A decade after the metabolomics standards initiative it's time for a revision.

A recent analysis of publicly available metabolomics data shows that the MSI guidelines are not well abided to in publicly shared metabolomics studies. We propose that the MSI guidelines should be revisited and revised, as has been done in other communities, to fit the current community needs

Compliance with minimum information guidelines in public metabolomics repositories.

The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards

Dissemination of metabolomics results: role of MetaboLights and COSMOS.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".

BACKGROUND: Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently no central repository for the depositing of data despite efforts by the Metabolomics Standard Initiative (MSI) to develop a standardised description of a metabolomic experiment. FINDINGS: In this manuscript we describe how the MSI description has been applied to a published dataset involving the identification of cross-species metabolic biomarkers associated with type II diabetes. The study describes sample collection of urine from mice, rats and human volunteers, and the subsequent acquisition of data by high resolution 1H NMR spectroscopy. The metadata is described to demonstrate how the MSI descriptions could be applied in a manuscript and the spectra have also been made available for the mouse and rat studies to allow others to process the data. CONCLUSIONS: The intention of this manuscript is to stimulate discussion as to whether the MSI description is sufficient to describe the metadata associated with metabolomic experiments and encourage others to make their data available to other researchers

Medical Students’ View about the Effects of Practical Courses on Learning the General Theoretical Concepts of Basic Medical Sciences

Introduction: The basic medical sciences section requires 2.5 years in the medical education curriculum. Practical courses complement theoretical knowledge in this period to improve their appreciation. Despite spending lots of disbursement and time, this period’s efficacy is not clearly known. Methods: One hundred thirty-three General Practitioner (GP) students have been included in this descriptive cross-sectional study and were asked by questionnaire about the positive impact of practical courses on learning theoretical knowledge. Data were analyzed by descriptive statistics. Result: The agreement in “Practical Head and Neck Anatomy” was 40.91% ± 29.45, in “Practical Trunk Anatomy” was 63.62% ± 2.32 and in “Practical Anatomy of Extremities” was 56.16% ± 2.57. In “Practical Histology”, agreement was 69.50%±2.19; “Practical Biophysics” was 45.97%±2.25, “Practical Physiology” 61.75%±2.17; “Practical Biochemistry” 36.28%±2.42; “Practical Pathology” 59.80%±2.53; “Practical Immunology” 56.25%±26.40; “Practical Microbiology and Virology” 60.39%±2.27 and “Practical Mycology and Parasitology” 68.2%± 2.16.Conclusion: GP students in Tabriz University of Medical Sciences are not optimistic about the applicability of practical courses of basic medical sciences lessons

Optimization of chemical conditions for metabolites production by Ganoderma lucidum using response surface methodology and investigation of antimicrobial as well as anticancer activities

Ganoderma lucidum (G. lucidum) is a medicinal mushroom that is known for its ability to produce compounds with physiological effects on human health. This research was undertaken to amplify the production of bioactive components of G. lucidum under optimal cultivation conditions, obtained in a submerged state and utilized in solid state fermentation, with the purpose of enhancing antimicrobial and anticancer activities. The results indicated that titanium dioxide (TiO2 NPs), magnesium oxide nanoparticles (MgO2 NPs), and B6, along with glucose syrup and CLS syrups, were the most effective for producing GA, while wheat starch and whey protein, along with MgO2 NPs and B6 vitamin, stimulated polysaccharide production using the One Factor at a Time (OFAT) method. After screening, the response surface method (RSM) statistically indicated that the media containing 42.11 g/L wheat starch with 22 g/L whey protein and 50 g/L glucose syrup with 30 g/L CSL were found to be the best conditions for polysaccharide (21.47% of dry weight biomass) and GA (20.35 mg/g dry weight biomass) production, respectively. The moss of the fruit body of G. lucidum produced under optimal GA conditions had the highest diversity in flavonoids and phenolic acids and significant antimicrobial activity against Esherichia coli (E. coli) and Bacillus subtilis (B. subtilis). In addition, the IC50 levels of shell and stem of G. lucidum were 465.3 and 485.7 μg/mL, respectively, while the moss did not reach 50% inhibition. In the end, the statistical approaches utilized in this research to elevate the levels of bioactive components in the fruiting body of G. lucidum produced a promising natural source of antimicrobial and anticancer agents

The Metabolomics Society-Current State of the Membership and Future Directions.

Background: In 2017, the Metabolomics Society conducted a survey among its members to assess the degree of its current success, define opportunities for improving its service to the community and make plans to establish future goals and direction of the Society. Methods: A 32-question online survey was sent via e-mail to all Metabolomics Society members as of 19 June 2017 (n = 644). In addition to the direct e-mails, the link to access the survey was made available through social media. The survey was open until 10 August 2017. Question-specific data were reported using the summary data generated by SurveyMonkey and additional stratified analyses performed using Stata 15. Results: The number of respondents was 394 (61%) with 348 (88%) completing the multiple-choice questions in survey. Metabolomics Society annual meetings, networking and the opportunity to join the global metabolomics community were among the most important benefits expressed by the Metabolomics Society members. Conclusions: The survey collected the first data focusing on membership issues from Society members. The Society should focus on collecting and monitoring of demographic data during the membership registration process; continuing to support the early-career members of the Society; and developing initiatives that focus on member networking to retain and increase Society membership

The metaRbolomics Toolbox in Bioconductor and beyond

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub

Effects of oleoylethanolamide supplementation on inflammatory biomarkers, oxidative stress and antioxidant parameters of obese patients with NAFLD on a calorie-restricted diet: A randomized controlled trial

Background: Oxidative stress is considered a major factor in the pathophysiology of non-alcoholic liver disease (NAFLD). A growing body of evidence indicates that oleoylethanolamide (OEA), a bioactive lipid mediator, has anti-inflammatory and antioxidant properties. This trial investigated the effects of OEA administration on inflammatory markers, oxidative stress and antioxidant parameters of patients with NAFLD.Methods: The present randomized controlled trial was conducted on 60 obese patients with NAFLD. The patients were treated with OEA (250 mg/day) or placebo along with a low-calorie diet for 12 weeks. Inflammatory markers and oxidative stress and antioxidant parameters were evaluated pre-and post-intervention.Results: At the end of the study, neither the between-group changes, nor the within-group differences were significant for serum levels of high-sensitivity C-reactive protein (hs-CRP), interleukin-1 beta (IL-1β), IL-6, IL-10, and tumor necrosis-factor α (TNF-α). Serum levels of total antioxidant capacity (TAC) and superoxide dismutase (SOD) significantly increased and serum concentrations of malondialdehyde (MDA) and oxidized-low density lipoprotein (ox-LDL) significantly decreased in the OEA group compared to placebo at study endpoint (p = 0.039, 0.018, 0.003 and 0.001, respectively). Although, no significant between-group alterations were found in glutathione peroxidase and catalase. There were significant correlations between percent of changes in serum oxidative stress and antioxidant parameters with percent of changes in some anthropometric indices in the intervention group.Conclusion: OEA supplementation could improve some oxidative stress/antioxidant biomarkers without any significant effect on inflammation in NAFLD patients. Further clinical trials with longer follow-up periods are demanded to verify profitable effects of OEA in these patients.Clinical Trial Registration:www.irct.ir, Iranian Registry of Clinical Trials IRCT20090609002017N32