Easyfig: a genome comparison visualizer

Summary: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures

Methods to improve recruitment to randomised controlled trials : Cochrane systematic review and meta-analysis

Peer reviewedPublisher PD

The impact of deliberate reflection with WISE-MD modules on surgical clerkship students\u27 critical thinking: a prospective, randomized controlled pilot study

Purpose: Critical thinking underlies several Association of American Medical Colleges (AAMC)-defined core entrustable professional activities (EPAs). Critical-thinking ability affects health care quality and safety. Tested tools to teach, assess, improve, and nurture good critical-thinking skills are needed. This prospective randomized controlled pilot study evaluated the addition of deliberate reflection (DR), guidance with Web Initiative in Surgical Education (WISE-MD) modules, to promote surgical clerks\u27 critical-thinking ability. The goal was to promote the application of reflective awareness principles to enhance learning outcomes and critical thinking about the module content. Participants and methods: Surgical clerkship (SC) students were recruited from two different blocks and randomly assigned to a control or intervention group. The intervention group was asked to record responses using a DR guide as they viewed two selected WISE-MD modules while the control group was asked to view two modules recording free thought. We hypothesized that the intervention group would show a significantly greater pre- to postintervention increase in critical-thinking ability than students in the control group. Results: Neither group showed a difference in pre- and posttest free-thought critical-thinking outcomes; however, the intervention group verbalized more thoughtful clinical reasoning during the intervention. Conclusion: Despite an unsupported hypothesis, this study provides a forum for discussion in medical education. It took a sponsored tool in surgical education (WISE-MD) and posed the toughest evaluation criteria of an educational intervention; does it affect the way we think? and not just what we learn, but how we learn it? The answer is significant and will require more resources before we arrive at a definitive answer

Tensile Properties of Amorphous Diamond Films

The strength and modulus of amorphous diamond, a new material for surface micromachined MEMS and sensors, was tested in uniaxial tension by pulling laterally with a flat tipped diamond in a nanoindenter. Several sample designs were attempted. Of those, only the single layer specimen with a 1 by 2 {micro}m gage cross section and a fixed end rigidly attached to the substrate was successful. Tensile load was calculated by resolving the measured lateral and normal forces into the applied tensile force and frictional losses. Displacement was corrected for machine compliance using the differential stiffness method. Post-mortem examination of the samples was performed to document the failure mode. The load-displacement data from those samples that failed in the gage section was converted to stress-strain curves using carefully measured gage cross section dimensions. Mean fracture strength was found to be 8.5 {+-} 1.4 GPa and the modulus was 831 {+-} 94 GPa. Tensile results are compared to hardness and modulus measurements made using a nanoindenter

The impact of deliberate reflection with WISE-MDTM modules on critical thinking of nurse practitioner students: A prospective, randomized controlled pilot study

Objective: Nurse practitioner (NP) students at our graduate school of nursing use WISE-MDTM simulation modules in the curriculum. This prospective randomized controlled pilot study was undertaken to evaluate critical-thinking outcomes associated with adding metacognitive deliberate-reflection guidance to the learning strategy with WISE-MDTM simulation modules. Methods: Of 33 NP students randomly assigned to intervention and control groups, 16 completed the study. The intervention group received WISE-MDTM learning modules with specific guidance or deliberate reflection. Controls used the modules with instructions for periodic free-thought reflections. Students’ tape-recorded reflections were categorized according to author-developed critical-thinking categories. Data were analyzed using NVIVOTM. Students’ feedback was collected by post-intervention anonymous survey. Results: Critical thinking outcomes (student responses to exercises after free-thinking or deliberate-reflection guidance) did not differ between groups. However, the intervention group demonstrated a higher level of critical thought after deliberate-reflection guidance. Post-intervention quantitative and qualitative feedback from both groups endorsed the value of the WISE-MDTM modules for NP education. Conclusions: Despite no difference in unprompted outcomes between groups, the intervention group often verbalized more thoughtful clinical decision-making. We speculate that the deliberate-reflection guidance intervention utilized with students throughout only two modules was insufficient for them to internalize the critical-thinking process. We propose using free-thought reflections with one or two WISE-MDTM modules to identify struggling students’ clinical decision-making process. These students’ remediation plan could include recording their deliberate-reflection process while viewing WISE-MDTM modules. Students would be guided to verbalize and record their critical-thinking processes for faculty review until students sufficiently integrate the process into their clinical decision-making

