Optimised access to user analysis data using the gLite DPM

The ScotGrid distributed Tier-2 now provides more that 4MSI2K and 500TB for LHC computing, which is spread across three sites at Durham, Edinburgh and Glasgow. Tier-2 sites have a dual role to play in the computing models of the LHC VOs. Firstly, their CPU resources are used for the generation of Monte Carlo event data. Secondly, the end user analysis data is distributed across the grid to the site's storage system and held on disk ready for processing by physicists' analysis jobs. In this paper we show how we have designed the ScotGrid storage and data management resources in order to optimise access by physicists to LHC data. Within ScotGrid, all sites use the gLite DPM storage manager middleware. Using the EGEE grid to submit real ATLAS analysis code to process VO data stored on the ScotGrid sites, we present an analysis of the performance of the architecture at one site, and procedures that may be undertaken to improve such. The results will be presented from the point of view of the end user (in terms of number of events processed/second) and from the point of view of the site, which wishes to minimise load and the impact that analysis activity has on other users of the system

Studies of the cholesterol-dependent cytolysins

The cholesterol-dependent cytolyslns (CDCs) are a group of toxins produced by several genera of Gram-positive bacteria, that bind to and form large oligomeric pores in target cell membranes that contain cholesterol. In addition to cell lysis, a great number of other biological functions have been described for many members of the group, including induction of cytokine release and complement activation. Some of the CDCs have been shown to be critical virulence factors of their producing organisms and immunisation with a number of the CDCs has been shown to be protective against disease caused by those producing organisms. The CDCs are also being used in a diverse array of applications that utilise their pore-forming and toxic properties, including anti-cancer therapy, anti-viral therapy and cell biology. Pneumolysin (PLY) is a member of the CDCs produced by S. pneumoniae and is an important virulence factor and vaccine candidate. A deletion mutant of PLY, Delta6PLY, has been described (Kirkham et al., 2006b), and this mutant is capable of cell binding but incapable of pore formation. Enhanced green fluorescent protein (eGFP) tagged forms of PLY and Delta6PLY were produced and the tagged toxins had similar haemolytic and cytotoxic effects to the parent toxins. Toxin binding to host cells was visualised by epifluorescence microscopy and laser scanning confocal fluorescence microscopy. Binding of the tagged toxins to erythrocytes could also be measured by flow cytometry and an increase in the quantity of bound toxin could be detected in a dose-dependent manner over a large range of toxin concentrations. Rod-like structures were observed on membranes treated with Delta6eGFPPLY and these were further studied by SEM. These rod-like structures may be responsible for the strong aggregation effect observed upon Delta6PLY treatment of erythrocytes. Intermedilysin (ILY) is a member of the CDCs produced by S. intermedius. It is unique within the group in that it exhibits human-specific cytolysis and initial studies suggested that this is due to binding of a different cellular receptor to other toxins of the family and that this receptor was a protein (Nagamune et al, 1996). eGFP-tagged forms of ILY and Delta6ILY were produced to allow tracking of the localisation of ILY and for use in development of a quantitative binding assay. It was confirmed that these proteins could be easily visualised by fluorescence microscopy and that binding could be detected by flow cytometry. A two-hybrid screen was also used to screen for proteins from a human brain cDNA library that were capable of interaction with ILY in order to identify candidate protein receptors for ILY, however no likely receptor candidates were identified. In order to determine which region is responsible for the human specificity of intermedilysin, a bank of chimeras between ILY and PLY was created. The chimeric toxins were expressed and purified and the specificity of the mutants was determined by haemolytic assay on human and rabbit erythrocytes. The specificity of the chimeric toxin was determined by the origin of the C-terminal 53/56 residues, indicating that the latter part of domain 4 is responsible for the human specificity of intermedilysin. To further resolve the region involved in human specificity or cholesterol-binding, a series of small substitution mutants was created. These revealed that the promiscuous cell binding activity of the other CDCs was conferred by residues in the undecapeptide loop as this property could be transferred to ILY by introduction of the typical undecapeptide sequence. Surface-plasmon resonance analysis of substitutions of PLY was used to detect any mutants possessing reduced binding affinity. However, problems with aggregation of purified proteins prevented quantitative data from being collected. Anthrolysin O (ALO) is a toxin produced by Bacillus anthracis, the causative agent of anthrax. It is a member of the cholesterol-dependent cytolysin (CDC) group of toxins, many of which are potential vaccine candidates that protect against their producing organisms. Pore formation by ALO was studied by transmission electron microscopy and pores were found to be consistent with those formed by other members of this toxin family. A novel genetic toxoid of anthrolysin O, Delta6mAL0, was constructed and characterised and was able to bind to cells but was incapable of pore- formation or haemolysis. The capacity of the haemolytic and non-haemolytic forms of ALO to protect against challenge with the toxin or B. anthracis was determined. Immunisation with both active and non-haemolytic forms of ALO elicited protection against lethal i.v. challenge with ALO but neither was protective against B. anthracis in a murine i.p. challenge model. Immunisation with another CDC, pneumolysin, did not confer cross-protection against challenge with ALO. Histopathological investigation following lethal i.v. challenge with ALO revealed acute pathology in the lungs with occlusion of alveolar vessels by fibrin deposits

