A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met

Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins

Bacillus subtilis pnpA gene product, polynucleotide phosphorylase (PNPase), is involved in double-strand break (DSB) repair via homologous recombination (HR) or non-homologous end-joining (NHEJ). RecN is among the first responders to localize at the DNA DSBs, with PNPase facilitating the formation of a discrete RecN focus per nucleoid. PNPase, which co-purifies with RecA and RecN, was able to degrade single-stranded (ss) DNA with a 3′ → 5′ polarity in the presence of Mn2+ and low inorganic phosphate (Pi) concentration, or to extend a 3′-OH end in the presence dNDP·Mn2+. Both PNPase activities were observed in evolutionarily distant bacteria (B. subtilis and Escherichia coli), suggesting conserved functions. The activity of PNPase was directed toward ssDNA degradation or polymerization by manipulating the Pi/dNDPs concentrations or the availability of RecA or RecN. In its dATP-bound form, RecN stimulates PNPase-mediated polymerization. ssDNA phosphorolysis catalyzed by PNPase is stimulated by RecA, but inhibited by SsbA. Our findings suggest that (i) the PNPase degradative and polymerizing activities might play a critical role in the transition from DSB sensing to end resection via HR and (ii) by blunting a 3′-tailed duplex DNA, in the absence of HR, B. subtilis PNPase might also contribute to repair via NHEJ

Can antibiotic prescriptions in respiratory tract infections be improved? A cluster-randomized educational intervention in general practice – The Prescription Peer Academic Detailing (Rx-PAD) Study [NCT00272155]

BACKGROUND: More than half of all antibiotic prescriptions in general practice are issued for respiratory tract infections (RTIs), despite convincing evidence that many of these infections are caused by viruses. Frequent misuse of antimicrobial agents is of great global health concern, as we face an emerging worldwide threat of bacterial antibiotic resistance. There is an increasing need to identify determinants and patterns of antibiotic prescribing, in order to identify where clinical practice can be improved. METHODS/DESIGN: Approximately 80 peer continuing medical education (CME) groups in southern Norway will be recruited to a cluster randomized trial. Participating groups will be randomized either to an intervention- or a control group. A multifaceted intervention has been tailored, where key components are educational outreach visits to the CME-groups, work-shops, audit and feedback. Prescription Peer Academic Detailers (Rx-PADs), who are trained GPs, will conduct the educational outreach visits. During these visits, evidence-based recommendations of antibiotic prescriptions for RTIs will be presented and software will be handed out for installation in participants PCs, enabling collection of prescription data. These data will subsequently be linked to corresponding data from the Norwegian Prescription Database (NorPD). Individual feedback reports will be sent all participating GPs during and one year after the intervention. Main outcomes are baseline proportion of inappropriate antibiotic prescriptions for RTIs and change in prescription patterns compared to baseline one year after the initiation of the tailored pedagogic intervention. DISCUSSION: Improvement of prescription patterns in medical practice is a challenging task. A thorough evaluation of guidelines for antibiotic treatment in RTIs may impose important benefits, whereas inappropriate prescribing entails substantial costs, as well as undesirable consequences like development of antibiotic resistance. Our hypothesis is that an educational intervention program will be effective in improving prescription patterns by reducing the total number of antibiotic prescriptions, as well as reducing the amount of broad-spectrum antibiotics, with special emphasis on macrolides

Effectiveness of student response systems in terms of learning environment, attitudes and achievement

In order to investigate the effectiveness of using Student Response Systems (SRS) among grade 7 and 8 science students in New York, the How Do You Feel About This Class? (HDYFATC) questionnaire was administered to 1097 students (532 students did use SRS and 565 students who did not use SRS). Data analyses attested to the sound factorial validity and internal consistency reliability of the HDYFATC, as well as its ability to differentiate between the perceptions of students in different classrooms. Very large differences between users and non-users of SRS, ranging from 1.17 to 2.45 standard deviations for various learning environment scales, attitudes and achievement, supported the efficacy of using SRS

Rates of DNA chain growth in Escherichia coli

The thymidylic acid step-time, σ T, was measured in two strains of Escherichia coli in order to obtain an estimate of the rate of DNA chain growth. ( σ T is defined as the average time required for adding the next deoxyribonucleotide to the end of a nascent DNA chain carrying thymidylic acid at its growing end.) For these measurements E. coli cultures were pulse-labeled with [ 3H]thymidine for 6, 10, 14 and 18 seconds. DNA was extracted from each sample and hydrolyzed enzymically to yield deoxyribonucleoside-3′-monophosphates from interior residues and dexoyribonucleosides from 3′-OH termini. Determination of the radioactivities in thymidine-3′-monophosphate and in thymidine showed that the ratio [ 3H]thymidine [ 3H]thymidine + [ 3H]thymidine-3′-monophosphate decreased continuously during the labeling period. Such a decrease is to be expected if deoxyribonucleoside-5′-phosphates are utilized as precursors of chromosome replication in vivo and if DNA chains grow in the direction 5′ → 3′. These data allowed a calculation of σ T. In E. coli BT − (thymine −) grown at 18.5, 20 and 25 °C in a minimal medium supplemented with glucose and 0.3 to 0.4 μg thymine/ml., σ T was found to be 20 to 23, 13 to 15 and 6 to 9 msec, respectively. The corresponding rates of DNA chain growth were estimated to be 43 to 50, 67 to 77 and 111 to 167 nucleotides per second. In these cultures the turbidity increased exponentially but DNA synthesis was partially inhibited by the low level of thymine in the medium. In E. coli B grown at 20.5 †C in minimal medium supplemented with glucose, turbidity and DNA content both increased exponentially. In this case σ T was found to be 4 to 7 msec and the rate of DNA chain growth was estimated to be 143 to 250 nucleotides per second. This estimate of the rate of chain growth is somewhat slower than the over-all rate of movement of the replication fork which was reckoned to be 300 to 420 nucleotides per second for E. coli B grown at 20.5 °C. It is, however, 11 to 19 times faster than the rate of RNA chain growth