StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction.

We propose a new deterministic methodology to predict the secondary structure of RNA sequences. What information of stem is important for structure prediction, and is it enough ? The proposed simple deterministic algorithm uses minimum stem length, Stem-Loop score, and co-existence of stems, to give good structure predictions for short RNA and tRNA sequences. The main idea is to consider all possible stem with certain stem loop energy and strength to predict RNA secondary structure. We use graph notation, where stems are represented as vertexes, and co-existence between stems as edges. This full Stem-graph presents all possible folding structure, and we pick sub-graph(s) which give the best matching energy for structure prediction. Stem-Loop score adds structure information and speeds up the computation. The proposed method can predict secondary structure even with pseudo knots. One of the strengths of this approach is the simplicity and flexibility of the algorithm, and it gives a deterministic answer. Numerical experiments are done on various sequences from Protein Data Bank and the Gutell Lab using a laptop and results take only a few seconds.

Effects of methionine synthase and methionine synthase reductase polymorphisms on hypertension susceptibility.

BACKGROUND: Polymorphisms of methylenetetrahydrofolate reductase (MTHFR) gene are strongly associated with hypertension incidence, although such association is inconsistent among ethnicities studied. However, effects of polymorphisms of other genes related to folate metabolism besides MTHFR on hypertension susceptibility are not well known yet. OBJECTIVE: The aim of this study was to elucidate whether methionine synthase (MTR) 2756A>G and methionine synthase reductase (MTRR) 66A>G polymorphisms might be associated with risks of hypertension susceptibility in the Korean population. METHODS: Genotyping of these two polymorphisms was performed for 232 hypertensive patients and 247 unrelated healthy controls using polymerase chain reaction-restriction fragment length polymorphism technique. RESULTS: In the present study, mutations of MTR 2756A>G and MTRR 66A>G polymorphisms were associated with increased and decreased susceptibility to hypertension, respectively. Allele combinations from these two polymorphisms were also related to hypertension prevalence. When polymorphism data were stratified according to clinical components of hypertension, The G allele of MTR 2756A>G polymorphism was significantly associated with an increased risk of hypertension in subjects with BMI < 26.1 kg/m2 (P = 0.004), WC < 87.2 in. (P = 0.021), FBG < 95.5 mg/dL (P = 0.011), triglyceride < 133.5 mg/dL (P = 0.034), and HDL-cholesterol < 52.2 mg/dL (P = 0.036). The G allele of MTRR 66A>G polymorphism was significantly associated with a decreased risk of hypertension in subjects with WC ≥ 87.2 in. (P = 0.029), FBG ≥ 95.5 mg/dL (P = 0.032) and triglyceride ≥ 133.5 mg/dL (P = 0.027). CONCLUSION: MTR 2756A>G and MTRR 66A>G polymorphisms related to folate metabolism might be genetic markers for risk of hypertension in the Korean population.

Variational models for image colorization via chromaticity and brightness decomposition.

Colorization refers to an image processing task which recovers color in grayscale images when only small regions with color are given. We propose a couple of variational models using chromaticity color components to colorize black and white images. We first consider total variation minimizing (TV) colorization which is an extension from TV inpainting to color using chromaticity model. Second, we further modify our model to weighted harmonic maps for colorization. This model adds edge information from the brightness data, while it reconstructs smooth color values for each homogeneous region. We introduce penalized versions of the variational models, we analyze their convergence properties, and we present numerical results including extension to texture colorization.

Prevalence of plasmid-mediated AmpC beta-lactamases in Escherichia coli and Klebsiella pneumoniae in Korea.

Cefoxitin-resistant Escherichia coli and Klebsiella pneumoniae are relatively prevalent in Korea, suggesting dissemination of plasmid-mediated AmpC beta-lactamases. In this study, 238 isolates of cefoxitin-resistant E. coli and K. pneumoniae (not including subspecies ozaenae and rhinoscleromatis) were collected in 2003 from 16 Korean hospitals. The prevalence of plasmid-mediated AmpC beta-lactamases was determined by PCR. The AmpC gene alleles detected in E. coli and K. pneumoniae were bla(DHA-1), 10 (8.6%) and 93 (76.2%); bla(CMY-1)-like, 14 (12.1%) and 2 (1.6%); and bla(CMY-2)-like, 38 (32.7%) and 1 (0.8%) isolates, respectively. The genes identified were bla(DHA-1), bla(CMY10)-like, and bla(CMY-2)-like, and a new variant, bla(CMY-18). Plasmidmediated AmpC gene allele-positive isolates were present both in large city and in small province hospitals, as well as in isolates from outpatients. The proportions of plasmid-mediated AmpC gene-positive isolates were similar in both expanded spectrum beta-lactamase (ESBL)-producing and -nonproducing isolates. In conclusion, DHA-1, CMY-2-like, and CMY-10-like plasmid-mediated AmpC beta-lactamase-producing K. pneumoniae and E. coli isolates are widely disseminated in both large city and small province hospitals. Absence of bla(CMY-1) and detection of a novel variant of bla(CMY-2), bla(CMY-18), indicate continued evolution of the prototype genes. Similar proportions of plasmid-mediated AmpC gene-positive isolates in both ESBL-producing and -nonproducing isolates suggest unhindered future spread of these resistances.

