myTea: Connecting the Web to Digital Science on the Desktop

Bioinformaticians regularly access the hundreds of databases and tools that are available to them on the Web. None of these tools communicate with each other, causing the scientist to copy results manually from a Web site into a spreadsheet or word processor. myGrids' Taverna has made it possible to create templates (workflows) that automatically run searches using these databases and tools, cutting down what previously took days of work into hours, and enabling the automated capture of experimental details. What is still missing in the capture process, however, is the details of work done on that material once it moves from the Web to the desktop: if a scientist runs a process on some data, there is nothing to record why that action was taken; it is likewise not easy to publish a record of this process back to the community on the Web. In this paper, we present a novel interaction framework, built on Semantic Web technologies, and grounded in usability design practice, in particular the Making Tea method. Through this work, we introduce a new model of practice designed specifically to (1) support the scientists' interactions with data from the Web to the desktop, (2) provide automatic annotation of process to capture what has previously been lost and (3) associate provenance services automatically with that data in order to enable meaningful interrogation of the process and controlled sharing of the results

First-principles calculations of 2x2 reconstructions of GaN(0001) surfaces involving N, Al, Ga, In, and as atoms

The ab initio studies presented here employed a pseudopotential-plane-wave method in order to obtain the minimum-energy configurations of various 22 GaN0001 surfaces involving N, Al, Ga, In, and As atoms. Comparison of the various possible reconstructions allows predictions to be made regarding the most energetically favorable configurations. Such comparisons depend on the value of the effective chemical potential of each atomic species, which can be related directly to experimental growth conditions. The most stable structure as a function of chemical potentials is determined. Based on these results we have characterized the effect of N in the adlayer surface and the stability dependence with number of substitutions as a function of the model employed and the possible surfactant character of some of the added atoms. Surface phase diagrams as a function of the chemical potential have been calculated to show the phase transition between the different reconstructions

The Trypanosome Rab-Related Proteins RabX1 and RabX2 Play No Role in IntraCellular Trafficking but May Be Involved in Fly Infectivity

BACKGROUND: Rab GTPases constitute the largest subgroup of the Ras superfamily and are primarily involved in vesicle targeting. The full extent of Rab family function is unexplored. Several divergent Rab-like proteins are known but few have been characterized. In Trypanosoma brucei there are sixteen Rab genes, but RabX1, RabX2 and RabX3 are divergent within canonical sequence regions. Where known, trypanosome Rab functions are broadly conserved when orthologous relationships may be robustly established, but specific functions for RabX1, X2 and X3 have yet to be determined. RabX1 and RabX2 originated via tandem duplication and subcellular localization places RabX1 at the endoplasmic reticulum, while RabX2 is at the Golgi complex, suggesting distinct functions. We wished to determine whether RabX1 and RabX2 are involved in vesicle transport or other cellular processes. METHODOLOGY/PRINCIPAL FINDINGS: Using comparative genomics we find that RabX1 and RabX2 are restricted to trypanosomatids. Gene knockout indicates that RabX1 and RabX2 are non-essential. Simultaneous RNAi knockdown of both RabX1 and RabX2, while partial, was also non-lethal and may suggest non-redundant function, consistent with the distinct locations of the proteins. Analysis of the knockout cell lines unexpectedly failed to uncover a defect in exocytosis, endocytosis or in the morphology or location of multiple markers for the endomembrane system, suggesting that neither RabX1 nor RabX2 has a major role in intracellular transport. However, it was apparent that RabX1 and RabX2 knockout cells displayed somewhat enhanced survival within flies. CONCLUSIONS/SIGNIFICANCE: RabX1 and RabX2, two members of the trypanosome Rab subfamily, were shown to have no major detectable role in intracellular transport, despite the localization of each gene product to highly specific endomembrane compartments. These data extend the functional scope of Rab proteins in trypanosomes to include non-canonical roles in differentiation-associated processes in protozoa

