Future socioeconomic changes

Development of socio-economic scenarios and translating them into suitable storylines and provide an overview of potential data to be used for a quantification of future disease vulnerabilitie

Evaluation of the ALMA Prototype Antennas

The ALMA North American and European prototype antennas have been evaluated by a variety of measurement systems to quantify the major performance specifications. Nearfield holography was used to set the reflector surfaces to 17 microns RMS. Pointing and fast switching performance was determined with an optical telescope and by millimeter wavelength radiometry, yielding 2 arcsec absolute and 0.6 arcsec offset pointing accuracies. Path length stability was measured to be less than or approximately equal to 20 microns over 10 minute time periods using optical measurement devices. Dynamical performance was studied with a set of accelerometers, providing data on wind induced tracking errors and structural deformation. Considering all measurements made during this evaluation, both prototype antennas meet the major ALMA antenna performance specifications.Comment: 83 pages, 36 figures, AASTex format, to appear in PASP September 2006 issu

An Experimental Investigation Into the Performance of a Flush Water-Jet Inlet

An experimental investigation of the flow within a generic flush type water-jet inlet has been carried out to identify the principal flow features and provide a basis for development of computational fluid dynamics (CFD) models. Tests were performed in a cavitation tunnel with the model inlet fitted to the test section ceiling, and effects of thickening the ingested tunnel wall boundary layer were investigated. The model was fitted with a range of instrumentation to investigate the ramp pressure distribution and boundary layer development, lip incidence, and pump face flow properties. Observations of lip and duct cavitation inception and behavior were also made. The results showed the inlet performance to be generally improved with the ingestion of a thicker boundary layer. The thickened boundary layer significantly reduced ramp boundary layer separation and distortion of flow at the notional pump face. However, a greater range of lip incidence occurred with the thickened boundary layer with consequent greater likelihood of lip separation and cavitation occurrence. Ideal lip incidence and pump face flow uniformity occurred at flow parameters significantly different from those for ideal pump face pressure recovery. Large developed cavities on the inlet lip were observed for a range of conditions typical of conventional high-speed vessel operation

Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1

Polycomb group proteins, as part of the Polycomb repressive complexes, are essential in gene repression through chromatin compaction by canonical PRC1, mono-ubiquitylation of histone H2A by non-canonical PRC1 and tri-methylation of histone H3K27 by PRC2. Despite prevalent models emphasizing tight functional coupling between PRC1 and PRC2, it remains unclear whether this paradigm indeed reflects the evolution and functioning of these complexes. Here, we conduct a comprehensive analysis of the presence or absence of cPRC1, nPRC1 and PRC2 across the entire eukaryotic tree of life, and find that both complexes were present in the Last Eukaryotic Common Ancestor (LECA). Strikingly, ~42% of organisms contain only PRC1 or PRC2, showing that their evolution since LECA is largely uncoupled. The identification of ncPRC1-defining subunits in unicellular relatives of animals and fungi suggests ncPRC1 originated before cPRC1, and we propose a scenario for the evolution of cPRC1 from ncPRC1. Together, our results suggest that crosstalk between these complexes is a secondary development in evolution

Toward automatic reconstruction of a highly resolved tree of life

Contains fulltext : 51078.pdf (publisher's version ) (Closed access)We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor

STRING: known and predicted protein–protein associations, integrated and transferred across organisms

A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical binding, but can also mean indirect interaction such as participation in the same metabolic pathway or cellular process. Currently, information about protein association is scattered over a wide variety of resources and model organisms. STRING aims to simplify access to this information by providing a comprehensive, yet quality-controlled collection of protein–protein associations for a large number of organisms. The associations are derived from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic context analysis. STRING integrates and ranks these associations by benchmarking them against a common reference set, and presents evidence in a consistent and intuitive web interface. Importantly, the associations are extended beyond the organism in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms, where applicable. STRING currently holds 730 000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells

10.1371/journal.pone.0017538PLoS ONE63

Cure of Helicobacter pylori infection in patients with reflux oesophagitis treated with long term omeprazole reverses gastritis without exacerbation of reflux disease: results of a randomised controlled trial

BACKGROUND: Helicobacter pylori gastritis may progress to glandular atrophy and intestinal metaplasia, conditions that predispose to gastric cancer. Profound suppression of gastric acid is associated with increased severity of H pylori gastritis. This prospective randomised study aimed to investigate whether H pylori eradication can influence gastritis and its sequelae during long term omeprazole therapy for gastro-oesophageal reflux disease (GORD). METHODS: A total of 231 H pylori positive GORD patients who had been treated for > or =12 months with omeprazole maintenance therapy (OM) were randomised to either continuation of OM (OM only; n = 120) or OM plus a one week course of omeprazole, amoxycillin, and clarithromycin (OM triple; n = 111). Endoscopy with standardised biopsy sampling as well as symptom evaluation were performed at baseline and after one and two years. Gastritis was assessed according to the Sydney classification system for activity, inflammation, atrophy, intestinal metaplasia, and H pylori density. RESULTS: Corpus gastritis activity at entry was moderate or severe in 50% and 55% of the OM only and OM triple groups, respectively. In the OM triple group, H pylori was eradicated in 90 (88%) patients, and activity and inflammation decreased substantially in both the antrum and corpus (p<0.001, baseline v two years). Atrophic gastritis also improved in the corpus (p<0.001) but not in the antrum. In the 83 OM only patients with continuing infection, there was no change in antral and corpus gastritis activity or atrophy, but inflammation increased (p<0.01). H pylori eradication did not alter the dose of omeprazole required, or reflux symptoms. CONCLUSIONS: Most H pylori positive GORD patients have a corpus predominant pangastritis during omeprazole maintenance therapy. Eradication of H pylori eliminates gastric mucosal inflammation and induces regression of corpus glandular atrophy. H pylori eradication did not worsen reflux disease or lead to a need for increased omeprazole maintenance dose. We therefore recommend eradication of H pylori in GORD patients receiving long term acid suppression

Transmembrane Protein Oxygen Content and Compartmentalization of Cells

Recently, there was a report that explored the oxygen content of transmembrane proteins over macroevolutionary time scales where the authors observed a correlation between the geological time of appearance of compartmentalized cells with atmospheric oxygen concentration. The authors predicted, characterized and correlated the differences in the structure and composition of transmembrane proteins from the three kingdoms of life with atmospheric oxygen concentrations in geological timescale. They hypothesized that transmembrane proteins in ancient taxa were selectively excluding oxygen and as this constraint relaxed over time with increase in the levels of atmospheric oxygen the size and number of communication-related transmembrane proteins increased. In summary, they concluded that compartmentalized and non-compartmentalized cells can be distinguished by how oxygen is partitioned at the proteome level. They derived this conclusion from an analysis of 19 taxa. We extended their analysis on a larger sample of taxa comprising 309 eubacterial, 34 archaeal, and 30 eukaryotic complete proteomes and observed that one can not absolutely separate the two groups of cells based on partition of oxygen in their membrane proteins. In addition, the origin of compartmentalized cells is likely to have been driven by an innovation than happened 2700 million years ago in the membrane composition of cells that led to the evolution of endocytosis and exocytosis rather than due to the rise in concentration of atmospheric oxygen