There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly, the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line discussion forum at http://msi-workgroups.sourceforge.net/ or http://Msiemail@example.com. Further, community input related to this document can also be provided via this electronic forum.
Abstract A non-linear poroelastic finite element model of the lumbar spine was developed to investigate spinal response during daily dynamic physiological activities. Swelling was simulated by imposing a boundary pore pressure of 0.25 MPa at all external surfaces. Partial saturation of the disc was introduced to circumvent the negative pressures otherwise computed upon unloading. The loading conditions represented a pre-conditioning full day followed by another day of loading: 8 h rest under a constant compressive load of 350 N, followed by 16 h loading phase under constant or cyclic compressive load varying in between 1000 and 1600 N. In addition, the effect of one or two short resting periods in the latter loading phase was studied. The model yielded fairly good agreement with in-vivo and in-vitro measurements. Taking the partial saturation of the disc into account, no negative pore pressures were generated during unloading and recovery phase. Recovery phase was faster than the loading period with equilibrium reached in only ∼3 h. With time and during the day, the axial displacement, fluid loss, axial stress and disc radial strain increased whereas the pore pressure and disc collagen fiber strains decreased. The fluid pressurization and collagen fiber stiffening were noticeable early in the morning, which gave way to greater compression stresses and radial strains in the annulus bulk as time went by. The rest periods dampened foregoing differences between the early morning and late in the afternoon periods. The forgoing diurnal variations have profound effects on lumbar spine biomechanics and risk of injury.
Guiyu, China is infamous for its involvement in primitive e-waste processing and recycling activities. Freshwater samples were collected in and outside of Guiyu for dissolved metal analysis. It was found that dissolved metal concentrations were higher in Lianjiang and Nanyang River within Guiyu than the reservoir outside of Guiyu. Lianjiang was enriched with dissolved As, Cr, Li, Mo, Sb and Se, while Nanyang River had elevated dissolved Ag, Be, Cd, Co, Cu, Ni, Pb and Zn. Temporal distributions of the metals suggested recent discharges of metals attributable to a strong acid leaching operation of e-waste, where dissolved Ag, Cd, Cu and Ni (0.344 ± 0.014, 0.547 ± 0.074, 87.6 ± 3.0 and 93.0 ± 1.4 μg/L, respectively) were significantly elevated. Pb isotopic composition of dissolved Pb confirmed that more than one non-indigenous Pb were present in Lianjiang and Nanyang River. In summary, it was evident that the riverine environment of Guiyu was heavily impacted by e-waste related activities. Proliferation of primitive e-waste processing activities significantly elevated levels of dissolved metals in the riverine environment of Guiyu.
We report enzymologic, thermodynamic and structural analyses of a series of six clinically derived mutant HIV proteases (PR) resistant to darunavir. We show that even very dramatic changes in PR sequence leading to the loss of hydrogen bonds with the inhibitor could be partially compensated by the entropy contribution due to burial of larger nonpolar surface area of the protein.
Highlights ► In florid stage significantly impaired sagittal plane kinematics on involved and non-involved side. ► Significantly reduced power generation and absorption mainly at the level of involved hip. ► In final stage impaired global hip function in 46, 2% of patients.
A detailed investigation was conducted to understand the contamination characteristics of a selected set of potentially toxic metals in Shanghai. The amount of Pb, Zn, Cu, Cr, Cd and Ni were determined from 273 soil/dust samples collected within urban area. The results indicated that concentration of all metals except Ni in soils was significant, and metal pollution was even severer in roadside dust. A series of metal spatial distribution maps were created through geostatistical analysis, and the pollution hotspots tended to associate with city core area, major road junctions, and the regions close to industrial zones. In attempt of identifying the source of metals through geostatistical and multivariate statistical analyses, it was concluded as follows: Pb, Zn and Cu mainly originated from traffic contaminants; soil Ni was associated with natural concentration; Cd largely came from point-sourced industrial pollution; and Cr, Ni in dust were mainly related to atmospheric deposition. Human activities have led to high accumulation of potentially toxic metals in urban soils and roadside dust of Shanghai.
First released in 2009, MetaboAnalyst (www.metaboanalyst.ca) was a relatively simple web server designed to facilitate metabolomic data processing and statistical analysis. With continuing advances in metabolomics along with constant user feedback, it became clear that a substantial upgrade to the original server was necessary. MetaboAnalyst 2.0, which is the successor to MetaboAnalyst, represents just such an upgrade. MetaboAnalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization. It also supports multi-group data analysis, two-factor analysis as well as time-series data analysis. These new functions have also been supplemented with: (i) a quality-control module that allows users to evaluate their data quality before conducting any analysis, (ii) a functional enrichment analysis module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis and visualization for 15 different model organisms. In developing MetaboAnalyst 2.0 we have also substantially improved its graphical presentation tools. All images are now generated using anti-aliasing and are available over a range of resolutions, sizes and formats (PNG, TIFF, PDF, PostScript, or SVG). To improve its performance, MetaboAnalyst 2.0 is now hosted on a much more powerful server with substantially modified code to take advantage the server's multi-core CPUs for computationally intensive tasks. MetaboAnalyst 2.0 also maintains a collection of 50 or more FAQs and more than a dozen tutorials compiled from user queries and requests. A downloadable version of MetaboAnalyst 2.0, along detailed instructions for local installation is now available as well.
MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which similar to 300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (similar to 50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta) genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.