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

In vitro growth characteristics of Fusarium langsethiae isolates recovered from oats and wheat grain in the UK

Fusarium langsethiae is a fungus that has recently been implicated in the contamination of small-grain cereal crops such as oats, wheat and barley with high levels of HT-2 and T-2 toxins in many European countries. The epidemiology of this fungus is not well known and may therefore be a bigger problem than currently thought to be. A study was carried out investigating the in vitro growth characteristics of F. langsethiae isolates from contaminated oats and wheat at various temperatures; 15, 20, 25 and 30 °C. Results indicated similar growth trends of oats and wheat isolates of F. langsethiae. Wheat isolates grew significantly (p<0.001) faster than oat isolates although this difference may have been confounded by the age of cultures, with oat isolates collected one year earlier. The estimated optimum growth temperature for all isolates was 24 °C. Isolates were macro-morphologically categorized as having lobed or entire colony margins, and either possessing one of the following colony colours: white, orange or purple. Since the estimated optimum growth temperature of F. langsethiae is typical in temperate summers when small-grain cereals are flowering, it is possible that this species can infect, colonise and possibly contaminate the developing grains with HT-2 and T-2 toxins which are of food safety concern

Chemical composition and antiglycoxidant activities of French organic propolis extracts

International audienc

Genomic surveillance of 4CMenB vaccine antigenic variants among disease-causing Neisseria meningitidis isolates, United Kingdom, 2010–2016

In September 2015, 4CMenB meningococcal vaccine was introduced into the United Kingdom infant immunization program without phase 3 trial information. Understanding the effect of this program requires enhanced surveillance of invasive meningococcal disease (IMD) Neisseria meningitidis isolates and comparison with prevaccination isolates. Bexsero Antigen Sequence Types (BASTs) were used to analyze whole-genome sequences of 3,073 prevaccine IMD N. meningitidis isolates obtained during 2010−2016. Isolates exhibited 803 BASTs among 31 clonal complexes. Frequencies of antigen peptide variants were factor H binding protein 1, 13.4%; Neisserial heparin-binding antigen 2, 13.8%; Neisseria adhesin A 8, 0.8%; and Porin A-VR2:P1.4,10.9%. In 2015−16, serogroup B isolates showed the highest proportion (35.7%) of exact matches to &#62;1 Bexsero components. Serogroup W isolates showed the highest proportion (93.9%) of putatively cross-reactive variants of Bexsero antigens. Results highlighted the likely role of cross-reactive antigens. BAST surveillance of meningococcal whole-genome sequence data is rapid, scalable, and portable and enables international comparisons of isolates

Polyphenolic content and pharmacological potential of french BFA propolis extracts

Propolis, or bee glue, is a natural resinous hive product collected by honeybees from buds and exudates of various trees and plants. Mixed with beewax and salivary enzymes, it is employed to fill cracks and embalm dead invaders in the hive. Propolis has been used in folk medecine since ancien times due to its pharmacological potential associated with antioxidant, antifungal, antibacterial as well as antitumoral properties. A batch of various French propolis extracts, supplied by “Ballot-Flurin Apiculteurs” (BFA), a company located in the South-West of France and specialized in apitherapy products, was fractionated and analysed by HPLC/MS. Its qualitative chemical composition highlights the presence of polyphenols such as hydroxycinnamic acid derivatives and flavonoids. Total polyphenol content and antioxidant activities were evaluated on six BFA propolis extracts, using respectively Folin-Ciocalteu, DPPH and ORAC assays. Preliminary antifungal (Candida albicans) and antibacterial (Staphylococcus aureus) evaluations will also be given

