Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

The state of the art in the analysis of two-dimensional gel electrophoresis images

Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field

Use of antibiotics in uncomplicated diverticulitis

The value of antibiotics in the treatment of acute uncomplicated left-sided diverticulitis is not well established. The aim of this review was to assess whether or not antibiotics contribute to the (uneventful) recovery from acute uncomplicated left-sided diverticulitis, and which types of antibiotic and route of administration are most effective. Medline, the Cochrane Library and Embase databases were searched. Randomized controlled trials (RCTs), prospective or retrospective cohort studies addressing conservative treatment of mild uncomplicated left-sided diverticulitis and use of antibiotics were included. No randomized or prospective studies were found on the topic of effect on outcome. One retrospective cohort study was retrieved that compared a group treated with antibiotics with observation alone. This study showed no difference in success rate between groups. Only one RCT of moderate quality compared intravenous and oral administration of antibiotics, and found no differences. One other RCT of very poor quality compared two different kinds of intravenous antibiotic and also found no difference. A small retrospective cohort study comparing antibiotics with and without anaerobe coverage showed no difference in group outcomes. Evidence on the use of antibiotics in mild or uncomplicated diverticulitis is sparse and of low quality. There is no evidence mandating the routine use of antibiotics in uncomplicated diverticulitis, although several guidelines recommend this. Copyright © 2011 British Journal of Surgery Society Ltd. Published by John Wiley & Sons, Lt