Analysis and visualisation of RDF resources in Ondex

An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a distributed knowledge base which has the potential to advance biomedical research [1]. This potential, however, cannot be realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need for tools that provide data reduction, visualization and interactive analysis capabilities.
Ondex is a data integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated with ontologies. This data model conforms to the Semantic Web framework, in particular to RDF, and therefore Ondex is ideally positioned as a platform that can exploit the semantic web. 
The Ondex system offers a range of features and analysis methods of potential value to semantic web users, including:
-	An interactive graph visualization interface (Ondex user client), which provides data reduction and representation methods that leverage the ontological annotation.
-	A suite of importers from a variety of data sources to Ondex (http://ondex.org/formats.html)
-	A collection of plug-ins which implement graph analysis, graph transformation and graph-matching functions.
-	An integration toolkit (Ondex Integrator) which allows users to compose workflows from these modular components
-	In addition, all importers and plug-ins are available as web-services which can be integrated in other tools, as for instance Taverna [3].
The developments that will be presented in this demo have made this functionality interoperable with the Semantic Web framework. In particular we have developed an interactive importer, based on SPARQL that allows the query-driven construction of datasets which brings together information from different RDF data resources into Ondex.
These datasets can then be further refined, analysed and annotated both interactively using the Ondex user client and via user-defined workflows. The results of these analyses can be exported in RDF, which can be used to enrich existent knowledge bases, or to provide application-specific views of the data. Both importer and exporter only focus on a subset of the Ondex and RDF data models, which are shared between these two data representations [4].
In this demo we will show how Ondex can be used to query, analyse and visualize Semantic Web knowledge bases. In particular we will present real use cases focused, but not limited to, resources relevant to plant biology. 
We believe that Ondex can be a valid contribution to the adoption of the Semantic Web in Systems Biology research and in biomedical investigation more generally. We welcome feedback on our current import/export prototype and suggestions for the advancement of Ondex for the Semantic Web.

References

1.	Ruttenberg, A. et. al.: Advancing translational research with the Semantic Web, BMC Bioinformatics, 8 (Suppl. 3): S2 (2007).
2.	Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Ruegg, A., Rawlings, C., Verrier, P., Philippi, S.: Graph-based analysis and visualization of experimental results with Ondex. Bioinformatics 22 (11):1383-1390 (2006).
3.	Rawlings, C.: Semantic Data Integration for Systems Biology Research, Technology Track at ISMB’09, http://www.iscb.org/uploaded/css/36/11846.pdf (2009).
4.	Splendiani, A. et. al.: Ondex semantic definition, (Web document) http://ondex.svn.sourceforge.net/viewvc/ondex/trunk/doc/semantics/ (2009).
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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

Phage display selected magnetite interacting Adhirons for shape controlled nanoparticle synthesis

Adhirons are robust, well expressing, peptide display scaffold proteins, developed as an effective alternative to traditional antibody binding proteins for highly specific molecular recognition applications. This paper reports for the first time the use of these versatile proteins for material binding, and as tools for controlling material synthesis on the nanoscale. A phage library of Adhirons, each displaying two variable binding loops, was screened to identify specific proteins able to interact with [100] faces of cubic magnetite nanoparticles. The selected variable regions display a strong preference for basic residues such as lysine. Molecular dynamics simulations of amino acid adsorption onto a [100] magnetite surface provides a rationale for these interactions, with the lowest adsorption energy observed with lysine. These proteins direct the shape of the forming nanoparticles towards a cubic morphology in room temperature magnetite precipitation reactions, in stark contrast to the high temperature, harsh reaction conditions currently used to produce cubic nanoparticles. These effects demonstrate the utility of the selected Adhirons as novel magnetite mineralization control agents using ambient aqueous conditions. The approach we outline with artificial protein scaffolds has the potential to develop into a toolkit of novel additives for wider nanomaterial fabrication

