Enhancements to the GW space-time method

We describe the following new features which significantly enhance the power of the recently developed real-space imaginary-time GW scheme (Rieger et al., Comp. Phys. Commun. 117, 211 (1999)) for the calculation of self-energies and related quantities of solids: (i) to fit the smoothly decaying time/energy tails of the dynamically screened Coulomb interaction and other quantities to model functions, treating only the remaining time/energy region close to zero numerically and performing the Fourier transformation from time to energy and vice versa by a combination of analytic integration of the tails and Gauss-Legendre quadrature of the remaining part and (ii) to accelerate the convergence of the band sum in the calculation of the Green's function by replacing higher unoccupied eigenstates by free electron states (plane waves). These improvements make the calculation of larger systems (surfaces, clusters, defects etc.) accessible.Comment: 10 pages, 6 figure

So what have data standards ever done for us? The view from metabolomics

The standardization of reporting of data promises to revolutionize biology by allowing community access to data generated in laboratories across the globe. This approach has already influenced genomics and transcriptomics. Projects that have previously been viewed as being too big to implement can now be distributed across multiple sites. There are now public databases for gene sequences, transcriptomic profiling and proteomic experiments. However, progress in the metabolomic community has seemed to falter recently, and whereas there are ontologies to describe the metadata for metabolomics there are still no central repositories for the datasets themselves. Here, we examine some of the challenges and potential benefits of further efforts towards data standardization in metabolomics and metabonomics

OrChem - An open source chemistry search engine for Oracle®

<p>Abstract</p> <p>Background</p> <p>Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world.</p> <p>Results</p> <p>Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets.</p> <p>Availability</p> <p>OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via <url>http://orchem.sourceforge.net</url>.</p

Lost in transition? Access to and uptake of adult health services and outcomes for young people with type 1 diabetes in regional New South Wales

Objective: To document diabetes health services use and indices of glycaemic management of young people with type 1 diabetes from the time of their first contact with adult services, for those living in regional areas compared with those using city and state capital services, and compared with clinical guideline targets. Design, setting and subjects: Case note audit of 239 young adults aged 18-28 years with type 1 diabetes accessing five adult diabetes services before 30 June 2008 in three geographical regions of New South Wales: the capital (86), a city (79) and a regional area (74). Main outcome measures: Planned (routine monitoring) and unplanned (hospital admissions and emergency department attendance for hypoglycaemia or hyperglycaemia) service contacts; recorded measures of glycated haemoglobin (HbA1c), body mass index (BMI), and blood pressure (BP). Results: Routine preventive service uptake during the first year of contact with adult services was significantly higher in the capital and city. Fewer regional area patients had records of complications assessment and measurements of HbA1c, BMI and BP across all audited years of contact (HbA1c: 73% v 94% city, 97% capital; P 8.0% (79% v 62% city, 56% capital) and lowest proportion < 7% (4% v 7%, 22%) (both P < 0.001). Fewer young people made unplanned use of acute services for diabetes crisis management in the capital (24% v 49% city, 50% regional area; P < 0.001). In the regional area, routine review did not occur reliably even annually, with marked attrition of patients from adult services after the first year of contact. Conclusion: Inadequate routine specialist care, poor diabetes self-management and frequent use of acute services for crisis management, particularly in regional areas, suggest service redesign is needed to encourage young people's engagement

Services doing the best they can: Service experiences of young adults with type 1 diabetes mellitus in rural Australia

Aims and objectives. To describe the healthcare experiences of young adults with type 1 diabetes who access diabetes services in rural areas of New South Wales, Australia. Background. The incidence of type 1 diabetes in childhood and adolescence is increasing worldwide; internationally, difficulties are encountered in supporting young people during their transition from children to adulthood. Consumers' experiences and views will be essential to inform service redesign. Design. This was a qualitative exploratory study. Methods. Semistructured telephone interviews were conducted with 26 people aged 18-28years living rurally, recruited through staff in four regional healthcare centres in 2008. Results. Two key themes were evident: lack of access (comprised of transfer to adult services, access to health professionals and access to up-to-date information) and age-appropriate provision. The impact of place of residence and personal motivation crossed all themes. Participants contrasted unfavourably the seamless care and support received from paediatric outreach services with the shortages in specialist and general practice-based care and information and practical problems of service fragmentation and lack of coordination experienced as adults. They identified a range of issues including need for ongoing education, age-appropriate services and support networks related to developing their ability to self-manage. They valued personal service; online and electronic support was seldom volunteered as an alternative. Conclusion. This was a first view of rural young people's experiences with adult diabetes services. Reported experiences were in line with previous reports from other settings in that they did not perceive services in this rural area of Australia as meeting their needs; suggestions for service redesign differed. Relevance to clinical practice. New models of age-appropriate service provision are required, to meet their needs for personal as well as other forms of support, whilst acknowledging the very real resource limitations of these locations. © 2012 Blackwell Publishing Ltd

