
Adolescent ; Busan ; Child ; Compensation and Redress ; Dental Clinics ; Humans ; Malocclusion ; Masks ; Maxilla ; Methods ; Molar ; Orthopedics ; Puberty ; Retrognathia ; Retrospective Studies

This study was performed to evaluate clinical use of laser fluorescence (LF) to identify early childhood caries lesions suitable for applying resin infiltration.20 exfoliated primary molars with proximal caries were selected and cut buccolingually cross the central pit for regarding the mesial and distal surfaces respectively. 27 specimens corresponding to ICDAS code 1 and 2 were selected and the LF values were measured. When infiltrant resin was applied, double staining for microscopy detection has done simultaneously. Tooth samples were sliced with 0.7 mm thick. The maximum lesion depth, maximum penetration depth, and average penetration rate were measured from the confocal scanning laser microscope image. Pearson correlation analysis was performed.The intraclass correlation coefficient of LF values shows excellent agreement. LF values had positive correlation with penetration rate, but not lesion depth and penetration depth. Significant correlation between LF readings and penetration rate was verified in deep enamel caries and dentin caries except shallow enamel caries.Infiltrant resin could penetrate with a higher rate and LF values could be increased in more active caries lesions. In assessing radiologically similar caries lesion, laser fluorescence might be useful for identifying caries activity.
Dental Enamel ; Dentin ; Fluorescence ; Microscopy ; Molar ; Reading ; Tooth ; Tooth, Deciduous

This study was aimed to assess the new trial for minimal cavity preparation in composite restoration combined with resin infiltration, focusing at application sequence.32 human primary molars with early carious lesions around small cavity were selected and randomly divided into two groups, according to the sequence of cavity preparation (P), composite filling (F) and resin infiltration (I) as IPF and PFI group. Each group was assessed about amount of tooth reduction, features of resin infiltration, and marginal leakage around restoration.Amount of tooth reduction evaluated using micro-CT was decreased compared with the original lesion size in both groups. Features of resin infiltration were verified under confocal laser scanning microscopy. In both groups, infiltrant resin was found on all around the composite and maintained in spite of extent of decalcification even after artificial caries induction. Marginal micro leakage assessed with silver nitrate immersion and micro-CT was found more frequently in PFI group.The technique combining resin infiltration and composite restoration might ensure better adhesion prognosis as applied by the sequence of resin infiltration, cavity preparation, and composite filling. This new trial was thought meaningful in minimizing the cavity size and contributing to minimal invasive dentistry.
Dentistry ; Humans ; Immersion ; Microscopy, Confocal ; Molar ; Prognosis ; Silver Nitrate ; Tooth

Genome-wise association studies (GWASs) have become popular approaches to identify genetic variants associated with human biological traits. In this study, we applied Structural Equation Models (SEMs) in order to model complex relationships between genetic networks and traits as risk factors. SEMs allow us to achieve a better understanding of biological mechanisms through identifying greater numbers of genes and pathways that are associated with a set of traits and the relationship among them. For efficient SEM analysis for GWASs, we developed a procedure, comprised of four stages. In the first stage, we conducted single-SNP analysis using regression models, where age, sex, and recruited area were included as adjusting covariates. In the second stage, Fisher's combination test was conducted for each gene to detect significant genes using p-values obtained from the single-SNP analysis. In the third stage, Fisher's exact test was adopted to determine which biological pathways were enriched with significant SNPs. Finally, based on a pathway that was associated with the four traits in common, a SEM was fit to model a causal relationship among the genetic factors and traits. We applied our SEM model to GWAS data with four central obesity related traits: suprailiac and subscapular measures for upper body fat, BMI, and hypertension. Study subjects were collected from two Korean cohort regions. After quality control, 327,872 SNPs for 8842 individuals were included in the analysis. After comparing two SEMs, we concluded that suprailiac and subscapular measures may indirectly affect hypertension susceptibility by influencing BMI. In conclusion, our analysis demonstrates that SEMs provide a better understanding of biological mechanisms by identifying greater numbers of genes and pathways.
Adipose Tissue ; Cohort Studies ; Humans ; Hypertension ; Obesity, Abdominal ; Polymorphism, Single Nucleotide ; Quality Control ; Risk Factors

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