The Abundances Of Neutron-Capture Species In The Very Metal-Poor Globular Cluster M15: A Uniform Analysis Of Red Giant Branch And Red Horizontal Branch Stars

The globular cluster M15 is unique in its display of star-to-star variations in the neutron-capture elements. Comprehensive abundance surveys have been previously conducted for handfuls of M15 red giant branch (RGB) and red horizontal branch (RHB) stars. No attempt has been made to perform a single, self-consistent analysis of these stars, which exhibit a wide range in atmospheric parameters. In the current effort, a new comparative abundance derivation is presented for three RGB and six RHB members of the cluster. The analysis employs an updated version of the line transfer code MOOG, which now appropriately treats coherent, isotropic scattering. The apparent discrepancy in the previously reported values for the metallicity of M15 RGB and RHB stars is addressed and a resolute disparity of Delta(RHB-RGB) approximate to 0.1 dex in the iron abundance was found. The anti-correlative behavior of the light neutron-capture elements (Sr, Y, Zr) is clearly demonstrated with both Ba and Eu, standard markers of the s- and r-process, respectively. No conclusive detection of Pb was made in the RGB targets. Consequently for the M15 cluster, this suggests that the main component of the s-process has made a negligible contribution to those elements normally dominated by this process in solar system material. Additionally for the M15 sample, a large Eu abundance spread is confirmed, which is comparable to that of the halo field at the same metallicity. These abundance results are considered in the discussion of the chemical inhomogeneity and nucleosynthetic history of M15.National Science Foundation AST 07-07447, AST 09-08978Astronom

Landmine Detection System

Solumspect\u27s proposed device is a low-cost ground penetrating radar machine for use as a landmine detector. The device will be a free standing machine that scans a given area and generates a threedimensional map of objects in the ground. The functionality is expected to be comparable to existing machines; however, using off-the-shelf components to build our device will allow it to be priced at a fraction of the cost.&nbsp

Double-negative-2 B cells are the major synovial plasma cell precursor in rheumatoid arthritis

B cells are key pathogenic drivers of chronic inflammation in rheumatoid arthritis (RA). There is limited understanding of the relationship between synovial B cell subsets and pathogenic antibody secreting cells (ASCs). This knowledge is crucial for the development of more targeted B-cell depleting therapies. While CD11c+ double-negative 2 (DN2) B cells have been suggested as an ASC precursor in lupus, to date there is no proven link between the two subsets in RA. We have used both single-cell gene expression and BCR sequencing to study synovial B cells from patients with established RA, in addition to flow cytometry of circulating B cells. To better understand the differentiation patterns within the diseased tissue, a combination of RNA-based trajectory inference and clonal lineage analysis of BCR relationships were used. Both forms of analysis indicated that DN2 B cells serve as a major precursors to synovial ASCs. This study advances our understanding of B cells in RA and reveals the origin of pathogenic ASCs in the RA synovium. Given the significant role of DN2 B cells as a progenitor to pathogenic B cells in RA, it is important to conduct additional research to investigate the origins of DN2 B cells in RA and explore their potential as therapeutic targets in place of the less specific pan-B cells depletion therapies currently in use

Immunological consequences of antihelminthic treatment in preschool children exposed to urogenital schistosome infection

Urogenital schistosomiasis, due to Schistosoma haematobium, is endemic in sub-Saharan Africa. Control is by targeted treatment with praziquantel but preschool age children are excluded from control programs. Immunological studies on the effect of treatment at this young age are scarce. In light of studies in older individuals showing that praziquantel alters antischistosome immune responses and responses to bystander antigens, this study aims to investigate how these responses would be affected by treatment at this young age. Antibody responses directed against schistosome antigens, Plasmodium falciparum crude and recombinant antigens, and the allergen house dust mite were measured in children aged 3 to 5 years before and 6 weeks after treatment. The change in serological recognition of schistosome proteins was also investigated. Treatment augmented antischistosome IgM and IgE responses. The increase in IgE responses directed against adult worm antigens was accompanied by enhanced antigen recognition by sera from the children. Antibody responses directed against Plasmodium antigens were not significantly affected by praziquantel treatment nor were levels of allergen specific responses. Overall, praziquantel treatment enhanced, quantitatively and qualitatively, the antiworm responses associated with protective immunity but did not alter Plasmodium-specific responses or allergen-specific responses which mediate pathology in allergic disease