CDK-Taverna: an open workflow environment for cheminformatics

<p>Abstract</p> <p>Background</p> <p>Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.</p> <p>Results</p> <p>Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.</p> <p>Conclusions</p> <p>The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.</p

Facebook as a recruitment tool for adolescent health research: A systematic review

BACKGROUND: Researchers are increasingly using social media to recruit participants to surveys and clinical studies. However, the evidence of the efficacy and validity of adolescent recruitment through Facebook is yet to be established. OBJECTIVE: To conduct a systematic review of the literature on the use of Facebook to recruit adolescents for health research. DATA SOURCES: Nine electronic databases and reference lists were searched for articles published between 2004 and 2013. STUDY ELIGIBILITY CRITERIA: Studies were included in the review if: 1) participants were aged 10 to 18 years, 2) studies addressed a physical or mental health issue, 3) Facebook was identified as a recruitment tool, 4) recruitment details using Facebook were outlined in the methods section and considered in the discussion, or information was obtained by contacting the authors, 5) results revealed how many participants were recruited using Facebook, and 6) studies addressed how adolescent consent and/or parental consent was obtained. STUDY APPRAISALS AND SYNTHESIS METHODS: Titles, abstracts, and keywords were scanned and duplicates removed by 2 reviewers. Full text was evaluated for inclusion criteria, and 2 reviewers independently extracted data. RESULTS: The search resulted in 587 publications, of which 25 full-text papers were analyzed. Six studies met all the criteria for inclusion in the review. Three recruitment methods using Facebook was identified: 1) paid Facebook advertising, 2) use of the Facebook search tool, and 3) creation and use of a Facebook Page. CONCLUSIONS: Eligible studies described the use of paid Facebook advertising and Facebook as a search tool as methods to successfully recruit adolescent participants. Online and verbal consent was obtained from participants recruited from Facebook

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".

BACKGROUND: Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently no central repository for the depositing of data despite efforts by the Metabolomics Standard Initiative (MSI) to develop a standardised description of a metabolomic experiment. FINDINGS: In this manuscript we describe how the MSI description has been applied to a published dataset involving the identification of cross-species metabolic biomarkers associated with type II diabetes. The study describes sample collection of urine from mice, rats and human volunteers, and the subsequent acquisition of data by high resolution 1H NMR spectroscopy. The metadata is described to demonstrate how the MSI descriptions could be applied in a manuscript and the spectra have also been made available for the mouse and rat studies to allow others to process the data. CONCLUSIONS: The intention of this manuscript is to stimulate discussion as to whether the MSI description is sufficient to describe the metadata associated with metabolomic experiments and encourage others to make their data available to other researchers

New developments on the cheminformatics open workflow environment CDK-Taverna

<p>Abstract</p> <p>Background</p> <p>The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego™-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public.</p> <p>Results</p> <p>The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios.</p> <p>Conclusions</p> <p>CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Taverna community and published on myexperiment.org enables molecular scientists to quickly calculate, process and analyse molecular data as typically found in e.g. today's systems biology scenarios.</p

Prader-Willi Syndrome Is Associated with Activation of the Innate Immune System Independently of Central Adiposity and Insulin Resistance

Background: Subjects with Prader-Willi syndrome (PWS) have a reduced life expectancy due to cardiovascular disease. Increased systemic low-grade inflammation is postulated as a contributor, despite reported lower visceral fat mass and increased insulin sensitivity. Objectives: Our aim was to compare inflammatory markers and arterial stiffness in PWS and adiposity-matched obese control subjects. Design: We conducted a cross-sectional cohort study comparing 12 PWS subjects, 12 obese subjects matched for percentage body fat and central abdominal fat mass, and 10 healthy normal-weight subjects. Main Outcome Measures: Dual-energy x-ray absorptiometry was used to assess body composition, flow cytometry to quantify activation markers on immune cells, and ELISA for measurement of C-reactive protein, adiponectin, and IL-6. Insulin resistance was estimated by homeostasis model assessment and arterial stiffness by applanation tonometry. Results: PWS and obese subjects had similarly increased homeostasis model assessment and arterial stiffness. Nevertheless, PWS subjects showed significantly higher IL-6 (4.9 ± 1.0 vs. 2.5 ± 0.4 pg/ml; P = 0.02) and nonsignificantly higher C-reactive protein (10.5 ± 3.2 vs. 4.0 ± 1.0 ng/ml; P = 0.08). Neutrophil activation markers CD66b and CD11b were higher in PWS compared to obese subjects (P < 0.01), reflecting an activated innate immune system. These markers were positively related to central adiposity in lean and obese subjects (r = 0.49; P < 0.05), but not in PWS subjects. Conclusions: PWS subjects compared to adiposity-matched obese subjects demonstrate similar insulin resistance but increased low-grade inflammation. The dissociation of inflammation and central adiposity suggests that activation of innate immunity may be either a specific genetic feature of PWS or linked to the commonly associated obstructive sleep apnea syndrome, and might offer a treatment target to reduce cardiovascular disease