Synthetic Strategies toward Ortho-3-propanoate Substituted Aryl Phosphonates by Three-Component Coupling Reactions of Arynes, Phosphites, and Acrylates.

Mild, metal-free, and operationally simple three-component coupling reactions involving arynes, phosphites, and acrylates have been achieved. The reaction proceeded well with α- or ß-substituted acrylates. Additionally, various functional groups were tolerated under these reaction conditions, resulting in diverse ortho-3-propanoate-substituted aryl phosphonates. Moreover, the reaction can be used to synthesize a range of organophosphorus compounds present in natural products, materials, and biologically active compounds.

MoNetExplorer: A Visual Analytics System for Analyzing Dynamic Networks with Temporal Network Motifs.

Partitioning a dynamic network into subsets (i.e., snapshots) based on disjoint time intervals is a widely used technique for understanding how structural patterns of the network evolve. However, selecting an appropriate time window (i.e., slicing a dynamic network into snapshots) is challenging and time-consuming, often involving a trial-and-error approach to investigating underlying structural patterns. To address this challenge, we present MoNetExplorer, a novel interactive visual analytics system that leverages temporal network motifs to provide recommendations for window sizes and support users in visually comparing different slicing results. MoNetExplorer provides a comprehensive analysis based on window size, including (1) a temporal overview to identify the structural information, (2) temporal network motif composition, and (3) node-link-diagram-based details to enable users to identify and understand structural patterns at various temporal resolutions. To demonstrate the effectiveness of our system, we conducted a case study with network researchers using two real-world dynamic network datasets. Our case studies show that the system effectively supports users to gain valuable insights into the temporal and structural aspects of dynamic networks.

RCMVis: A Visual Analytics System for Route Choice Modeling.

We present RCMVis, a visual analytics system to support interactive Route Choice Modeling analysis. It aims to model which characteristics of routes, such as distance and the number of traffic lights, affect travelers' route choice behaviors and how much they affect the choice during their trips. Through close collaboration with domain experts, we designed a visual analytics framework for Route Choice Modeling. The framework supports three interactive analysis stages: exploration, modeling, and reasoning. In the exploration stage, we help analysts interactively explore trip data from multiple origin-destination (OD) pairs and choose a subset of data they want to focus on. To this end, we provide coordinated multiple OD views with different foci that allow analysts to inspect, rank, and compare OD pairs in terms of their multidimensional attributes. In the modeling stage, we integrate a k-medoids clustering method and a path-size logit model into our system to enable analysts to model route choice behaviors from trips with support for feature selection, hyperparameter tuning, and model comparison. Finally, in the reasoning stage, we help analysts rationalize and refine the model by selectively inspecting the trips that strongly support the modeling result. For evaluation, we conducted a case study and interviews with domain experts. The domain experts discovered unexpected insights from numerous modeling results, allowing them to explore the hyperparameter space more effectively to gain better results. In addition, they gained OD- and road-level insights into which data mainly supported the modeling result, enabling further discussion of the model.

Shotgun metagenomics of Cheonggukjang, a fermented soybean food of Korea: Community structure, predictive functionalities and amino acids profile.

Cheonggukjang is a naturally fermented soybean food of Korea. The present study was aimed to reveal the whole microbial community structure of naturally fermented cheonggukjang along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. Metataxonomic profile of cheonggukjang samples showed different domains viz. bacteria (95.83%), virus (2.26%), unclassified (1.84%), eukaryotes (0.05%) and archaea (0.005%). Overall, 44 phyla, 286 families, 722 genera and 1437 species were identified. Firmicutes was the most abundant phylum (98.04%) followed by Proteobacteria (1.49%), Deinococcus-Thermus (0.14%). Bacillus thermoamylovorans was the most abundant species in cheonggukjang followed by Bacillus licheniformis, Bacillus glycinifermentans, Bacillus subtilis, Bacillus paralicheniformis, Bacillus amyloliquifaciens, Brevibacillus borstelensis, Brevibacillus sonorensis Brevibacillus, Acinetobacter, Carnobacterium, Paenibacillus, Cronobacter Enterococcus, Enterobacter, Terriglobus, Psychrobacter and Virgibacillus. A colossal diversity of the genus Bacillus was detected with 150 species. Functional analysis of cheonggukjang metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including, various essential amino acids, conjugated amino acids, different vitamins, flavonoids, and enzymes. Amino acid profiles obtained from KEGG annotation in cheonggukjang were validated with experimental result of amino acid profiles.

Functional Properties of Microorganisms in Fermented Foods.

Fermented foods have unique functional properties imparting some health benefits to consumers due to presence of functional microorganisms, which possess probiotics properties, antimicrobial, antioxidant, peptide production, etc. Health benefits of some global fermented foods are synthesis of nutrients, prevention of cardiovascular disease, prevention of cancer, gastrointestinal disorders, allergic reactions, diabetes, among others. The present paper is aimed to review the information on some functional properties of the microorganisms associated with fermented foods and beverages, and their health-promoting benefits to consumers.

XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data.

BACKGROUND: Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. RESULTS: In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. CONCLUSIONS: Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results.

Improved cognitive performance following supplementation with a mixed-grain diet in high school students: a randomized controlled trial.

OBJECTIVE: Adolescence is a stage of rapid growth, when rich nutritional supplementation is important. Maintaining optimal cognitive functioning is critical in high school students, who are under considerable academic pressure. The objectives of this study were to identify the effects of a 9-wk randomly assigned diet of mixed grains versus a regular diet on cognitive performance and on levels of plasma brain-derived neurotrophic factor (BDNF) and S100B, a calcium-binding protein produced by astroglial cells, in healthy high school students (grades 10 and 11). METHODS: In this 9-wk, single-blind, controlled study, subjects were randomly allocated to either a mixed-grain or a regular diet. Cognitive assessments and measurements of plasma BDNF and S100B levels were performed at baseline and after the 9-wk intake of a mixed-grain or regular diet. Computerized neuropsychological tests and self-rating scales were used for the cognitive assessments. RESULTS: Significant improvements in some neuropsychological tests were found after 9 wk in both the mixed-grain and the regular-diet groups, but the changes from baseline between the two groups were not significantly different. Significant impairments on the AX-continuous performance test were observed at the endpoint in the regular-diet group, and the changes from baseline between the two groups were also significantly different for this test. A significant difference in changes in BDNF levels was observed between the two groups. CONCLUSIONS: These results suggest that intake of mixed grains for 9 wk is beneficial for cognitive performance and plasma BDNF levels in high school students. These beneficial effects seem to be related to the prevention of cognitive deterioration in a mental-fatigue test with the mixed-grain diet, rather than cognitive enhancement per se.

Effect of Cheonggukjang supplementation upon hepatic acyl-CoA synthase, carnitine palmitoyltransferase I, acyl-CoA oxidase and uncoupling protein 2 mRNA levels in C57BL/6J mice fed with high fat diet.

This study investigated the effect of Cheonggukjang on mRNA levels of hepatic acyl-CoA synthase (ACS), carnitine palmitoyltransferase I (CPT-I), acyl-CoA oxidase (ACO) and uncoupling protein 2 (UCP2), and on serum lipid profiles in C57BL/6J mice. Thirty male C57BL/6J mice were divided into three groups; normal diet (ND), high fat diet (HD) and high fat diet with 40% Cheonggukjang (HDC). Energy intake was significantly higher in the HDC group than in the ND and HD groups. The HDC group normalized in weight gain, epididymal and back fat (g/100 g) accumulation which are increased by high fat diet. Serum concentrations of triglyceride and total cholesterol in the HDC were significantly lower than those in the HD group. These results were confirmed by hepatic mRNA expression of enzymes and protein (ACS, CPT-1, ACO, UCP2) which is related with lipid metabolism by RT-PCR. Hepatic CPT-I, ACO and UCP2 mRNA expression was increased by Cheonggukjang supplementation. We demonstrated that Cheonggukjang supplement leads to increased mRNA expressions of enzymes and protein involved in fatty acid oxidation in liver, reduced accumulation of body fat and improvement of serum lipids in high fat diet fed mice.

Growth inhibitory effects of kimchi (Korean traditional fermented vegetable product) against Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus.

Kimchi is a unique Korean traditional vegetable product that is fermented by lactic acid bacteria (LAB) and is mainly consumed as a side dish with boiled rice. Its main ingredients are brined Chinese cabbage, red pepper powder, and fermented fish sauce, and these are combined with many spices such as garlic, green onion, ginger, and some seaweed. The relationship between the concentration of LAB or the pH and the growth of three gram-positive foodborne pathogens (Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus) was evaluated. Heat treatment (HT; 85 degrees C for 15 min) or neutralization treatment (NT; pH 7.0) was conducted on day 0 (0-D group) and day 3 (3-D group) of incubation. The pH in the control group and the NT group dropped sharply to 4.12 to 4.30 after 2 days of incubation and slightly decreased thereafter, whereas the pH in the control group and HT group stayed at 7.0 during incubation. LAB were not detected in the HT kimchi during incubation. B. cereus in the NT-0-D, NT-3-D, and HT-3-D groups was reduced by 1.5 to 3.1 log CFU/ml but increased slightly in the HT-0-D group. L. monocytogenes in HT-3-D and NT-3-D groups disappeared after 5 days of incubation, and S. aureus in the NT-0-D group disappeared after 4 days. These findings indicate that growth of all the foodborne pathogens was inhibited by NT-0-D, HT-3-D, and NT-3-D, but B. cereus was not inhibited by HT-0-D. Thus, growth of LAB in kimchi is an important factor in the control of foodborne pathogens.

The isoflavonoid aglycone-rich fractions of Chungkookjang, fermented unsalted soybeans, enhance insulin signaling and peroxisome proliferator-activated receptor-gamma activity in vitro.

