Single event upset studies for the ATLAS SCT and pixel optical links

Optical data transmission has been chosen for the ATLAS Pixel and SemiConductor Tracker to deliver both timing and control information to the detector modules and transmit tracking data to the remote computer room. Radiation hardness of individuals optical components and their ASICs drivers have been reported in previous papers. We will report here the Single Event Upset studies carried out on a customised optopackage using a high-energy pion beam. It will be shown that the system is sufficiently robust to SEU at the ATLAS SCT level

Transgenic avidin maize is resistant to storage insect pests

Avidin is a glycoprotein found in chicken egg white, that sequesters the vitamin biotin. Here we show that when present in maize at levels of ≥100 p.p.m., avidin is toxic to and prevents development of insects that damage grains during storage. Insect toxicity is caused by a biotin deficiency, as shown by prevention of toxicity with biotin supplementation. The avidin maize is not, however, toxic to mice when administered as the sole component of their diet for 21 days. These data suggest that avidin expression in food or feed grain crops can be used as a biopesticide against a spectrum of stored-product insect pests

Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?

<p>Abstract</p> <p>Background</p> <p>In ribonucleic acid (RNA) molecules whose function depends on their final, folded three-dimensional shape (such as those in ribosomes or spliceosome complexes), the secondary structure, defined by the set of internal basepair interactions, is more consistently conserved than the primary structure, defined by the sequence of nucleotides.</p> <p>Results</p> <p>The research presented here investigates the possibility of applying a progressive, pairwise approach to the alignment of multiple RNA sequences by simultaneously predicting an energy-optimized consensus secondary structure. We take an existing algorithm for finding the secondary structure common to two RNA sequences, Dynalign, and alter it to align profiles of multiple sequences. We then explore the relative successes of different approaches to designing the tree that will guide progressive alignments of sequence profiles to create a multiple alignment and prediction of conserved structure.</p> <p>Conclusion</p> <p>We have found that applying a progressive, pairwise approach to the alignment of multiple ribonucleic acid sequences produces highly reliable predictions of conserved basepairs, and we have shown how these predictions can be used as constraints to improve the results of a single-sequence structure prediction algorithm. However, we have also discovered that the amount of detail included in a consensus structure prediction is highly dependent on the order in which sequences are added to the alignment (the guide tree), and that if a consensus structure does not have sufficient detail, it is less likely to provide useful constraints for the single-sequence method.</p

HerMES: SPIRE Science Demonstration Phase maps

We describe the production and verification of sky maps of the five Spectral and Photometric Imaging Receiver (SPIRE) fields observed as part of the Herschel Multi-tiered Extragalactic Survey (HerMES) during the Science Demonstration Phase (SDP) of the Herschel mission. We have implemented an iterative map-making algorithm [The SPIRE-HerMES Iterative Mapper (SHIM)] to produce high fidelity maps that preserve extended diffuse emission on the sky while exploiting the repeated observations of the same region of the sky with many detectors in multiple scan directions to minimize residual instrument noise. We specify here the SHIM algorithm and outline the various tests that were performed to determine and characterize the quality of the maps and verify that the astrometry, point source flux and power on all relevant angular scales meet the needs of the HerMES science goals. These include multiple jackknife tests, determination of the map transfer function and detailed examination of the power spectra of both sky and jackknife maps. The map transfer function is approximately unity on scales from 1 arcmin to 1°. Final maps (v1.0), including multiple jackknives, as well as the SHIM pipeline, have been used by the HerMES team for the production of SDP papers

A phase II study of mitomycin C, cisplatin and continuous infusion 5-fluorouracil (MCF) in the treatment of patients with carcinoma of unknown primary site

Carcinoma of unknown primary site remains a common clinical diagnosis, accounting for between 5 and 10% of all cancer patients. Numerous combination chemotherapy regimens have been used in the management of carcinoma of unknown primary site, resulting in response rates of 0–48%. We present the results of a single centre phase II study of the use of the combination of mitomycin C (7 mg m−2 on day 1 of cycles 1, 3 and 5) cisplatin (60 mg m−2 on day 1) and continuous infusion 5-fluorouracil (300 mg m−2 daily), MCF, delivered as a 21-day cycle, in patients with carcinoma of unknown primary site. Thirty-one patients with a diagnosis of carcinoma of unknown primary site were treated in Aberdeen Royal Infirmary between 1997 and 2001 with MCF. In total, 136 cycles of MCF were delivered (median of 5 cycles per patient). Toxicity was acceptable, with 19% grade 3 or 4 neutropenia, 16% grade 3 or 4 thrombocytopenia and 13% grade 3 or 4 nausea and vomiting. No cases of neutropenic sepsis were seen and there were no treatment-related deaths, however, six patients developed thrombotic complications. The overall response rate was 27% (CR 3%; PR 23%). Median time to progression was 3.4 months (95% CI 1.1–5.6 months) and median overall survival was 7.7 months (95% CI 5.7–9.8 months). Survival at 1 year was 28%, and at 2 years, 10%. MCF is a tolerable regimen with comparable toxicity, response rates and survival data to most platinum-based combination chemotherapy regimens in use for this devastating disease

MSDmotif: exploring protein sites and motifs

<p>Abstract</p> <p>Background</p> <p>Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB) is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure.</p> <p>Results</p> <p>We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS) protocol. An additional entry point facilitates XML requests with XML responses.</p> <p>Conclusion</p> <p>MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.</p

