Semantic Web meets Web 2.0 (and vice versa): The Value of the Mundane for the Semantic Web

Web 2.0, not the Semantic Web, has become the face of “the next generation Web” among the tech-literate set, and even among many in the various research communities involved in the Web. Perceptions in these communities of what the Semantic Web is (and who is involved in it) are often misinformed if not misguided. In this paper we identify opportunities for Semantic Web activities to connect with the Web 2.0 community; we explore why this connection is of significant benefit to both groups, and identify how these connections open valuable research opportunities “in the real” for the Semantic Web effort

A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

ApuA, a multifunctional x-glucan-degrading enzyme of Streptococcus suis, mediates adhesion to porcine epithelium and mucus

We have identified apuA in Streptococcus suis, which encodes a bifunctional amylopullulanase with conserved -amylase and pullulanase substrate-binding domains and catalytic motifs. ApuA exhibited properties typical of a Gram-positive surface protein, with a putative signal sequence and LPKTGE cell-wall-anchoring motif. A recombinant protein containing the predicted N-terminal -amylase domain of ApuA was shown to have -(1,4) glycosidic activity. Additionally, an apuA mutant of S. suis lacked the pullulanase -(1,6) glycosidic activity detected in a cell-surface protein extract of wild-type S. suis. ApuA was required for normal growth in complex medium containing pullulan as the major carbon source, suggesting that this enzyme plays a role in nutrient acquisition in vivo via the degradation of glycogen and food-derived starch in the nasopharyngeal and oral cavities. ApuA was shown to promote adhesion to porcine epithelium and mucus in vitro, highlighting a link between carbohydrate utilization and the ability of S. suis to colonize and infect the host

Past, Present And Future Implications Of Human Supervisory Control In Space Missions

Achieving the United States’ Vision for future Space Exploration will necessitate far greater collaboration between humans and automated technology than previous space initiatives. However, the development of methodologies to optimize this collaboration currently lags behind development of the technologies themselves, thus potentially decreasing mission safety, efficiency and probability of success. This paper discusses the human supervisory control (HSC) implications for use in space, and outlines several areas of current automated space technology in which the function allocation between humans and machines/automation is sub-optimal or under dispute, including automated spacecraft landings, Mission Control, and wearable extra-vehicular activity computers. Based on these case studies, we show that a more robust HSC research program will be crucial to achieving the Vision for Space Exploration, especially given the limited resources under which it must be accomplished

Addressing health literacy in patient decision aids

MethodsWe reviewed literature for evidence relevant to these two aims. When high-quality systematic reviews existed, we summarized their evidence. When reviews were unavailable, we conducted our own systematic reviews.ResultsAim 1: In an existing systematic review of PtDA trials, lower health literacy was associated with lower patient health knowledge (14 of 16 eligible studies). Fourteen studies reported practical design strategies to improve knowledge for lower health literacy patients. In our own systematic review, no studies reported on values clarity per se, but in 2 lower health literacy was related to higher decisional uncertainty and regret. Lower health literacy was associated with less desire for involvement in 3 studies, less question-asking in 2, and less patient-centered communication in 4 studies; its effects on other measures of patient involvement were mixed. Only one study assessed the effects of a health literacy intervention on outcomes; it showed that using video to improve the salience of health states reduced decisional uncertainty. Aim 2: In our review of 97 trials, only 3 PtDAs overtly addressed the needs of lower health literacy users. In 90% of trials, user health literacy and readability of the PtDA were not reported. However, increases in knowledge and informed choice were reported in those studies in which health literacy needs were addressed.ConclusionLower health literacy affects key decision-making outcomes, but few existing PtDAs have addressed the needs of lower health literacy users. The specific effects of PtDAs designed to mitigate the influence of low health literacy are unknown. More attention to the needs of patients with lower health literacy is indicated, to ensure that PtDAs are appropriate for lower as well as higher health literacy patients

Quartic Gauge Couplings and the Radiation Zero in pp to l nu gamma gamma events at the LHC

We report a study of the process pp to l nu gamma gamma at CERN's Large Hadron Collider, using a leading order partonic-level event generator interfaced to the Pythia program for showering and hadronisation and a with a generic detector simulation. The process is sensitive to possible anomalous quartic gauge boson couplings of the form W W gamma gamma. It is shown how unitarity-safe limits may be placed on these anomalous couplings by applying a binned maximum likelihood fit to the distribution of the two-photon invariant mass, M(gamma gamma), below a cutoff of 1TeV. Assuming 30fb-1 of integrated luminosity, the expected limits are two orders of magnitude tighter than those available from LEP. It is also demonstrated how the Standard Model radiation zero feature of the qq to W gamma gamma process may be observed in the difference between the two-photon and charged lepton pseudo-rapidities.Comment: 9 pages, 7 figure

The Honey Bee Parasite Nosema ceranae: Transmissible via Food Exchange?

Nosema ceranae, a newly introduced parasite of the honey bee, Apis mellifera, is contributing to worldwide colony losses. Other Nosema species, such as N. apis, tend to be associated with increased defecation and spread via a fecal-oral pathway, but because N. ceranae does not induce defecation, it may instead be spread via an oral-oral pathway. Cages that separated older infected bees from young uninfected bees were used to test whether N. ceranae can be spread during food exchange. When cages were separated by one screen, food could be passed between the older bees and the young bees, but when separated by two screens, food could not be passed between the two cages. Young uninfected bees were also kept isolated in cages, as a solitary control. After 4 days of exposure to the older bees, and 10 days to incubate infections, young bees were more likely to be infected in the 1-Screen Test treatment vs. the 2-Screen Test treatment (P = 0.0097). Young bees fed by older bees showed a 13-fold increase in mean infection level relative to young bees not fed by older bees (1-Screen Test 40.8%; 2-Screen Test 3.4%; Solo Control 2.8%). Although fecal-oral transmission is still possible in this experimental design, oral-oral infectivity could help explain the rapid spread of N. ceranae worldwid

Three point SUSY Ward identities without Ghosts

We utilise a non-local gauge transform which renders the entire action of SUSY QED invariant and respects the SUSY algebra modulo the gauge-fixing condition, to derive two- and three-point ghost-free SUSY Ward identities in SUSY QED. We use the cluster decomposition principle to find the Green's function Ward identities and then takes linear combinations of the latter to derive identities for the proper functions.Comment: 20 pages, no figures, typos correcte