Chemical composition, antioxidant and anti-AGEs activities of a French propolis

Accumulation in tissues and serum of advanced glycation end-products (AGEs) plays an important role in pathologies such as Alzheimer\u27s disease or, in the event of complications of diabetes, atherosclerosis or renal failure. Therefore there is a potential therapeutic interest in natural antioxidants with true anti-AGEs capabilities for the prevention of this kind of pathologies. The aim of this study was to evaluate the antioxidant and anti-AGEs potential of a French propolis batch (natural resinous substance collected by honeybees from differents plants and trees), then to identify the main compounds responsible for this anti-AGEs effect. For this purpose, the phytochemical composition of a 70% ethanolic extract of propolis (EEP70) was determined, using HPLC/DAD/MS and/or 1H and 13C NMR (1D and 2D) analysis. This study showed the presence of phenolic acids and their esters as well as flavonoids. Then, the evaluation of the antioxidant, using DPPH and ORAC assays, and the anti-AGEs potential, using an automated test recently developed in our laboratory, showed that EEP70 exhibited both high antioxidant (1650 ± 149 µmol TE/g) and anti-AGEs (IC50=0.03 mg/ml) activities. A bio-guided fractionation allowed us to identify the most active anti-AGEs compounds: pinobanksin-3-acetate (IC50=0.06 mM) which is the major compound of EEP70. Thus, EEP70 represents a good candidate as food additive to prevent glycoxidation. Boisard S, Le Ray A-M, Gatto J, Aumond M-C, Blanchard P, Derbré S, Flurin C, Richomme P: Chemical Composition, Antioxidant and Anti-AGEs Activities of a French Poplar Type Propolis. J Agric Food Chem 2014, 62:1344–1351

Studies on the Interactions Between Fungicides, Alternaria tenuissima, Cladosporium herbarum and Microdochium spp., on Fusarium Head Blight (FHB) Development and Deoxynivalenol (DON) Concentration in Grain Caused by Fusarium culmorum

Saprophytic microflora and non-toxin producing Microdochium spp. capable of causing Fusarium head blight (FHB) have been suggested to affect the development of FHB caused by Fusarium spp., the occurrence of mycotoxins and the efficacy of fungicides for the control of the disease. The effects of metconazole and azoxystrobin on the interactions between Fusarium culmorum and Microdochium spp., Alternaria tenuissima or Cladosporium herbarum on FHB symptom development, Tri5 DNA concentration and deoxynivalenol (DON) production were studied under glasshouse conditions. Results indicated that the sequence of infection of wheat heads and the relative timing of fungicide application can significantly affect FHB severity and the resulting mycotoxin contamination of harvested grain. Introduction of A. tenuissima, C. herbarum or Microdochium spp. to wheat heads at GS 57 before inoculation with F. culmorum at GS 65 generally resulted in increased FHB severity, Tri5 DNA and DON concentration in harvested grain. The greatest increases of FHB severity (266%), Tri5 DNA (79%) and DON (152%) were observed when Microdochium spp. were introduced first at GS 57 and F. culmorum inoculation followed at GS 65. Metconazole generally reduced FHB severity, Tri5 DNA and DON concentration in grain but azoxystrobin was most efficient at reducing DNA of Microdochium spp. in grain

Nuclear transparencies in relativistic A(e,e'p) models

Relativistic and unfactorized calculations for the nuclear transparency extracted from exclusive A(e,e'p) reactions for 0.3 \leq Q^2 \leq 10 (GeV/c)^2 are presented for the target nuclei C, Si, Fe and Pb. For Q^2 \geq 0.6 (GeV/c)^2, the transparency results are computed within the framework of the recently developed relativistic multiple-scattering Glauber approximation (RMSGA). The target-mass and Q^2 dependence of the RMSGA predictions are compared with relativistic distorted-wave impulse approximation (RDWIA) calculations. Despite the very different model assumptions underlying the treatment of the final-state interactions in the RMSGA and RDWIA frameworks, they predict comparable nuclear transparencies for kinematic regimes where both models are applicable.Comment: 15 pages, 4 figure

The Swinburne Intermediate Latitude Pulsar Survey

We have conducted a survey of intermediate Galactic latitudes using the 13-beam 21-cm multibeam receiver of the Parkes 64-m radio telescope. The survey covered the region enclosed by 5 deg < |b| < 15 deg and -100 deg < l < 50 deg with 4,702 processed pointings of 265 s each, for a total of 14.5 days of integration time. Thirteen 2x96-channel filterbanks provided 288 MHz of bandwidth at a centre frequency of 1374 MHz, one-bit sampled every 125 microsec and incurring ~DM/13.4 cm^-3 pc samples of dispersion smearing. The system was sensitive to slow and most millisecond pulsars in the region with flux densities greater than approximately 0.3--1.1 mJy. Offline analysis on the 64-node Swinburne workstation cluster resulted in the detection of 170 pulsars of which 69 were new discoveries. Eight of the new pulsars, by virtue of their small spin periods and period derivatives, may be recycled and have been reported elsewhere. The slow pulsars discovered are typical of those already known in the volume searched, being of intermediate to old age. Several pulsars experience pulse nulling and two display very regular drifting sub-pulses. We discuss the new discoveries and provide timing parameters for the 48 slow pulsars for which we have a phase-connnected solution.Comment: 19 pages, 11 figures, accepted to MNRA