Hiding the complexity: building a distributed ATLAS Tier-2 with a single resource interface using ARC middleware

Since their inception, Grids for high energy physics have found management of data to be the most challenging aspect of operations. This problem has generally been tackled by the experiment's data management framework controlling in fine detail the distribution of data around the grid and the careful brokering of jobs to sites with co-located data. This approach, however, presents experiments with a difficult and complex system to manage as well as introducing a rigidity into the framework which is very far from the original conception of the grid.<p></p> In this paper we describe how the ScotGrid distributed Tier-2, which has sites in Glasgow, Edinburgh and Durham, was presented to ATLAS as a single, unified resource using the ARC middleware stack. In this model the ScotGrid 'data store' is hosted at Glasgow and presented as a single ATLAS storage resource. As jobs are taken from the ATLAS PanDA framework, they are dispatched to the computing cluster with the fastest response time. An ARC compute element at each site then asynchronously stages the data from the data store into a local cache hosted at each site. The job is then launched in the batch system and accesses data locally.<p></p> We discuss the merits of this system compared to other operational models and consider, from the point of view of the resource providers (sites), and from the resource consumers (experiments); and consider issues involved in transitions to this model

A Longitudinal Study of Streptococcus mutans Colonization in Infants after Tooth Eruption

We previously reported that, before tooth eruption, over one-half of infants aged 6 mos were already infected with Streptococcus mutans. The aim of this investigation was to determine the colonization of S. mutans after tooth eruption in the same cohort of 111 infants (35 pre-term, 76 full-term). Our results showed that S. mutans colonization increased with increasing age, so that by 24 mos of age, 84% harbored the bacteria (p 10(5) CFU/mL (p < 0.02). In contrast, non-colonization of S. mutans was associated with toothbrushing (p < 0.03) and multiple courses of antibiotics (p < 0.001). Analysis of our data establishes the timing of S. mutans colonization in children from birth to 24 mos of age

Interpretation of Photoemission Spectra of (TaSe4)2I as Evidence of Charge Density Wave Fluctuations

The competition between different and unusual effects in quasi-one-dimensional conductors makes the direct interpretation of experimental measurements of these materials both difficult and interesting. We consider evidence for the existence of large charge-density-wave fluctuations in the conducting phase of the Peierls insulator (TaSe4)2I, by comparing the predictions of a simple Lee, Rice and Anderson theory for such a system with recent angle-resolved photoemission spectra. The agreement obtained suggests that many of the unusual features of these spectra may be explained in this way. This view of the system is contrasted with the behaviour expected of a Luttinger liquid.Comment: Archive copy of published paper. 19 pages, 12 figures, uses IOP macro

Comparing computer-generated and pathologist-generated tumour segmentations for immunohistochemical scoring of breast tissue microarrays

BACKGROUND: Tissue microarrays (TMAs) have become a valuable resource for biomarker expression in translational research. Immunohistochemical (IHC) assessment of TMAs is the principal method for analysing large numbers of patient samples, but manual IHC assessment of TMAs remains a challenging and laborious task. With advances in image analysis, computer-generated analyses of TMAs have the potential to lessen the burden of expert pathologist review. METHODS: In current commercial software computerised oestrogen receptor (ER) scoring relies on tumour localisation in the form of hand-drawn annotations. In this study, tumour localisation for ER scoring was evaluated comparing computer-generated segmentation masks with those of two specialist breast pathologists. Automatically and manually obtained segmentation masks were used to obtain IHC scores for thirty-two ER-stained invasive breast cancer TMA samples using FDA-approved IHC scoring software. RESULTS: Although pixel-level comparisons showed lower agreement between automated and manual segmentation masks (κ=0.81) than between pathologists' masks (κ=0.91), this had little impact on computed IHC scores (Allred; [Image: see text]=0.91, Quickscore; [Image: see text]=0.92). CONCLUSIONS: The proposed automated system provides consistent measurements thus ensuring standardisation, and shows promise for increasing IHC analysis of nuclear staining in TMAs from large clinical trials

Hole dynamics in noble metals

We present a detailed analysis of hole dynamics in noble metals (Cu and Au), by means of first-principles many-body calculations. While holes in a free-electron gas are known to live shorter than electrons with the same excitation energy, our results indicate that d-holes in noble metals exhibit longer inelastic lifetimes than excited sp-electrons, in agreement with experiment. The density of states available for d-hole decay is larger than that for the decay of excited electrons; however, the small overlap between d- and sp-states below the Fermi level increases the d-hole lifetime. The impact of d-hole dynamics on electron-hole correlation effects, which are of relevance in the analysis of time-resolved two-photon photoemission experiments, is also addressed.Comment: 4 pages, 2 figures, to appear in Phys. Rev. Let

Lifetime of d-holes at Cu surfaces: Theory and experiment

We have investigated the hole dynamics at copper surfaces by high-resolution angle-resolved photoemission experiments and many-body quasiparticle GW calculations. Large deviations from a free-electron-like picture are observed both in the magnitude and the energy dependence of the lifetimes, with a clear indication that holes exhibit longer lifetimes than electrons with the same excitation energy. Our calculations show that the small overlap of d- and sp-states below the Fermi level is responsible for the observed enhancement. Although there is qualitative good agreement of our theoretical predictions and the measured lifetimes, there still exist some discrepancies pointing to the need of a better description of the actual band structure of the solid.Comment: 15 pages, 7 figures, 1 table, to appear in Phys. Rev.

