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

BACKGROUND: Liquid chromatographyetandem mass spectrometry (LC-MSMS) for simultaneous analysis of multiple microbial secondary metabolites (MSMs) is potentially subject to interference by matrix components. METHODS: We examined potential matrix effects (MEs) in analyses of 31 MSMs using ultraperformance LC-MSMS. Twenty-one dust aliquots from three buildings (seven aliquots/building) were spiked with seven concentrations of each of the MSMs (6.2 pg/µl–900 pg/µl) and then extracted. Another set of 21 aliquots were first extracted and then, the extract was spiked with the same concentrations. We added deepoxy-deoxynivalenol (DOM) to all aliquots as a universal internal standard. Ten microliters of the extract was injected into the ultraperformance LC-MSMS. ME was calculated by subtracting the percentage of the response of analyte in spiked extract to that in neat standard from 100. Spiked extract results were used to create a matrix-matched calibration (MMC) curve for estimating MSM concentration in dust spiked before extraction. RESULTS: Analysis of variance was used to examine effects of compound (MSM), building and concentration on response. MEs (range: 63.4%–99.97%) significantly differed by MSM (p < 0.01) and building (p < 0.05). Mean percent recoveries adjusted with DOM and the MMC method were 246.3% (SD = 226.0) and 86.3% (SD = 70.7), respectively. CONCLUSION: We found that dust MEs resulted in substantial underestimation in quantifying MSMs and that DOM was not an optimal universal internal standard for the adjustment but that the MMC method resulted in more accurate and precise recovery compared with DOM. More research on adjustment methods for dust MEs in the simultaneous analyses of multiple MSMs using LC-MSMS is warranted.
2,5-Dimethoxy-4-Methylamphetamine ; Calibration ; Dust ; Mass Spectrometry ; Methods

BACKGROUND/AIMS: Prokinetics are commonly used for the treatment of functional dyspesia, but their methods of action are different. First, we compared the efficacy and safety of the dopamine receptor antagonists, which were domperidone maleate and levosulpiride, in a 2 week treatment in functional dyspepsia, then investigated the efficacy and safety of cisapride tartrate in a 2 week treatment in those who were resistant to domperidone maleate or levosulpiride. METHODS: One hundred Forty-nine patients, who were diagnosed with functional dyspepsia, were selected. The subjects were randomly divided into two groups, domperidone maleate (75) and levosupiride (74). Daily they took 30mg of domperidone maleate (DOM) or 75mg of levosulpiride (LEV) for 2 weeks. Then the subjects who didn't respond to these treatments took 30mg of cisapride tartrate for the following 2 weeks. RESULTS: At week 0, the total symptom scores of the DOM group and LEV group were 8.01+/-2.57 and 8.14+/-2.65 respectively, which were not statistically different. At week 2, the total symptom scores of the DOM and LEV groups were significantly reduced to 4.28+/-3.30 and 4.85+/-3.53(p=0.0001). The efficacy rates of the DOM and LEV groups at week 2 were 50.8% vs. 44.1%. The rate of adverse events in the LEV groups was much higher than in the DOM group(17.7% vs. 8.0%). In addition the rate of change from normal to abnomal in prolactin level was markedly higher in the LEV than that of the DOM group(80.0% vs. 8.3%). After 2 weeks of treatment with cisapride tartrate, the total symptom score was significantly reduced to 3.77+/-2.49(p=0.0001), and the efficacy rate was 75.0%. The satisfaction of the resistant subjects in efficacy of cisapride compared with the previous treatment was 73.3%. The rate of adverse events of cisapride tartrate was 5.0%. CONCLUSIONS: Considering efficacy and safety of domperidone maleate and levosulpiride, domperidone maleate was the safer drug for the treatment of functional dyspepsia, and cisapride tartrate can be a useful drug in those patients who are resistant to dopamine antagonists like domperidone maleate and levosulpiride.
2,5-Dimethoxy-4-Methylamphetamine ; Cisapride* ; Domperidone ; Dopamine Antagonists* ; Dopamine* ; Dyspepsia* ; Gastroesophageal Reflux ; Humans ; Prolactin

