Computing inelastic neutron scattering spectra from molecular dynamics trajectories

Inelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation method that is frequently used to simulate semicrystalline/amorphous materials. We illustrate the technique by analyzing spectra of a well-studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) and conclude that our technique provides improved volume and structural variety, but that the classical force field requires improvement before the morphology can be accurately interpreted

Meningococcal genetic variation mechanisms viewed through comparative analysis of Serogroup C strain FAM18

Copyright @ 2007 Public Library of ScienceThe bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.This work was supported by the Wellcome Trust through the Beowulf Genomics Initiative

Prevalence and microbiological characteristics of clinically infected foot-ulcers in patients with rheumatoid arthritis: A retrospective exploratory study

Background: The prevalence of foot ulcers in patients with rheumatoid arthritis (RA) has been reported at almost 10 %. These foot ulcers often occur at multiple sites and are reoccurring, with the potential risk of infection increased due to RA diagnosis and disease modifying medications. The objective of this study was to estimate the prevalence of clinical infection in foot-ulcers of patients with RA; describe the microbiological characteristics and investigate risk factors. Methods: Retrospective clinical data was collected for all patients attending a rheumatology foot ulcer clinic between 1st May 2012 and 1st May 2013: wound swab data was collected from those with clinical infection. Results: Twenty-eight patients with RA and foot-ulcers were identified; eight of these patients had clinical infection and wound swabs taken (29 %). Of these eight patients there were equal men and women, with median age 74 years, and average disease duration 22 years. Cardiovascular disease/peripheral-vascular disease (CVD/PVD) were reported in six patients, diabetes in two patients. Six patients were treated with disease-modifying anti-rheumatic drugs (DMARDs); three were on biologic medications and two on steroids. Five wound swabs cultured skin flora, one staphylococcus aureus, one had no growth after culture; and one was rejected due to labelling error. Conclusion: Almost a third of people with RA and foot ulcers attending clinic over one year had clinical infection, however microbiological analysis failed to isolate pathogens in six of seven wound swabs. This may be due to inaccurate diagnosis of ulcer infection or to issues with sampling, collection, transport, analysis or reporting. There was insufficient data to relate risk of clinical infection with risk factors. Further research is required to identify the most appropriate techniques for infection diagnosis, wound sampling and processing. Trial registration: Ethical approval was obtained from University of Leeds, Faculty of Medicine and Health (Reference number: SHREC/RP/349)

Immunocytochemical determination of the subcellular distribution of ascorbate in plants

Ascorbate is an important antioxidant in plants and fulfills many functions related to plant defense, redox signaling and modulation of gene expression. We have analyzed the subcellular distribution of reduced and oxidized ascorbate in leaf cells of Arabidopsis thaliana and Nicotiana tabacum by high-resolution immuno electron microscopy. The accuracy and specificity of the applied method is supported by several observations. First, preadsorption of the ascorbate antisera with ascorbic acid or dehydroascorbic acid resulted in the reduction of the labeling to background levels. Second, the overall labeling density was reduced between 50 and 61% in the ascorbate-deficient Arabidopsis mutants vtc1-2 and vtc2-1, which correlated well with biochemical measurements. The highest ascorbate-specific labeling was detected in nuclei and the cytosol whereas the lowest levels were found in vacuoles. Intermediate labeling was observed in chloroplasts, mitochondria and peroxisomes. This method was used to determine the subcellular ascorbate distribution in leaf cells of plants exposed to high light intensity, a stress factor that is well known to cause an increase in cellular ascorbate concentration. High light intensities resulted in a strong increase in overall labeling density. Interestingly, the strongest compartment-specific increase was found in vacuoles (fourfold) and in plastids (twofold). Ascorbate-specific labeling was restricted to the matrix of mitochondria and to the stroma of chloroplasts in control plants but was also detected in the lumen of thylakoids after high light exposure. In summary, this study reveals an improved insight into the subcellular distribution of ascorbate in plants and the method can now be applied to determine compartment-specific changes in ascorbate in response to various stress situations

Synchronous online CPD: empirical support for the value of webinars in career settings

The careers profession in England is facing unprecedented challenges. Initiatives to improve service delivery while keeping costs low are attractive and online training holds the promise of high impact at low cost. The present study employs a qualitative methodology to evaluate a series of online ‘webinars’ conducted with 15 careers advisers. Results showed that the technology itself could impede learning, and participants missed out on the peer-to-peer interaction that takes place in a ‘bricks and mortar’ setting, but overall participants found that access to relevant, good quality training from the convenience of their workplace more than compensated for the challenges. The article offers conceptual support for the viability of online learning through the theory of equivalency, andragogy and transactional distance theory, and makes recommendations for practice

What impact do posters have on academic knowledge transfer? A pilot survey on author attitudes and experiences

<p>Abstract</p> <p>Background</p> <p>Research knowledge is commonly facilitated at conferences via oral presentations, poster presentations and workshops. Current literature exploring the efficacy of academic posters is however limited. The purpose of this initial study was to explore the perceptions of academic poster presentation, together with its benefits and limitations as an effective mechanism for academic knowledge transfer and contribute to the available academic data.</p> <p>Methods</p> <p>A survey was distributed to 88 delegates who presented academic posters at two Releasing Research and Enterprise Potential conferences in June 2007 and June 2008 at Bournemouth University. This survey addressed attitude and opinion items, together with their general experiences of poster presentations. Descriptive statistics were performed on the responses.</p> <p>Results</p> <p>A 39% return was achieved with the majority of respondents believing that posters are a good medium for transferring knowledge and a valid form of academic publication. Visual appeal was cited as more influential than subject content, with 94% agreeing that poster imagery is most likely to draw viewer's attention. Respondents also believed that posters must be accompanied by their author in order to effectively communicate the academic content.</p> <p>Conclusion</p> <p>This pilot study is the first to explore perceptions of the academic poster as a medium for knowledge transfer. Given that academic posters rely heavily on visual appeal and direct author interaction, the medium requires greater flexibility in their design to promote effective knowledge transfer. This paper introduces the concept of the IT-based 'MediaPoster' so as to address the issues raised within published literature and subsequently enhance knowledge-transfer within the field of academic medicine.</p

