'Datafication': Making sense of (big) data in a complex world

This is a pre-print of an article published in European Journal of Information Systems. The definitive publisher-authenticated version is available at the link below. Copyright @ 2013 Operational Research Society Ltd.No abstract available (Editorial

Gbrowse Moby: a Web-based browser for BioMoby Services

BACKGROUND: The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client – Gbrowse Moby – that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. RESULTS: Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. CONCLUSION: Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment

The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 angstrom resolution

Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7 angstrom and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3'-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites

Public-private health sector partnerships for STD control in South Africa perspectives from the Hlabisa experience

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A Dynamical Fossil in the Ursa Minor Dwarf Spheroidal Galaxy

The nearby Ursa Minor dwarf spheroidal (UMi dSph) is one of the most dark matter dominated galaxies known, with a central mass to light ratio roughly equal to 70. Somewhat anomalously, it appears to contain morphological substructure in the form of a second peak in the stellar number density. It is often argued that this substructure must be transient because it could not survive for the > 10 Gyr age of the system, given the crossing time implied by UMi's 8.8 km/s internal velocity dispersion. In this paper, however, we present evidence that the substructure has a cold kinematical signature, and argue that UMi's clumpiness could indeed be a primordial artefact. Using numerical simulations, we demonstrate that substructure is incompatible with the cusped dark matter haloes predicted by the prevailing Cold Dark Matter (CDM) paradigm, but is consistent with an unbound stellar cluster sloshing back and forth within the nearly harmonic potential of a cored dark matter halo. Thus CDM appears to disagree with observation at the least massive, most dark matter dominated end of the galaxy mass spectrum.Comment: Astrophysical Journal (Letters), in pres

Dynamical Mass Estimates for the Halo of M31 from Keck Spectroscopy

The last few months have seen the measurements of the radial velocities of all of the dwarf spheroidal companions to the Andromeda galaxy (M31) using the spectrographs (HIRES and LRIS) on the Keck Telescope. This paper summarises the data on the radial velocities and distances for all the companion galaxies and presents new dynamical modelling to estimate the mass of extended halo of M31. The best fit values for the total mass of M31 are between 7 and 10 x 10^{11} solar masses, depending on the details of the modelling. The mass estimate is accompanied by considerable uncertainty caused by the smallness of the dataset; for example, the upper bound on the total mass is roughly 24 x 10^{11} solar masses, while the lower bound is about 3 x 10^{11} solar masses. These values are less than the most recent estimates of the most likely mass of the Milky Way halo. Bearing in mind all the uncertainties, a fair conclusion is that the M31 halo is roughly as massive as that of the Milky Way halo. There is no dynamical evidence for the widely held belief that M31 is more massive -- it may even be less massive.Comment: In press, The Astrophysical Journal (Letters

Time-resolved multi-mass ion imaging: femtosecond UV-VUV pump-probe spectroscopy with the PImMS camera

The Pixel-Imaging Mass Spectrometry (PImMS) camera allows for 3D charged particle imaging measurements, in which the particle time-of-flight is recorded along with $(x,y)$ position. Coupling the PImMS camera to an ultrafast pump-probe velocity-map imaging spectroscopy apparatus therefore provides a route to time-resolved multi-mass ion imaging, with both high count rates and large dynamic range, thus allowing for rapid measurements of complex photofragmentation dynamics. Furthermore, the use of vacuum ultraviolet wavelengths for the probe pulse allows for an enhanced observation window for the study of excited state molecular dynamics in small polyatomic molecules having relatively high ionization potentials. Herein, preliminary time-resolved multi-mass imaging results from C$_2$F$_3$I photolysis are presented. The experiments utilized femtosecond UV and VUV (160.8~nm and 267~nm) pump and probe laser pulses in order to demonstrate and explore this new time-resolved experimental ion imaging configuration. The data indicates the depth and power of this measurement modality, with a range of photofragments readily observed, and many indications of complex underlying wavepacket dynamics on the excited state(s) prepared

Strömgren uvby photometry of the peculiar globular cluster NGC 2419

NGC 2419 is a peculiar Galactic globular cluster offset from the others in the size-luminosity diagram, and showing several chemical abundance anomalies. Here, we present Strömgren uvby photometry of the cluster. Using the gravity- and metallicity-sensitive c1 and m1 indices, we identify a sample of likely cluster members extending well beyond the formal tidal radius. The estimated contamination by cluster non-members is only one per cent, making our catalogue ideally suited for spectroscopic follow-up. We derive photometric [Fe/H] of red giants, and depending on which metallicity calibration from the literature we use, we find reasonable to excellent agreement with spectroscopic [Fe/H], both for the cluster mean metallicity and for individual stars. We demonstrate explicitly that the photometric uncertainties are not Gaussian and this must be accounted for in any analysis of the metallicity distribution function. Using a realistic, non-Gaussian model for the photometric uncertainties, we find a formal internal [Fe/H] spread of σ=0.11+0.02-0.01 dex. This is an upper limit to the cluster’s true [Fe/H] spread and may partially, and possibly entirely, reflect the limited precision of the photometric metallicity estimation and systematic effects. The lack of correlation between spectroscopic and photometric [Fe/H] of individual stars is further evidence against a [Fe/H] spread on the 0.1 dex level. Finally, the CN-sensitive δ4, among other colour indices, anti-correlates strongly with magnesium abundance, indicating that the second-generation stars are nitrogen enriched. The absence of similar correlations in some other CN-sensitive indices supports the second generation being enriched in He, which in these indices approximately compensates the shift due to CN. Compared to a single continuous distribution with finite dispersion, the observed δ4 distribution of red giants is slightly better fit by two distinct populations with no internal spread, with the nitrogen-enhanced second generation accounting for 53 ± 5 per cent of stars. Despite its known peculiarities, NGC 2419 appears to be very similar to other metal-poor Galactic globular clusters with a similarly nitrogen-enhanced second generation and little or no variation in [Fe/H], which sets it apart from other suspected accreted nuclei such as ωCen

Effect of Time of Access to Pasture and the Provision of a Total Mixed Ration on the Performance and Methane Production of High Yielding Dairy Cows

Allowing cows to spend time on pasture may improve their welfare, although high yielding cows are unable to consume sufficient amounts of grass to maintain milk yield and require supplementation (Charlton et al. 2011). The inclusion of grass in the diet of high yielding cows may have benefits as grass contains polyunsaturated fatty acids which can reduce methane production (Martin et al. 2008). Additionally, the soluble carbohydrate content in grass is higher in the afternoon which may increase intake (Trevaskis et al. 2004). The aim of the experiment was to determine the effects of timing of pasture access and the provision of access to total mixed ration (TMR) when at grass on the performance and methane production of high yielding dairy cows