To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In this respect, a format conversion tool, as well as quality conversion tool would be the minimum requirements to integrate reads from different platforms. We have developed the Pyrus NGS Sequencing Format Converter, a simple software toolkit which allows to convert three kinds of Next Generation Sequencing reads, into commonly used fasta or fastq formats. The converter modules are all implemented, uniformly, in Java GUI modules that can be integrated in software applications for displaying the data content in the same format.
Indonesia ; Pyrus

BACKGROUND/OBJECTIVE: Chronic hyperglycemia induces oxidative stress via accumulation of reactive oxygen species (ROS) and contributes to diabetic complications. Hyperglycemia induces mitochondrial superoxide anion production through the increased activity of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. This study aimed to determine whether fisetin and luteolin treatments suppress the oxidative stress by modulating the expression of sirtuins (SIRTs) and forkhead box O3a (FOXO3a) under hyperglycemic conditions in human monocytes. MATERIALS/METHODS: Human monocytic cells (THP-1) were cultured under osmotic control (14.5 mmol/L mannitol), normoglycemic (NG, 5.5 mmol/L glucose), or hyperglycemic (HG, 20 mmol/L glucose) conditions, in the absence or presence of fisetin and luteolin for 48 h. To determine the effect of fisetin and luteolin treatments on high glucose-induced oxidative stress, western blotting and intracellular staining were performed. RESULTS: Hyperglycemic conditions increased the ROS production, as compared to normoglycemic condition. However, fisetin and luteolin treatments inhibited ROS production under hyperglycemia. To obtain further insight into ROS production in hyperglycemic conditions, evaluation of p47phox expression revealed that fisetin and luteolin treatments inhibited p47phox expression under hyperglycemic conditions. Conversely, the expression levels of SIRT1, SIRT3, SIRT6, and FOXO3a were decreased under high glucose conditions compared to normal glucose conditions, but exposure to fisetin and luteolin induced the expression of SIRT1, SIRT3, SIRT6, and FOXO3a. The above findings suggest that fisetin and luteolin inhibited high glucose-induced ROS production in monocytes through the activation of SIRTs and FOXO3a. CONCLUSIONS: The results of our study supports current researches that state fisetin and luteolin as potential agents for the development of novel strategies for diabetes.
Blotting, Western ; Diabetes Complications ; Diabetes Mellitus ; Glucose ; Humans ; Hyperglycemia ; In Vitro Techniques* ; Luteolin* ; Monocytes ; NADP ; Oxidative Stress* ; Oxidoreductases ; Reactive Oxygen Species ; Sirtuins* ; Superoxides

Dietary intake and nutritional status of individuals are important factors affecting mental health and the development of psychiatric disorders. Majority of scientific evidence relating to mental health focuses on depression, cognitive function, and dementia, and limited evidence is available about other psychiatric disorders including schizophrenia. As life span of human being is increasing, the more the prevalence of mental disorders is, the more attention rises. Lists of suggested nutritional components that may be beneficial for mental health are omega-3 fatty acids, phospholipids, cholesterol, niacin, folate, vitamin B6, and vitamin B12. Saturated fat and simple sugar are considered detrimental to cognitive function. Evidence on the effect of cholesterol is conflicting; however, in general, blood cholesterol levels are negatively associated with the risk of depression. Collectively, the aims of this review are to introduce known nutritional factors for mental health, and to discuss recent issues of the nutritional impact on cognitive function and healthy brain aging.
Aging ; Brain ; Cholesterol ; Cognition ; Dementia ; Depression ; Fatty Acids, Omega-3 ; Folic Acid ; Humans ; Mental Disorders ; Mental Health* ; Niacin ; Nutritional Status ; Phospholipids ; Prevalence ; Schizophrenia ; Vitamin B 12 ; Vitamin B 6

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
2,5-Dimethoxy-4-Methylamphetamine ; Biology ; Computational Biology ; Indonesia ; Systems Biology

The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in twoand- a-half dimensions (2.5D) as an alternative to three dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.
Hypogonadism ; Metabolic Networks and Pathways ; Mitochondrial Diseases ; Ophthalmoplegia

BACKGROUND: Cut-off values for visceral fat area (VFA) measured by computed tomography (CT) for identifying individuals at risk of metabolic syndrome (MetS) have not been clearly established in Korean adults, particularly for large populations. We aimed to identify optimal VFA and waist circumference (WC) cut-off values and compare the ability of VFA and WC to predict the presence of ≥2 metabolic risk factors. METHODS: We included 36,783 subjects aged 19–79 years undergoing abdominal fat CT during regular health checkups between January 2007 and February 2015 in Seoul. The risk factors for MetS except WC were based on the International Diabetes Federation criteria. Receiver operating characteristic curve analyses were used to determine the appropriate VFA and WC cut-off values for MetS. RESULTS: VFA was a more significant predictor of metabolic risk factors than WC and body mass index (BMI). The optimal cut-off values for VFA and WC were 134.6 cm2 and 88 cm for men and 91.1 cm2 and 81 cm for women, respectively. We estimated age-specific cut-off values for VFA, WC, and BMI. VFA cut-off values increased with age, particularly among women. CONCLUSION: This large population study proposed the cut-off values for VFA and WC for identifying subjects at risk of MetS among Korean adults. For more accurate diagnosis, different age-specific cut-off values for VFA and WC may be considered.
Abdominal Fat ; Adult* ; Body Mass Index ; Diagnosis ; Female ; Humans ; Intra-Abdominal Fat* ; Male ; Obesity, Abdominal ; Risk Factors ; ROC Curve ; Seoul ; Waist Circumference