Surface characterization and surface electronic structure of organic quasi-one-dimensional charge transfer salts

We have thoroughly characterized the surfaces of the organic charge-transfer salts TTF-TCNQ and (TMTSF)2PF6 which are generally acknowledged as prototypical examples of one-dimensional conductors. In particular x-ray induced photoemission spectroscopy turns out to be a valuable non-destructive diagnostic tool. We show that the observation of generic one-dimensional signatures in photoemission spectra of the valence band close to the Fermi level can be strongly affected by surface effects. Especially, great care must be exercised taking evidence for an unusual one-dimensional many-body state exclusively from the observation of a pseudogap.Comment: 11 pages, 12 figures, v2: minor changes in text and figure labellin

The effects of chlorhexidine gel on Streptococcus mutans infection in 10-month-old infants: A longitudinal, placebo-controlled, double-blind trial

This study investigated the long-term effects of 0.2% chlorhexidine gel, used as a weekly brush-on gel, on Streptoccocus mutans infection in 10-month-old infants.The investigation followed the criteria of a placebo-controlled, double-blind, longitudinal clinical trial. Infants were recruited at birth and oral microbiological swabs were taken at 3 monthly intervals, together with medical, dental, dietary and brushing histories. Children who were found to be colonized with S. mutans were randomly assigned to either the chlorhexidine-gel group (N = 50) or placebo gel group (N = 46), and parents were instructed to brush the gel on the teeth once per week for 12 weeks. In another control group (N = 210), infants did not use either chlorhexidine or placebo gels. Saliva samples were cultured using S. mutans-selective tryptone-yeast extract-cysteine-sucrose-bacitracin (TYCSB) agar. The mean age of the children was 10.2 +/- 2.6 months at the start of the trial and subjects were followed until the ages of 18 months.In the children with initial low S. mutans counts of < 300 CFU/mL, there was a significant percentage reduction in S. mutans counts in the chlorhexidine-gel group compared to the placebo gel and no-gel control groups after 3 months of weekly gel brushing. However, no significant differences with the placebo group were observed after 15 months of follow-up. There were 39 children (41%) who achieved reduction of their S. mutans to 0 CFU/mL. Compared to those who remained infected with S. mutans, these children had higher toothbrushing frequencies (P < .001) and toothpaste use (P < .001), as well as lower frequencies of daily feeds (P < .01), and lesser weekly frequencies of sweet solids and liquids (P < .001).Children with relatively low initial S. mutans counts (< 300 CFU/mL) showed a reduction in S. mutans counts in the first 3 months when 0.2% chlorhexidine gel was brushed on the teeth weekly. No differences were observed when compared with the placebo and no-treatment groups at later follow-up periods

Identification of Rigosertib for the Treatment of Recessive Dystrophic Epidermolysis Bullosa–Associated Squamous Cell Carcinoma

PURPOSE: Squamous cell carcinoma (SCC) of the skin is the leading cause of death in patients with the severe generalized form of the genetic disease recessive dystrophic epidermolysis bullosa (RDEB). Although emerging data are identifying why patients suffer this fatal complication, therapies for treatment of RDEB SCC are in urgent need. EXPERIMENTAL DESIGN: We previously identified polo-like kinase 1 (PLK1) as a therapeutic target in skin SCC, including RDEB SCC. Here, we undertake a screen of 6 compounds originally designated as PLK1 inhibitors, and detail the efficacy of the lead compound, the multipathway allosteric inhibitor ON-01910, for targeting RDEB SCC in vitro and in vivo. RESULTS: ON-01910 (or rigosertib) exhibited significant specificity for RDEB SCC: in culture rigosertib induced apoptosis in 10 of 10 RDEB SCC keratinocyte populations while only slowing the growth of normal primary skin cells at doses 2 orders of magnitude higher. Furthermore, rigosertib significantly inhibited the growth of two RDEB SCC in murine xenograft studies with no apparent toxicity. Mechanistically, rigosertib has been shown to inhibit multiple signaling pathways. Comparison of PLK1 siRNA with MEK inhibition, AKT inhibition, and the microtubule-disrupting agent vinblastine in RDEB SCC shows that only PLK1 reduction exhibits a similar sensitivity profile to rigosertib. CONCLUSIONS: These data support a “first in RDEB” phase II clinical trial of rigosertib to assess tumor targeting in patients with late stage, metastatic, and/or unresectable SCC