Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

The impact of the Netherlandish landscape tradition on poetry and painting in early modern England

Copyright © 2013 The University of Chicago Press.The relationship between poetry and painting has been one of the most debated issues in the history of criticism. The present article explores this problematic relationship in the context of sixteenth- and seventeenth-century England, taking into account theories of rhetoric, visual perception, and art. It analyzes a rare case in which a specific school of painting directly inspired poetry: in particular, the ways in which the Netherlandish landscape tradition influenced natural descriptions in the poem Poly-Olbion (1612, 1622) by Michael Drayton (1563–1631). Drayton — under the influence of the artistic principles of landscape depiction as explained in Henry Peacham’s art manuals, as well as of direct observation of Dutch and Flemish landscape prints and paintings — successfully managed to render pictorial landscapes into poetry. Through practical examples, this essay will thoroughly demonstrate that rhetoric is capable of emulating pictorial styles in a way that presupposes specialized art-historical knowledge, and that pictorialism can be the complex product as much of poetry and rhetoric as of painting and art-theoretical vocabulary

Someone is pulling the strings: hypersensitive agency detection and belief in conspiracy theories

We hypothesized that belief in conspiracy theories would be predicted by the general tendency to attribute agency and intentionality where it is unlikely to exist. We further hypothesized that this tendency would explain the relationship between education level and belief in conspiracy theories, where lower levels of education have been found to be associated with higher conspiracy belief. In Study 1 (N=202) participants were more likely to agree with a range of conspiracy theories if they also tended to attribute intentionality and agency to inanimate objects. As predicted, this relationship accounted for the link between education level and belief in conspiracy theories. We replicated this finding in Study 2 (N=330), whilst taking into account beliefs in paranormal phenomena. These results suggest that education may undermine the reasoning processes and assumptions that are reflected in conspiracy belief

Role of students' context in predicting academic performance at a medical school: a retrospective cohort study

OBJECTIVES: This study examines associations between medical students’ background characteristics (postcode-based measures of disadvantage, high school attended, sociodemographic characteristics), and academic achievement at a Russell Group University. DESIGN: Retrospective cohort analysis. SETTING: Applicants accepted at the University of Liverpool medical school between 2004 and 2006, finalising their studies between 2010 and 2011. PARTICIPANTS: 571 students (with an English home postcode) registered on the full-time Medicine and Surgery programme, who successfully completed their medical degree. MAIN OUTCOME MEASURES: Final average at year 4 of the medical programme (represented as a percentage). RESULTS: Entry grades were positively associated with final attainment (p<0.001). Students from high-performing schools entered university with higher qualifications than students from low-performing schools (p<0.001), though these differences did not persist at university. Comprehensive school students entered university with higher grades than independent school students (p<0.01), and attained higher averages at university, though differences were not significant after controlling for multiple effects. Associations between school type and achievement differed between sexes. Females attained higher averages than males at university. Significant academic differences were observed between ethnic groups at entry level and university. Neither of the postcode-based measures of disadvantage predicted significant differences in attainment at school or university. CONCLUSIONS: The findings of this study suggest that educational attainment at school is a good, albeit imperfect, predictor of academic attainment at medical school. Most attainment differences observed between students either decreased or disappeared during university. Unlike previous studies, independent school students did not enter university with the highest grades, but achieved the lowest attainment at university. Such variations depict how patterns may differ between subjects and higher-education institutions. Findings advocate for further evidence to help guide the implementation of changes in admissions processes and widen participation at medical schools fairly

Left-handers look before they leap:handedness influences reactivity to novel Tower of Hanoi tasks

A sample of 203 task naïve left- and right-handed participants were asked to complete a combination of the 3- and 4-disk Towers of Hanoi (ToH), manipulating novelty and complexity. Self-reported state anxiety and latency to respond (initiation time) were recorded before each ToH. Novelty had a major effect on initiation time, particularly for left-handers. Left-handers had a longer latency to start and this was significantly longer on the first trial. Irrespective of hand-preference, initiation time reduced on the second trial, however, this was greatest for left-handers. Condition of task did not systematically influence initiation time for right handers, but did for left-handers. State anxiety was influenced by task novelty and complexity in a more complicated way. During the first trial, there was a significant handedness × number of disks interaction with left-handers having significantly higher state anxiety levels before the 3-disk ToH. This suggests that the initial reaction to this task for left-handers was not simply due to perceived difficulty. On their second trial, participants completing a novel ToH had higher state anxiety scores than those completing a repeated version. Overall, left-handers had a larger reduction in their state anxiety across trials. Relating to this, the expected strong positive correlation between state and trait anxiety was absent for left-handed females in their first tower presentation, but appeared on their second. This was driven by low trait anxiety individuals showing a higher state anxiety response in the first (novel) trial, supporting the idea that left-handed females respond to novelty in a way that is not directly a consequence of their trait anxiety. A possible explanation may be stereotype threat influencing the behavior of left-handed females