Tumor necrosis factor alpha (TNFalpha) is a multifunctional cytokine that is elevated in inflammatory diseases such as atherosclerosis, diabetes and rheumatoid arthritis. Recent evidence has suggested that beta2 adrenergic receptor (beta2AR) activation in osteoblasts suppresses osteogenic activity. In the present study, we explored whether TNFalpha modulates betaAR expression in osteoblastic cells and whether this regulation is associated with the inhibition of osteoblast differentiation by TNFalpha. In the experiments, we used C2C12 cells, MC3T3-E1 cells and primary cultured mouse bone marrow stromal cells. Among the three subtypes of betaAR, beta2 and beta3AR were found in our analysis to be upregulated by TNFalpha. Moreover, isoproterenol-induced cAMP production was observed to be significantly enhanced in TNFalpha-primed C2C12 cells, indicating that TNFalpha enhances beta2AR signaling in osteoblasts. TNFalpha was further found in C2C12 cells to suppress bone morphogenetic protein 2-induced alkaline phosphatase (ALP) activity and the expression of osteogenic marker genes including Runx2, ALP and osteocalcin. Propranolol, a beta2AR antagonist, attenuated this TNFalpha suppression of osteogenic differentiation. TNFalpha increased the expression of receptor activator of NF-kappaB ligand (RANKL), an essential osteoclastogenic factor, in C2C12 cells which was again blocked by propranolol. In summary, our data show that TNFalpha increases beta2AR expression in osteoblasts and that a blockade of beta2AR attenuates the suppression of osteogenic differentiation and stimulation of RANKL expression by TNFalpha. These findings imply that a crosstalk between TNFalpha and beta2AR signaling pathways might occur in osteoblasts to modulate their function.
Alkaline Phosphatase ; Animals ; Arthritis, Rheumatoid ; Atherosclerosis ; Bone Morphogenetic Proteins ; Durapatite ; Mesenchymal Stromal Cells ; Mice ; Osteoblasts ; Osteocalcin ; Propranolol ; Receptor Activator of Nuclear Factor-kappa B ; Receptors, Adrenergic ; Tumor Necrosis Factor-alpha

The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to this thorny issue, we propose J2dpathway, a metabolic pathway atlas viewer that has node-abstracting features.
Metabolic Networks and Pathways ; Pliability

Background: Group genetic counseling has been implemented to meet growing demand.A metaverse platform, in which a society is built and activities are carried out in the virtual world, has not yet been implemented in group genetic counseling. We investigated whether a metaverse platform could be an alternative service-delivery model for group genetic counseling. Methods: Participants (N=131) were divided into three groups: patient (N=45), family (N= 43), and interested (N = 43) groups. Participants entered the metaverse through a link sent to their mobile phones and attended a 20-min group genetic counseling session reviewing hereditary breast cancer, followed by a 10-min question-and-answer period. Results: The overall median score of post-educational knowledge (9.0, range 8.0–10.0) significantly increased compared to that of pre-educational knowledge (6.0, range 3.0– 8.0) (P < 0.001). There was no significant difference in the pre- and post-educational knowledge scores among the three groups (P > 0.05). Most participants (95%) responded that their understanding of hereditary breast cancer had increased after the group genetic counseling session and that their satisfaction was high. The main advantage noted with metaverse was no limit of space and location while attending the session (97%), and the main disadvantage was a possibility of missing content due to an unstable internet connection (67%). Conclusions The metaverse platform would be acceptable as an alternative group genetic counseling service. More studies are needed to investigate how, for whom, and in what circumstances metaverse can be effectively utilized.

The association between vitamin D levels and nonalcoholic fatty liver disease (NAFLD) has been recognized. However, few studies showed independent associations between vitamin D deficiency and NAFLD after a sex-related adjustment for metabolic factors. We aimed to study whether vitamin D deficiency is an independent risk factor of NAFLD even after controlling for metabolic syndrome and visceral fat in both sexes. In this cross-sectional study, 7,514 Korean adults (5,278 men, 2,236 women) participated in a health check-up program. They underwent blood tests, abdominal computed tomography (CT) of the visceral fat area, and ultrasonography for NAFLD screening. Multiple logistic regression analysis was used to investigate the association of vitamin D deficiency with NAFLD according to the sex differences. Vitamin D deficiency is associated with NAFLD. The adjusted odds ratio (aOR) for NAFLD increased sequentially with decreasing vitamin D level, even after adjusting for metabolic syndrome and visceral fat. The subjects in the vitamin D sufficiency group (20–30 ng/mL) had an aOR for NAFLD of 1.18 (95% CI, 1.00–1.39), whereas the deficiency group (< 20 ng/mL) had an aOR of 1.29 (95% CI, 1.10–1.52). However, we have detected a significant sex-related interaction when analyzing the results. A significant relationship between vitamin D deficiency and NAFLD was found in men (aOR, 1.33; 95% CI, 1.11–1.60) but not in women.
Adult ; Cross-Sectional Studies ; Female ; Hematologic Tests ; Humans ; Intra-Abdominal Fat ; Logistic Models ; Male ; Mass Screening ; Metabolic Syndrome X ; Non-alcoholic Fatty Liver Disease* ; Odds Ratio ; Risk Factors* ; Sex Characteristics ; Ultrasonography ; Vitamin D Deficiency ; Vitamin D* ; Vitamins*