Deep-Inelastic Inclusive ep Scattering at Low x and a Determination of alpha_s

A precise measurement of the inclusive deep-inelastic e^+p scattering cross section is reported in the kinematic range 1.5<= Q^2 <=150 GeV^2 and 3*10^(-5)<= x <=0.2. The data were recorded with the H1 detector at HERA in 1996 and 1997, and correspond to an integrated luminosity of 20 pb^(-1). The double differential cross section, from which the proton structure function F_2(x,Q^2) and the longitudinal structure function F_L(x,Q^2) are extracted, is measured with typically 1% statistical and 3% systematic uncertainties. The measured partial derivative (dF_2(x,Q^2)/dln Q^2)_x is observed to rise continuously towards small x for fixed Q^2. The cross section data are combined with published H1 measurements at high Q^2 for a next-to-leading order DGLAP QCD analysis.The H1 data determine the gluon momentum distribution in the range 3*10^(-4)<= x <=0.1 to within an experimental accuracy of about 3% for Q^2 =20 GeV^2. A fit of the H1 measurements and the mu p data of the BCDMS collaboration allows the strong coupling constant alpha_s and the gluon distribution to be simultaneously determined. A value of alpha _s(M_Z^2)=0.1150+-0.0017 (exp) +0.0009-0.0005 (model) is obtained in NLO, with an additional theoretical uncertainty of about +-0.005, mainly due to the uncertainty of the renormalisation scale.Comment: 68 pages, 24 figures and 18 table

Echinacea purpurea and osteopathic manipulative treatment in children with recurrent otitis media: a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Recurrent otitis media is a common problem in young children. Echinacea and osteopathic manipulative treatment have been proposed as preventive measures, but have been inadequately studied. This study was designed to assess the efficacy of <it>Echinacea purpurea </it>and/or osteopathic manipulative treatment (OMT) for prevention of acute otitis media in otitis-prone children.</p> <p>Methods</p> <p>A randomized, placebo-controlled, two-by-two factorial trial with 6-month follow-up, conducted 1999 – 2002 in Tucson, Arizona. Patients were aged 12–60 months with recurrent otitis media, defined as three or more separate episodes of acute otitis media within six months, or at least four episodes in one year. Ninety children (44% white non-Hispanic, 39% Hispanic, 57% male) were enrolled, of which 84 had follow-up for at least 3 months. Children were randomly assigned to one of four protocol groups: double placebo, echinacea plus sham OMT, true OMT (including cranial manipulation) plus placebo echinacea, or true echinacea plus OMT. An alcohol extract of <it>Echinacea purpurea </it>roots and seeds (or placebo) was administered for 10 days at the first sign of each common cold. Five OMT visits (or sham treatments) were offered over 3 months.</p> <p>Results</p> <p>No interaction was found between echinacea and OMT. Echinacea was associated with a borderline increased risk of having at least one episode of acute otitis media during 6-month follow-up compared to placebo (65% versus 41%; relative risk, 1.59, 95% CI 1.04, 2.42). OMT did not significantly affect risk compared to sham (44% versus 61%; relative risk, 0.72, 95% CI 0.48, 1.10).</p> <p>Conclusion</p> <p>In otitis-prone young children, treating colds with this form of echinacea does not decrease the risk of acute otitis media, and may in fact increase risk. A regimen of up to five osteopathic manipulative treatments does not significantly decrease the risk of acute otitis media.</p> <p>Trial registration</p> <p>ClinicalTrials.gov Identifier: NCT00010465</p

Directed acyclic graph kernels for structural RNA analysis

<p>Abstract</p> <p>Background</p> <p>Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the similarities between two RNA sequences from the viewpoint of secondary structures. However, applying stem kernels directly to large data sets of ncRNAs is impractical due to their computational complexity.</p> <p>Results</p> <p>We have developed a new technique based on directed acyclic graphs (DAGs) derived from base-pairing probability matrices of RNA sequences that significantly increases the computation speed of stem kernels. Furthermore, we propose profile-profile stem kernels for multiple alignments of RNA sequences which utilize base-pairing probability matrices for multiple alignments instead of those for individual sequences. Our kernels outperformed the existing methods with respect to the detection of known ncRNAs and kernel hierarchical clustering.</p> <p>Conclusion</p> <p>Stem kernels can be utilized as a reliable similarity measure of structural RNAs, and can be used in various kernel-based applications.</p

Do financial incentives for delivering health promotion counselling work? Analysis of smoking cessation activities stimulated by the quality and outcomes framework

<p>Abstract</p> <p>Background</p> <p>A substantial fraction of UK general practitioners' salaries is now intended to reflect the quality of care provided. This performance-related pay system has probably improved aspects of primary health care but, using the observational data available, disentangling the impacts of different types of targets set within this unique payment system is challenging.</p> <p>Discussion</p> <p>Financial incentives undoubtedly influence GPs' activities, however, those aimed at encouraging GPs' delivery of health promotion counselling may not always have the effects intended. There is strong, observational evidence that targets and incentives intended to increase smoking cessation counselling by GPs have merely increased their propensity to record this activity in patients' medical records. The limitations of using financial incentives to stimulate the delivery of counselling in primary care are discussed and a re-appraisal of their use within UK GPs' performance-related pay system is argued for.</p> <p>Summary</p> <p>The utility of targets employed by the system for UK General Practitioners' performance related pay may be inappropriate for encouraging the delivery of health promotion counselling interventions. An evaluation of these targets is essential before they are further developed or added to.</p