ReseArch with Patient and Public invOlvement: a RealisT evaluation - the RAPPORT study

Background Patient and public involvement (PPI) is a prerequisite for many funding bodies and NHS research ethics approval. PPI in research is defined as research carried out with or by the public rather than to, about or for them. While the benefits of PPI have been widely discussed, there is a lack of evidence on the impact and outcomes of PPI in research. Objectives To determine the types of PPI in funded research, describe key processes, analyse the contextual and temporal dynamics of PPI and explore the experience of PPI in research for all those involved. Mechanisms contributing to the routine incorporation of PPI in the research process were assessed, the impact of PPI on research processes and outcomes evaluated, and barriers and enablers to effective PPI identified. Design A three-staged realist evaluation drawing on Normalisation Process Theory to understand how far PPI was embedded within health-care research in six areas: diabetes mellitus, arthritis, cystic fibrosis, dementia, public health and learning disabilities. The first two stages comprised a scoping exercise and online survey to chief investigators to assess current PPI activity. The third stage consisted of case studies tracked over 18 months through interviews and document analysis. The research was conducted in four regions of England. Participants Non-commercial studies currently running or completed within the previous 2 years eligible for adoption on the UK Clinical Research Network portfolio. A total of 129 case study participants included researchers and PPI representatives from 22 research studies, and representatives from funding bodies and PPI networks

The performance effects of creative imitation on original products: Evidence from lab and field experiments

Research Summary: A market entrant often challenges the incumbent using creative imitation: The entrant creatively combines imitated aspects of the original with its own innovative characteristics to create a distinct offering. Using lab and field experiments to examine creative imitation in China, we find the effects of creative imitations on the originals depend on the creative imitation's quality. We explore the underlying mechanisms, and show that including a low-quality creative imitation in the retail choice set increases satisfaction with and choice of the original, while a moderate-quality creative imitation does the opposite. Moreover, creative imitation affects consumers' satisfaction with the original by influencing whether their experience with the original verifies their expectations. Our paper reveals creative imitation effects to help incumbent firms effectively address them. Managerial Summary: When the incumbent is challenged by an entrant using creative imitation, consumers may react differently to the incumbent, and understanding consumers' reactions allows the incumbent to make better strategic decisions about how to address the challenge. Using lab and field experiments, we investigate creative imitations with two quality levels common in our empirical context, low quality and moderate quality, and examine how and why they differentially affect the originals. We find the presence of a low-quality creative imitation actually increased choice of the original by enhancing consumers' satisfaction with it, while a moderate-quality creative imitation reduced choice of the original by undermining satisfaction with it. Our research suggests the incumbent should address moderate-quality creative imitations' challenges to customer satisfaction, while temporarily tolerating low-quality creative imitations

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

D* Production in Deep Inelastic Scattering at HERA

This paper presents measurements of D^{*\pm} production in deep inelastic scattering from collisions between 27.5 GeV positrons and 820 GeV protons. The data have been taken with the ZEUS detector at HERA. The decay channel $D^{*+}\to (D^0 \to K^- \pi^+) \pi^+$ (+ c.c.) has been used in the study. The $e^+p$ cross section for inclusive D^{*\pm} production with $5<Q^2<100 GeV^2$ and $y<0.7$ is 5.3 \pms 1.0 \pms 0.8 nb in the kinematic region {$1.3<p_T(D^{*\pm})<9.0$ GeV and $| \eta(D^{*\pm}) |<1.5$}. Differential cross sections as functions of p_T(D^{*\pm}), $\eta(D^{*\pm}), W$ and $Q^2$ are compared with next-to-leading order QCD calculations based on the photon-gluon fusion production mechanism. After an extrapolation of the cross section to the full kinematic region in p_T(D^{*\pm}) and $\eta$(D^{*\pm}), the charm contribution $F_2^{c\bar{c}}(x,Q^2)$ to the proton structure function is determined for Bjorken $x$ between 2 $\cdot$ 10$^{-4}$ and 5 $\cdot$ 10$^{-3}$.Comment: 17 pages including 4 figure

Observation of Scaling Violations in Scaled Momentum Distributions at HERA

Charged particle production has been measured in deep inelastic scattering (DIS) events over a large range of $x$ and $Q^2$ using the ZEUS detector. The evolution of the scaled momentum, $x_p$, with $Q^2,$ in the range 10 to 1280 $GeV^2$, has been investigated in the current fragmentation region of the Breit frame. The results show clear evidence, in a single experiment, for scaling violations in scaled momenta as a function of $Q^2$.Comment: 21 pages including 4 figures, to be published in Physics Letters B. Two references adde