Near-Infrared Studies of V1280 Sco (Nova Scorpii 2007)

We present spectroscopic and photometric results of Nova V1280 Sco which was discovered in outburst in early 2007 February. The large number of spectra obtained of the object leads to one of the most extensive, near-infrared spectral studies of a classical nova. The spectra evolve from a P-Cygni phase to an emission-line phase and at a later stage is dominated by emission from the dust that formed in this nova. A detailed model is computed to identify and study characteristics of the spectral lines. Inferences from the model address the vexing question of which novae have the ability to form dust. It is demonstrated, and strikingly corroborated with observations, that the presence of lines in the early spectra of low-ionization species like Na and Mg - indicative of low temperature conditions - appear to be reliable indicators that dust will form in the ejecta. It is theoretically expected that mass loss during a nova outburst is a sustained process. Spectroscopic evidence for such a sustained mass loss, obtained by tracing the evolution of a P-Cygni feature in the Brackett gamma line, is presented here allowing a lower limit of 25-27 days to be set for the mass-loss duration. Photometric data recording the nova's extended 12 day climb to peak brightness after discovery is used to establish an early fireball expansion and also show that the ejection began well before maximum brightness. The JHK light curves indicate the nova had a fairly strong second outburst around 100 days after the first.Comment: Accepted in MNRAS. The paper contains 8 figures and 4 tables. Few typographical errors were correcte

Statistical ensembles for money and debt

We build a statistical ensemble representation of two economic models describing respectively, in simplified terms, a payment system and a credit market. To this purpose we adopt the Boltzmann-Gibbs distribution where the role of the Hamiltonian is taken by the total money supply (i.e. including money created from debt) of a set of interacting economic agents. As a result, we can read the main thermodynamic quantities in terms of monetary ones. In particular, we define for the credit market model a work term which is related to the impact of monetary policy on credit creation. Furthermore, with our formalism we recover and extend some results concerning the temperature of an economic system, previously presented in the literature by considering only the monetary base as conserved quantity. Finally, we study the statistical ensemble for the Pareto distribution.Comment: Final version published on Physica A: Statistical Mechanics and its Application

Membrane proteins: always an insoluble problem?

Membrane proteins play crucial roles in cellular processes and are often important pharmacological drug targets. The hydrophobic properties of these proteins make full structural and functional characterization challenging because of the need to use detergents or other solubilizing agents when extracting them from their native lipid membranes. To aid membrane protein research, new methodologies are required to allow these proteins to be expressed and purified cheaply, easily, in high yield and to provide water soluble proteins for subsequent study. This mini review focuses on the relatively new area of water soluble membrane proteins and in particular two innovative approaches: the redesign of membrane proteins to yield water soluble variants and how adding solubilizing fusion proteins can help to overcome these challenges. This review also looks at naturally occurring membrane proteins, which are able to exist as stable, functional, water soluble assemblies with no alteration to their native sequence

Magnetosomes and Magnetosome Mimics: Preparation, Cancer Cell Uptake and Functionalization for Future Cancer Therapies.

Magnetic magnetite nanoparticles (MNP) are heralded as model vehicles for nanomedicine, particularly cancer therapeutics. However, there are many methods of synthesizing different sized and coated MNP, which may affect their performance as nanomedicines. Magnetosomes are naturally occurring, lipid-coated MNP that exhibit exceptional hyperthermic heating, but their properties, cancer cell uptake and toxicity have yet to be compared to other MNP. Magnetosomes can be mimicked by coating MNP in either amphiphilic oleic acid or silica. In this study, magnetosomes are directly compared to control MNP, biomimetic oleic acid and silica coated MNP of varying sizes. MNP are characterized and compared with respect to size, magnetism, and surface properties. Small (8 ± 1.6 nm) and larger (32 ± 9.9 nm) MNP are produced by two different methods and coated with either silica or oleic acid, increasing the size and the size dispersity of the MNP. The coated larger MNP are comparable in size (49 ± 12.5 nm and 61 ± 18.2 nm) to magnetosomes (46 ± 11.8 nm) making good magnetosome mimics. All MNP are assessed and compared for cancer cell uptake in MDA-MB-231 cells and importantly, all are readily taken up with minimal toxic effect. Silica coated MNP show the most uptake with greater than 60% cell uptake at the highest concentration, and magnetosomes showing the least with less than 40% at the highest concentration, while size does not have a significant effect on uptake. Finally, surface functionalization is demonstrated for magnetosomes and silica coated MNP using biotinylation and EDC-NHS, respectively, to conjugate fluorescent probes. The modified particles are visualized in MDA-MB-231 cells and demonstrate how both naturally biosynthesized magnetosomes and biomimetic silica coated MNP can be functionalized and readily up taken by cancer cells for realization as nanomedical vehicles