Observed photodetachment in parallel electric and magnetic fields

We investigate photodetachment from negative ions in a homogeneous 1.0-T magnetic field and a parallel electric field of approximately 10 V/cm. A theoretical model for detachment in combined fields is presented. Calculations show that a field of 10 V/cm or more should considerably diminish the Landau structure in the detachment cross section. The ions are produced and stored in a Penning ion trap and illuminated by a single-mode dye laser. We present preliminary results for detachment from S- showing qualitative agreement with the model. Future directions of the work are also discussed.Comment: Nine pages, five figures, minor revisions showing final publicatio

Trophic relationships in an intertidal rockpool fish assemblage in the gulf of Cádiz (NE Atlantic)

Many species of littoral fish that live in rocky substrates are syntopic, sharing the same coastal habitat. They have similar feeding behaviours and use small hollows as places to hide and spawn. In the present study, we identified a total of 16 resident fish species in a rockpool assemblage in the Gulf of Cádiz and studied their patterns of co-occurrence. The dietary analysis performed showed the occurrence of 2 mainly herbivorous species (Lipophrys canevae and Parablennius sanguinolentus), 8 mainly carnivorous species with a percentage occurrence of algae in the diet below 10% (Gobius paganellus, Gobius cobitis, Gobius bucchichi, Clinitrachus argentatus, Tripterygion delaisi, Lepadogaster lepadogaster, Lepadogaster purpurea and Lepadogaster candolii), and 6 species that are carnivorous in the earlier phases of their lives and gradually increase the proportion of algae in their diet (Lipophrys pholis, Paralipophrys trigloides, Parablennius incognitus, Salaria pavo, Coryphoblennius galerita and Symphodus roissali). The dietary overlap among the different species does not explain the different patterns of abundance found among co-occurring species. In the present study, the common use of abundant resources coupled with specialized use of other types of resources was observed, and this allows the different species to minimise the effects of possible trophic competition

Efficient Recursion Method for Inverting Overlap Matrix

A new O(N) algorithm based on a recursion method, in which the computational effort is proportional to the number of atoms N, is presented for calculating the inverse of an overlap matrix which is needed in electronic structure calculations with the the non-orthogonal localized basis set. This efficient inverting method can be incorporated in several O(N) methods for diagonalization of a generalized secular equation. By studying convergence properties of the 1-norm of an error matrix for diamond and fcc Al, this method is compared to three other O(N) methods (the divide method, Taylor expansion method, and Hotelling's method) with regard to computational accuracy and efficiency within the density functional theory. The test calculations show that the new method is about one-hundred times faster than the divide method in computational time to achieve the same convergence for both diamond and fcc Al, while the Taylor expansion method and Hotelling's method suffer from numerical instabilities in most cases.Comment: 17 pages and 4 figure

B-cell dysregulation in Crohn's disease is partially restored with infliximab therapy

Background: B-cell depletion can improve a variety of chronic inflammatory diseases, but does not appear beneficial for patients with Crohn's disease. Objective: To elucidate the involvement of B cells in Crohn's disease, we here performed an 'in depth' analysis of intestinal and blood B-cells in this chronic inflammatory disease. Methods: Patients with Crohn's disease were recruited to study B-cell infiltrates in intestinal biopsies (n = 5), serum immunoglobulin levels and the phenotype and molecular characteristics of blood B-cell subsets (n = 21). The effects of infliximab treatment were studied in 9 patients. Results: Granulomatous tissue showed infiltrates of B lymphocytes rather than Ig-secreting plasma cells. Circulating transitional B cells and CD21low B cells were elevated. IgM memory B cells were reduced and natural effector cells showed decreased replication histories and somatic hypermutation (SHM) levels. In contrast, IgG and IgA memory B cells were normally present and their Ig gene transcripts carried increased SHM levels. The numbers of transitional and natural effector cells were normal in patients who responded clinically well to infliximab. Conclusions: B cells in patients with Crohn's disease showed signs of chronic stimulation with localization to granulomatous tissue and increased molecular maturation of IgA and IgG. Therapy with TNFα-blockers restored the defect in IgM memory B-cell generation and normalized transitional B-cell levels, making these subsets candidate markers for treatment monitoring. Together, these results suggest a chronic, aberrant B-cell response in patients with Crohn's disease, which could be targeted with new therapeutics that specifically regulate B-cell function