Polyglucosan Body Structure in Lafora Disease

Abnormal carbohydrate structures known as polyglucosan bodies (PGBs) are associated with neurodegenerative disorders, glycogen storage diseases (GSDs), and aging. A hallmark of the GSD Lafora disease (LD), a fatal childhood epilepsy caused by recessive mutations in the EPM2A or EPM2B genes, are cytoplasmic PGBs known as Lafora bodies (LBs). LBs result from aberrant glycogen metabolism and drive disease progression. They are abundant in brain, muscle and heart of LD patients and Epm2a-/- and Epm2b-/- mice. LBs and PGBs are histologically reminiscent of starch, semicrystalline carbohydrates synthesized for glucose storage in plants. In this study, we define LB architecture, tissue-specific differences, and dynamics. We propose a model for how small polyglucosans aggregate to form LBs. LBs are very similar to PGBs of aging and other neurological disorders, and so these studies have direct relevance to the general understanding of PGB structure and formation

'This is what democracy looks like' : New Labour's blind spot and peripheral vision

New Labour in government since 1997 has been roundly criticized for not possessing a clear, coherent and consistent democratic vision. The absence of such a grand vision has resulted, from this critical perspective, in an absence of 'joined-up' thinking about democracy in an evolving multi-level state. Tensions have been all too apparent between the government's desire to exert central direction - manifested in its most pathological form as 'control freakery' - and its democratising initiatives derived from 'third-way' obsessions with 'decentralising', 'empowering' and 'enabling'. The purpose of this article is to examine why New Labour displayed such apparently impaired democratic vision and why it appeared incapable of conceiving of democratic reform 'in the round'. This article seeks to explain these apparent paradoxes, however, through utilising the notion of 'macular degeneration'. In this analysis, the perceived democratic blind spot of New Labour at Westminster is connected to a democratic peripheral vision, which has envisaged innovative participatory and decentred initiatives in governance beyond Westminster

Entropy-induced smectic phases in rod-coil copolymers

We present a self-consistent field theory (SCFT) of semiflexible (wormlike) diblock copolymers, each consisting of a rigid and a flexible part. The segments of the polymers are otherwise identical, in particular with regard to their interactions, which are taken to be of an Onsager excluded-volume type. The theory is developed in a general three-dimensional form, as well as in a simpler one-dimensional version. Using the latter, we demonstrate that the theory predicts the formation of a partial-bilayer smectic-A phase in this system, as shown by profiles of the local density and orientational distribution functions. The phase diagram of the system, which includes the isotropic and nematic phases, is obtained in terms of the mean density and rigid-rod fraction of each molecule. The nematic-smectic transition is found to be second order. Since the smectic phase is induced solely by the difference in the rigidities, the onset of smectic ordering is shown to be an entropic effect and therefore does not have to rely on additional Flory-Huggins-type repulsive interactions between unlike chain segments. These findings are compared with other recent SCFT studies of similar copolymer models and with computer simulations of several molecular models.Comment: 13 pages, 8 figure

Molecular-size dependence of glycogen enzymatic degradation and its importance for diabetes

Glycogen, a hyperbranched glucose polymer, is the blood-sugar reservoir in animals. Liver glycogen comprises small β particles, which can join together as large composite α particles. It had been shown that the binding between β in α particles in the liver of diabetic mice is more fragile than in healthy mice. This could be linked to the loss of blood-sugar control characteristic of diabetes if the rate per monomer unit of the enzymatic degradation to glucose of α particles were significantly slower than that of β particles. This is tested here by examining the in vitro time evolution of the molecular size distribution of glycogen from the livers of healthy and diabetic mice and rats, containing distinct components of both α and β particles; this treatment is analogous to the “competitive growth” method used to explore mechanisms in emulsion polymerization. Simulations for the time evolution of the molecular size distribution were also performed. It is found that the degradation rate per monomer unit is indeed faster for the smaller particles, supporting the hypothesis of a causal link between chemical fragility of glycogen from diabetic liver with poor control of blood-sugar release. Comparison between simulations and experiment indicate that α and β particles have significant structural differences