LIPID MAPS online tools for lipid research

The LIPID MAPS consortium has developed a number of online tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry (MS) data. A simple online interface has been developed to enable an end-user to rapidly generate a variety of lipid chemical structures, along with corresponding systematic names and ontological information. The structure-drawing tools are available for six categories of lipids: (i) fatty acyls, (ii) glycerolipids, (iii) glycerophospholipids, (iv) cardiolipins, (v) sphingolipids and (vi) sterols. Within each category, the structure-drawing tools support the specification of various parameters such as chain lengths at a specific sn position, head groups, double bond positions and stereochemistry to generate a specific lipid structure. The structure-drawing tools have also been integrated with a second set of online tools which predict possible lipid structures from precursor-ion and product-ion MS experimental data. The MS prediction tools are available for three categories of lipids: (i) mono/di/triacylglycerols, (ii) glycerophospholipids and (iii) cardiolipins. The LIPID MAPS online tools are publicly available at www.lipidmaps.org/tools/

Gradual distraction for treatment of severe knee flexion contractures using the Ilizarov’s apparatus

Background: Knee flexion contractures result in a significant amount of functional disability due to reduced mobility and limb length discrepancy. Treatment options include non-surgical methods like serial casting, dynamic splinting and traction or surgical methods like osteotomies and soft tissue procedures. External fixation has emerged as a highly successful means of achieving controlled gradual correction of joint contractures with low rates of complications including recurrence. The aim of this study is to evaluate the functional outcome in terms of residual deformity and change in ambulatory status following correction using the Ilizarov’s apparatus.Methods: 12 patients with knee flexion contractures ranging from 20°-70° underwent correction using the Ilizarov’s external fixator (IEF). The use of simple mathematic formulae enabled us to calculate and estimate the rate and duration of distraction. End results were assessed at one year by the residual contracture as: Excellent: 0-5°, Good: 6-15°, Fair: 16-30° and Poor: >30°.Results: The functional assessment was graded as excellent in 7, good in 4 and fair in 1 out of 12 patients. All patients were independent ambulators and only 1 out of 12 patients required an additional orthosis for maintenance of the correction.Conclusions: The IEF is a safe and precise modality even for the most complex contractures of the knee. Accurate placement of the hinges along the center of rotation of the knee avoids undue subluxation of the tibia during correction. In order to ensure a low rate of complications, it is imperative to have a detailed pre-operative plan and all principles of fixation should be meticulously adhered to.

A comparative study of functional outcome of external fixation and volar plating in unstable distal radius fractures

Background: Distal radius fractures are amongst the most common injuries seen in the emergency department. It is imperative to restore the anatomy as much as possible in order to restore wrist function. Identifying a fracture as ‘unstable’ is critical in predicting the final outcome of treatment. The present study compares two primary modalities of treatment: external fixation and volar plating in terms of the functional outcome post-surgery.  Aim of the study was to compare the functional outcome of fixation of unstable distal radius fractures by external fixation to that of volar plating by the Disabilities of the Arm, Shoulder and Hand (DASH) scoring system and analysis of recovery of grip strength and range of motion. Settings and design: Hospital-based; randomized control trial.Methods: 80 patients presenting with unstable distal radius fractures were randomized into two groups of 40 each. One group received external fixation and the second received open reduction with volar plate fixation as the primary intervention. DASH scores were obtained and compared at specified time intervals following surgery.Results: The results of our study show a better improvement in the mean DASH scores at 3, 6 and 12 months in the volar plating group as compared to the external fixation group.Conclusions: Volar plating, with its definitive advantage of direct fracture visualization, has an overall better functional outcome with greater postoperative wrist motion and a lower incidence of complications.

Metabolomics Workbench: An International Repository for Metabolomics Data and Metadata, Metabolite Standards, Protocols, Tutorials and Training, and Analysis Tools

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund\u27s Metabolomics Program, provides data from the Common Fund\u27s Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world

LMSD: LIPID MAPS structure database

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available a

Discovering and linking public omics data sets using the Omics Discovery Index.

Biomedical data are being produced at an unprecedented rate owing to the falling cost of experiments and wider access to genomics, transcriptomics, proteomics and metabolomics platforms1, 2. As a result, public deposition of omics data is on the increase. This presents new challenges, including finding ways to store, organize and access different types of biomedical data stored on different platforms. Here, we present the Omics Discovery Index (OmicsDI; http://www.omicsdi.org), an open-source platform that enables access, discovery and dissemination of omics data sets

MayaChemTools: An Open Source Package for Computational Drug Discovery

MayaChemTools is a growing collection of Perl scripts, modules, and classes to support a variety of computational drug discovery needs, such as manipulation and analysis of data, generation of two-dimensional (2D) fingerprints, similarity searching, and calculation of physicochemical properties. MayaChemTools provides command line scripts for the following tasks: manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files; calculation of a key set of physicochemical properties, such as molecular weight, hydrogen bond donors and acceptors, logP, and topological polar surface area; generation of 2D fingerprints corresponding to atom neighborhoods, atom types, E-state indices, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets; similarity searching and calculation of similarity matrices using available 2D fingerprints; listing properties of elements in the periodic table, amino acids, and nucleic acids; and exporting data from relational databases. An extensive set of modules and classes are also available for custom development. MayaChemTools is freely available online at www.MayaChemTools.org, under the terms of the GNU LGPL, as published by the Free Software Foundation