An Assay of Measuring Platelet Reactivity Using Monoclonal Antibody against Activated Platelet Glycoprotein IIb/IIIa in Patients Taking Clopidogrel.

BACKGROUND AND OBJECTIVES: Residual platelet reactivity in patients who are taking clopidogrel is commonly measured with VerifyNow assay, which is based on the principle of light transmission aggregometry. However, to evaluate the residual platelet reactivity, it would be more accurate if the reactivity of platelet glycoprotein (GP) IIb/IIIa is directly monitored. In this study, PAC1, a monoclonal antibody against activated platelet GP IIb/IIIa, was used to measure the residual platelet reactivity. SUBJECTS AND METHODS: Twenty seven patients with coronary artery disease taking clopidogrel were enrolled. Platelets in whole blood were stained with fluorescein isothiocyanate (FITC)-conjugated PAC1. Mean fluorescence intensity (MFI) and % positive platelets (PP) were measured with flow cytometry, and the binding index (BI; MFI × %PP/100) was calculated. P2Y12 reaction unit (PRU) and % inhibition of VerifyNow assay were also measured in the usual manner. RESULTS: PRU of VerifyNow assay correlated significantly with MFI, %PP, and BI at 10 µM (r=0.59, 0.73, and 0.60, respectively, all p<0.005) and 20 µM of adenosine diphosphate (ADP; r=0.61, 0.75, and 0.63, respectively, all p<0.005). The % inhibition also correlated significantly with MFI, %PP, and BI at 10 µM (r=-0.60, -0.69, and -0.59, respectively, all p<0.005) and 20 µM of ADP (r=-0.63, -0.71, and -0.62, respectively, all p<0.005). CONCLUSION: Direct measurements of the reactivity of platelet GP IIb/IIIa were feasible using PAC1 and flow cytometry in patients taking clopidogrel. Further clinical studies are required to determine the cut-off values which would define high residual platelet reactivity in patients on this treatment protocol.

Korean nationwide surveillance of antimicrobial resistance in 2000 with special reference to vancomycin resistance in enterococci, and expanded-spectrum cephalosporin and imipenem resistance in gram-negative bacilli.

Antimicrobial resistance surveillance is necessary to determine the size of the problem and to guide empirical selection of antimicrobial agents for treating infected patients. The aim of this study was to analyze the results of susceptibility tests performed by hospitals participating in the Korean Nationwide Surveillance of Antimicrobial Resistance (KONSAR) program. The rates of oxacillin-resistant staphylococci, penicillin-nonsusceptible pneumococci, and ampicillin-resistant E. faecium were over 70%. Ampicillin-resistant H. influenzae increased to 68%. Expanded-spectrum cephalosporin-resistant K. pneumoniae, fluoroquinolone-resistant E. coli, and imipenem-resistant P. aeruginosa remained at 16% through 27%, depending on the species. The proportions of vancomycin- resistant E. faecium and imipenem-resistant P. aeruginosa were 18 - 24% and 19-21%, respectively, indicating the seriousness of antimicrobial resistance. In conclusion, the increasing prevalence of resistant bacteria indicates that more concerted effort is required to conserve the usefulness of precious new antimicrobial agents.

Association of CYP11B2 polymorphisms with metabolic syndrome patients.