OBJECTIVES: Haloperidol has been widely used for treating schizophrenia with somewhat limitation due to the side effects. Some of these side effects are anticholinergic side effects such as dry mouth, constipation, urinary difficulty, blurred vision, sexual dysfunction, etc. Some kinds strategies to minimize these side effects are tried, one of which is the use of bethanechol. The authors studied the effects of bethanechol on the anticholinergic side effects of typical antipsychotics. METHODS: The subjects of this study consisted of 60 chronic schizophrenics who had used haloperidol since 4 weeks before the study and whose score of 'Askers side effects rating scale' was above 7. They were assigned evenly to three groups (placebo group, bethanechol 40mg group, bethanechol 80mg group). Benztropin had been washed out for 2 weeks before the study. The authors measured ASRS for evaluating the anticholinergic side effect and BPRS for evaluating the effects of bethanechol on the psychopathology, at baseline, the 2nd week and the 4th week from baseline, respectively. RESULTS: At baseline, the mean age of patients was 38.00(+/- 10.55) years, the mean duration of illness was 11.12(+/- 8.09) years, and the mean dosage of the haloperidol was 15.07(+/- 6.03)mg. At baseline, mean score of BFRS was 50.25(+/- 5.24), and mean score of ASRS was 9.27 (+/- 3.04). There were no significant differences of ages, duration of illness, dosage of haloperidol, scores of BPRS and ASRS among 3 groups at baseline. There were no significant changes in BPRS at the 2nd week and the 4th week as compared with baseline, and also there were no changes among groups. The total sums of ASRS showed the statistically significant changes in the 80mg group at the 2nd week and the 4th week. The 80mg group showed statistically significant changes in dry mouth, constipation and urinary difficulty dom the 2nd week, and orthostatic symptoms from the 4th week. CONCLUSION: The authors found that the use of bethanechol for the chronic schizophrenics treating with haloperidol greatly improved the anticholinergic side effects with no change in psychopathology. The 80mg group showed more significant results than the placebo group and the 40mg group, especially in dry mouth, constipation, urinary diffculty and orthostatic symptoms. The authors suggest that high doses of bethanechol decrease the anticholinergic side effects and increase the drug compliance of chronic schizophrenics with anticholinergic side effects.
2,5-Dimethoxy-4-Methylamphetamine ; Antipsychotic Agents ; Bethanechol* ; Compliance ; Constipation ; Haloperidol* ; Humans ; Mouth ; Psychopathology ; Schizophrenia

OBJECTIVE: To investigate the efficacy of commonly available analgesics in the management of delayed-onset muscle soreness (DOMS) over an 8-day period, and to compare the efficacy between aspirin and acetaminophen. METHOD: Forty-two subjects were recruited. DOMS was induced by using the isokinetic dynamometer (KinCom(R)) in standardized fashion in the nondominant knee extensor with subjects seated at 30 degree-angle velocity. Subjects were asked to extend their non-dominant knee with concentric method and to hold the knee with eccentric flexion force at 30 degree-angle velocity, with maximal efforts. On this way, they did 10 repetitions, and then 3 cycles. We categorized four groups (n=10, for each group), that were control group with no medication, placebo group with placebo medication (antacid tablets), aspirin group with medication of 900 mg of aspirin, and acetaminophen group with medication with 3,900 mg of acetaminophen. Visual Analogue Scale (VAS: twice a day, until on day 8). and McGill Pain Questionnaire (MPQ: on day 1 and 3) were measured. RESULTS: We didn't find any significant difference of peak VAS score and relief time between four groups (P>0.05), The score of MPQ was not different between four groups (P>0.05). CONCLUSION: We concluded that the medication may not be beneficial, at least at the doses stated, in the management of DOMS.
2,5-Dimethoxy-4-Methylamphetamine ; Acetaminophen* ; Analgesics ; Anti-Inflammatory Agents, Non-Steroidal ; Aspirin* ; Knee ; Myalgia* ; Pain Measurement