We investigated anti-diabetic candidates and their mechanisms from the fractions of Chungkookjang (CKJ), a traditional fermented unsalted soybean, by investigating insulin signaling, peroxisome proliferator-activated receptor (PPAR)-gamma activity and glucose-stimulated insulin secretion, in vitro. Cooked soybeans (CSB) and CKJ, fermented predominantly with Bacillus subtilis, were extracted by 70% EtOH followed by an XAD-4 column chromatography with a serial mixture of solvents comprised of MeOH and water. During fermentation, the contents of isoflavonoid aglycones were elevated, and the fractions enriched with aglycones enhanced insulin-stimulated glucose uptake in 3T3-L1 adipocytes. This increase in glucose uptake resulted from stimulating a translocation of the glucose transporter (GLUT)-4 into the plasma membrane through the phosphorylation of insulin receptor substrate (IRS)-1 and Akt. Especially, daidzein enriched fractions elevated insulin-stimulated glucose uptake by acting as PPAR-gamma agonist up to levels exhibited when 10 nM insulin is administered. Fractions containing small peptides with low polarity in CKJ slightly increased glucose-stimulated insulin secretion. The data suggest that an increase in isoflavonoid aglycones in CKJ, in comparison to CSB, enhances glucose utilization via activating insulin signaling and stimulates PPAR-gamma activity in adipocytes. In addition, CKJ contains small peptides improving glucose-stimulated insulin secretion in insulinoma cells. Overall, CKJ is superior to CSB in anti-diabetic action.

Volatile constituents from the leaves of Callicarpa japonica Thunb. and their antibacterial activities.

Volatile substances of Callicarpa japonica Thunb. were examined for their antibacterial activities against six foodborne microorganisms using the optical densitometer Bioscreen C. Extracts of C. japonica were obtained by simultaneous steam distillation and solvent extraction (SDE), and those extracted for 1.5 and 2.0 h at pH 6.0 strongly inhibited the growth of Bacillus cereus and Salmonella typhimurium; the content of the volatile substances of leaves at these pH levels were 543.1 and 706.7 mg/kg, respectively. All foodborne microorganisms tested were strongly inhibited by the addition of >8% (v/v) of the SDE extracts to broth medium. The major volatile components of the SDE extracts obtained at 1.5 h and pH 6.0 were gamma-caryophyllene, 1-octen-3-ol, 2-hexenal, germacrene B, and aromadendrene II, with corresponding peak areas of 44.14, 15.6, 9.86, 5.24, and 4.01%, respectively, and major antibacterial components were 1-octen-3-ol and 2-hexenal. Among the 32 materials identified as volatile flavor components, 2-hexenal, 2,4-hexadienal, 1-octen-3-ol, 2,4-heptadienal, and epiglobulol strongly inhibited microorganism growth. In particular, 2-hexenal (107.52 mg/L) and 1-octen-3-ol (678.64 mg/L) inhibited the growth of most microorganisms tested by >90%.

Isolation and characterization of lactic acid bacteria from feces of newborn baby and from dongchimi.

Lactic acid bacteria were screened from feces of newborn baby and from dongchimi. Selection criteria employed included the ability of strains to withstand environmental conditions such as low pH, high bile concentration, and oxygen. The isolates were applied to the juice of various vegetables, and fermentabilities of isolates were compared. Strains F20-3, F35-3, and F35-6 showed high stability compared to the other strains at pH 3.0 and 2.3. Strains D1 and D2 showed the highest survival at pH 3.0 and survived at 1% high bile concentration. The selected strains were able to survive at low pH and relatively high bile concentration and were not affected by oxygen. The growth of isolates was >10(7) cfu/mL in natural media, and strains were not affected by the pH values of the vegetables. Therefore, isolated strains are thought to survive through the intestinal ecosystem and are considered to be suitable for application of the fermented product using various vegetables for their functionality. The isolates were identified as Lactobacillus plantarum and Lactobacillus fermentum.

Antimicrobial synergistic effect of linolenic acid and monoglyceride against Bacillus cereus and Staphylococcus aureus.

The antimicrobial effect of linolenic acid with or without monoglyceride (glycerol laurate or glycerol myristate) against six food-borne microorganisms was determined in broth medium. Minimum inhibitory concentration of linolenic acid on Bacillus cereus and Staphylococcus aureus was 20 and 50 ppm, respectively. The growth of B. cereus treated with linolenic acid at 10 ppm with 10 ppm monoglyceride was more inhibitory than that of linolenic acid alone, and the viable cell population was reduced 2-4 log cycles compared to that of the control. When linolenic acid was added at that level, the adenosine triphosphate (ATP) concentration of extracellular fluid was drastically increased compared with that of the control, and the combined effect with monoglyceride was higher than that with linolenic acid alone. However, the intracellular ATP concentration decreased compared with that of the control. From these results, we concluded that linolenic acid has a strong antimicrobial activity against B. cereus and S. aureus, and that linolenic acid combined with monoglyceride showed stronger antimicrobial activity than using linolenic acid alone.