Myc stimulates B lymphocyte differentiation and amplifies calcium signaling

Deregulated expression of the Myc family of transcription factors (c-, N-, and L-myc) contributes to the development of many cancers by a mechanism believed to involve the stimulation of cell proliferation and inhibition of differentiation. However, using B cell–specific c-/N-myc double-knockout mice and Eμ-myc transgenic mice bred onto genetic backgrounds (recombinase-activating gene 2−/− and Btk−/− Tec−/−) whereby B cell development is arrested, we show that Myc is necessary to stimulate both proliferation and differentiation in primary B cells. Moreover, Myc expression results in sustained increases in intracellular Ca2+ ([Ca2+]i), which is required for Myc to stimulate B cell proliferation and differentiation. The increase in [Ca2+]i correlates with constitutive nuclear factor of activated T cells (NFAT) nuclear translocation, reduced Ca2+ efflux, and decreased expression of the plasma membrane Ca2+–adenosine triphosphatase (PMCA) efflux pump. Our findings demonstrate a revised model whereby Myc promotes both proliferation and differentiation, in part by a remarkable mechanism whereby Myc amplifies Ca2+ signals, thereby enabling the concurrent expression of Myc- and Ca2+-regulated target genes

model predictive control tools for evolutionary plants

The analysis and design of control system configurations for automated production systems is generally a challenging problem, in particular given the increasing number of automation devices and the amount of information to be managed. This problem becomes even more complex when the production system is characterized by a fast evolutionary behaviour in terms of tasks to be executed, production volumes, changing priorities, and available resources. Thus, the control solution needs to be optimized on the basis of key performance indicators like flow production, service level, job tardiness, peak of the absorbed electrical power and the total energy consumed by the plant. This paper proposes a prototype control platform based on Model Predictive Control (MPC) that is able to impress to the production system the desired functional behaviour. The platform is structured according to a two-level control architecture. At the lower layer, distributed MPC algorithms control the pieces of equipment in the production system. At the higher layer an MPC coordinator manages the lower level controllers, by taking full advantage of the most recent advances in hybrid control theory, dynamic programming, mixed‐integer optimization, and game theory. The MPC-based control platform will be presented and then applied to the case of a pilot production plant

The Imprint of Nova Nucleosynthesis in Presolar Grains

Infrared and ultraviolet observations of nova light curves have confirmed grain formation in their expanding shells that are ejected into the interstellar medium by a thermonuclear runaway. In this paper, we present isotopic ratios of intermediate-mass elements up to silicon for the ejecta of CO and ONe novae, based on 20 hydrodynamic models of nova explosions. These theoretical estimates will help to properly identify nova grains in primitive meteorites. In addition, equilibrium condensation calculations are used to predict the types of grains that can be expected in the nova ejecta, providing some hints on the puzzling formation of C-rich dust in O>C environments. These results show that SiC grains can condense in ONe novae, in concert with an inferred (ONe) nova origin for several presolar SiC grains.Comment: 42 pages. Accepted for publication in The Astrophysical Journa