Does peer learning or higher levels of e-learning improve learning abilities? A randomized controlled trial

Background and aims : The fast development of e-learning and social forums demands us to update our understanding of e-learning and peer learning. We aimed to investigate if higher, pre-defined levels of e-learning or social interaction in web forums improved students&#x2019; learning ability. Methods : One hundred and twenty Danish medical students were randomized to six groups all with 20 students (eCases level 1, eCases level 2, eCases level 2+, eTextbook level 1, eTextbook level 2, and eTextbook level 2+). All students participated in a pre-test, Group 1 participated in an interactive case-based e-learning program, while Group 2 was presented with textbook material electronically. The 2+ groups were able to discuss the material between themselves in a web forum. The subject was head injury and associated treatment and observation guidelines in the emergency room. Following the e-learning, all students completed a post-test. Pre- and post-tests both consisted of 25 questions randomly chosen from a pool of 50 different questions. Results : All students concluded the study with comparable pre-test results. Students at Level 2 (in both groups) improved statistically significant compared to students at level 1 (p&#x003E;0.05). There was no statistically significant difference between level 2 and level 2+. However, level 2+ was associated with statistically significant greater student&#x0027;s satisfaction than the rest of the students (p&#x003E;0.05). Conclusions : This study applies a new way of comparing different types of e-learning using a pre-defined level division and the possibility of peer learning. Our findings show that higher levels of e-learning does in fact provide better results when compared with the same type of e-learning at lower levels. While social interaction in web forums increase student satisfaction, learning ability does not seem to change. Both findings are relevant when designing new e-learning materials

Alterations in anatomic and functional imaging parameters with repeated FDG PET-CT and MRI during radiotherapy for head and neck cancer: a pilot study

Background: The use of imaging to implement on-treatment adaptation of radiotherapy is a promising paradigm but current data on imaging changes during radiotherapy is limited. This is a hypothesis-generating pilot study to examine the changes on multi-modality anatomic and functional imaging during (chemo)radiotherapy treatment for head and neck squamous cell carcinoma (HNSCC). Methods: Eight patients with locally advanced HNSCC underwent imaging including computed tomography (CT), Fluorine-18 fluorodeoxyglucose (FDG) positron emission tomography (PET)-CT and magnetic resonance imaging (MRI) (including diffusion weighted (DW) and dynamic contrast enhanced (DCE)) at baseline and during (chemo)radiotherapy treatment (after fractions 11 and 21). Regions of interest (ROI) were drawn around the primary tumour at baseline and during treatment. Imaging parameters included gross tumour volume (GTV) assessment, SUVmax, mean ADC value and DCE-MRI parameters including Plasma Flow (PF). On treatment changes and correlations between these parameters were analysed using a Wilcoxon rank sum test and Pearson’s linear correlation coefficient respectively. A p-value <0.05 was considered statistically significant. Results: Statistically significant reductions in GTV-CT, GTV-MRI and GTV-DW were observed between all imaging timepoints during radiotherapy. Changes in GTV-PET during radiotherapy were heterogeneous and non-significant. Significant changes in SUVmax, mean ADC value, Plasma Flow and Plasma Volume were observed between the baseline and the fraction 11 timepoint, whilst only changes in SUVmax between baseline and the fraction 21 timepoint were statistically significant. Significant correlations were observed between multiple imaging parameters, both anatomical and functional; 20 correlations between baseline to the fraction 11 timepoint; 12 correlations between baseline and the fraction 21 timepoints; and 4 correlations between the fraction 11 and fraction 21 timepoints. Conclusions: Multi-modality imaging during radiotherapy treatment demonstrates early changes (by fraction 11) in both anatomic and functional imaging parameters. All functional imaging modalities are potentially complementary and should be considered in combination to provide multi-parametric tumour assessment, to guide potential treatment adaptation strategies. Trial Registration: ISRCTN Registry: ISRCTN34165059. Registered 2nd February 2015

Nanocarbon-Based photovoltaics

Carbon materials are excellent candidates for photovoltaic solar cells: they are Earth-abundant, possess high optical absorption, and superior thermal and photostability. Here we report on solar cells with active layers made solely of carbon nanomaterials that present the same advantages of conjugated polymer-based solar cells - namely solution processable, potentially flexible, and chemically tunable - but with significantly increased photostability and the possibility to revert photodegradation. The device active layer composition is optimized using ab-initio density functional theory calculations to predict type-II band alignment and Schottky barrier formation. The best device fabricated is composed of PC70BM fullerene, semiconducting single-walled carbon nanotubes and reduced graphene oxide. It achieves a power conversion efficiency of 1.3% - a record for solar cells based on carbon as the active material - and shows significantly improved lifetime than a polymer-based device. We calculate efficiency limits of up to 13% for the devices fabricated in this work, comparable to those predicted for polymer solar cells. There is great promise for improving carbon-based solar cells considering the novelty of this type of device, the superior photostability, and the availability of a large number of carbon materials with yet untapped potential for photovoltaics. Our results indicate a new strategy for efficient carbon-based, solution-processable, thin film, photostable solar cells