Aldosterone synthase is a key enzyme in aldosterone production. Polymorphisms of the aldosterone synthase gene, CYP11B2, have been suggested to be involved in the pathogenesis of diabetes mellitus (DM), hypertension and cardiovascular diseases. In the light of these findings, we hypothesized that CYP11B2 genetic polymorphisms play a role in metabolic syndrome (MetS). Therefore, we investigated the associations of three CYP11B2 polymorphisms [-344T>C, K173R and intron 2 conversion (IC)] with Korean MetS patients. In total, 640 subjects comprising 320 cases and 320 control individuals) were included in the present study. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques were used to assess CYP11B2 polymorphisms. The CYP11B2 -344T>C, K173R and IC polymorphisms did not exhibit a significant difference in the genotype and allele frequencies between the MetS and control groups. However, the -344T>C polymorphism in males and haplotypes comprising the three polymorphisms were associated with susceptibility to MetS. Thus, the pattern of haplotype associations was gender-specific. Based on these results, the -344T>C polymorphism in males and haplotypes of the CYP11B2 gene potentially affect MetS susceptibility. These findings remain to be confirmed in various ethnic populations with a larger sample size.

CD26/DPP4 levels in peripheral blood and T cells in patients with type 2 diabetes mellitus.

CONTEXT: Dipeptidyl peptidase 4 (CD26/DPP4) is expressed on blood T cells and also circulates in a soluble form (sCD26/DPP4). OBJECTIVE: We aimed to evaluate blood T cell and circulating CD26/DPP4 and its association with metabolic parameters in patients with type 2 diabetes mellitus (T2DM). DESIGNS: We measured CD26/DPP4 expression (percentage of CD26(+) cells using flow cytometry) on CD4(+) and CD8(+) T cells, serum CD26/DPP4 level and activity, and various metabolic parameters in T2DM patients not on DPP4 inhibitor therapy (n = 148). Nondiabetic subjects (n = 50) were included as a control group. RESULTS: Compared with the healthy controls, CD26/DPP4 expression on CD4(+) T cells and CD8(+) T cells was higher in T2DM patients. Serum CD26/DPP4 levels and enzymatic activities were also higher in patients with T2DM than in the control group only when metformin and/or thiazolidinedione-treated T2DM patients were excluded; metformin and/or thiazolidinedione-treated T2DM patients had lower values compared with other T2DM patients. Various parameters in T2DM patients were related to CD26/DPP4 expression on the T cells (hemoglobin A1c), serum sCD26/DPP4 (hemoglobin A1c and insulin resistance assessed by updated homeostasis model assessment), and serum CD26/DPP4 activity (insulin resistance assessed by updated homeostasis model assessment, γ-glutamyl transferase, and alanine aminotransferase) by multivariate analyses. After active glucose control for 12 weeks in drug-naive T2DM patients (n = 50), CD26/DPP4 expression on blood T cells was significantly decreased. CONCLUSIONS: Our results suggest that the CD26/DPP4 level on blood T cells was associated with glucose control status in patients with T2DM.

Unsupervised multiphase segmentation: a phase balancing model.

Variational models have been studied for image segmentation application since the Mumford-Shah functional was introduced in the late 1980s. In this paper, we focus on multiphase segmentation with a new regularization term that yields an unsupervised segmentation model. We propose a functional that automatically chooses a favorable number of phases as it segments the image. The primary driving force of the segmentation is the intensity fitting term while a phase scale measure complements the regularization term. We propose a fast, yet simple, brute-force numerical algorithm and present experimental results showing the robustness and stability of the proposed model.

Clinical features of Plasmodium vivax malaria.

BACKGROUND: Since its reemergence in 1993, a number of cases of Plasmodium vivax malaria have been reported in Korea. We analyzed the cases of malaria patients living in Chuncheon and its neighboring communities, to characterize its clinical manifestations and laboratory findings, and to identify any differences between our clinical findings and those of previous studies. METHODS: We reviewed the clinical records of cases that were confirmed as malaria by peripheral blood smear at Chuncheon Sacred Heart Hospital from July 1998 to September 2001. RESULTS: Forty-four cases were included in the study. All patients were infected with Plasmodium vivax, and presented with high fever; however, tertian fever developed in only 15 patients (35.7%). A number of cases showed various symptoms, which included headache, abdominal pain, nausea and vomiting. Of the 44 cases identified, 41 (93.2%) developed malaria between June and September. Thrombocytopenia was a prominent finding in 75% of the cases at diagnosis, but resolved during or after therapy. Other laboratory abnormalities such as, anemia, elevated transamines, coagulopathies, and elevated lactose dehydrogenase (LDH) were also noted. Cerebrospinal fluid (CSF) studies were performed in five cases, one of which showed pleocytosis in the CSF. CONCLUSION: We noted only 15 patients (35.7%) with tertian fever; the other patients showed variable fever patterns. Thrombocytopenia was the most prominent laboratory finding. Therefore, we suggest that malaria should be included in the differential diagnosis of febrile diseases with an onset between June to and September, regardless of the pattern of the fever.