eGenomics: Cataloguing our complete genome collection III

This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27–29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database

Efficient Photoionization-Loading of Trapped Cadmium Ions with Ultrafast Pulses

Atomic cadmium ions are loaded into radiofrequency ion traps by photoionization of atoms in a cadmium vapor with ultrafast laser pulses. The photoionization is driven through an intermediate atomic resonance with a frequency-quadrupled mode-locked Ti:Sapphire laser that produces pulses of either 100 fsec or 1 psec duration at a central wavelength of 229 nm. The large bandwidth of the pulses photoionizes all velocity classes of the Cd vapor, resulting in high loading efficiencies compared to previous ion trap loading techniques. Measured loading rates are compared with a simple theoretical model, and we conclude that this technique can potentially ionize every atom traversing the laser beam within the trapping volume. This may allow the operation of ion traps with lower levels of background pressures and less trap electrode surface contamination. The technique and laser system reported here should be applicable to loading most laser-cooled ion species.Comment: 11 pages, 12 figure

Multi-junction surface ion trap for quantum computing

Surface ion traps with two-dimensional layouts of trapping regions are natural architectures for storing large numbers of ions and supporting the connectivity needed to implement quantum algorithms. Many of the components and operations needed to fully exploit this architecture have already been demonstrated, including operation at cryogenic temperatures with low heating, low excitation transport, and ion control and detection with integrated photonics. Here we demonstrate a trap that addresses the scaling challenge of increasing power dissipation as the RF electrode increases in size. By raising the RF electrode and removing most of the insulating dielectric layer below it we reduce both ohmic and dielectric power dissipation. We also measure heating rates across a range of motional frequencies and for different voltage sources in a trap with a raised RF electrode but solid dielectric.Comment: 7 pages, 4 figure

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets

In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources

Modules, networks and systems medicine for understanding disease and aiding diagnosis

Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation

Discrimination between oral corticosteroid-treated and oral corticosteroid-non-treated severe asthma patients by an electronic nose platform

Rationale: Some severe asthma patients require oral corticosteroids (OCS) likely due to greater disease severity. Exhaled molecular markers can provide phenotypic information in asthma. Objectives: Determine whether patients on OCS (OCS+) have a different breathprint compared with those who were not on OCS (OCS-); determine the classification accuracy of eNose as compared to FEV1 % pred, % sputum eosinophils, and exhaled nitric oxide (FENO). Methods: This was a cross-sectional analysis of the U-BIOPRED cohort. Severe asthma was defined by IMI-criteria [Bel Thorax 2011]. OCS+ patients had daily OCS. OCS- patients had never had OCS and were on maintenance inhaled fluticasone equivalent >1000 μg/day. Exhaled volatile organic compounds trapped on adsorption tubes were analysed by centralized eNose platform (Owlstone Lonestar, Cyranose 320, Comon Invent, Tor Vergata TEN) including a total of 190 sensors. t test was used for comparing groups and support vector machine with leave-one-out cross-validation as a classifier. Results: 33 OCS+ (age 55±11yr, mean±SD, 52% female, 27% smokers, pre-bronchodilator FEV1 64.1±24% pred) and 40 OCS- severe asthma patients (age 54±15yr, mean±SD, 55% female, 35% smokers, pre-bronchodilator FEV1 61.8±24% pred) were studied. Sensor by sensor analysis showed that 56 sensors provided different mean values (change in sensor resistance or frequency) between groups (P<0.05). Accuracy of classification was as follows: eNose 71% (n=73), FENO 71% (n=70), FEV1 62% (n=73) and sputum eosinophils 59% (n=37). Conclusions: Preliminary results suggest OCS+ and OCS- severe asthma patients can be distinguished by an eNose platform

Postoperative IOP prophylaxis practice following uncomplicated cataract surgery: a UK-wide consultant survey

BACKGROUND: In order to minimise postoperative intraocular pressure (IOP) rise, after routine uncomplicated cataract surgery, prophylaxis may be adopted. Currently, there are no specific guidelines in this regard resulting in wide variation in practice across the UK. We sought to document these variations through a questionnaire survey. METHODS: A questionnaire was sent to all consultant ophthalmic surgeons in the UK. RESULTS: 62.6% of surgeons did not use any IOP lowering agents. 37.4% surgeons routinely prescribed some form of medication. The majority (86.8%) used oral diamox. 20.6% of surgeons said they based their practice on evidence, 43.3% on personal experience, and 17.6% on unit policy. Surprisingly, among the two groups of surgeons (those who gave routine prophylaxis, and those who did not) the percentages of surgeons quoting personal experience, unit policy, or presence of evidence was strikingly similar. The timing of the first postoperative IOP check varied from the same day to beyond 2 weeks. Only 20.2% of surgeons had ever seen an adverse event related to IOP rise; this complication is thus very rare. CONCLUSION: This survey highlights a wide variation in the practice and postoperative management of phacoemulsification cataract surgery. What is very striking is that there is a similar proportion of surgeons in the diametrically opposite groups (those who give or do not give routine IOP lowering prophylaxis) who believe that there practice is evidence based. The merits of this study suggests that consideration must be given to drafting a uniform guideline in this area of practice