NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies. It also can be customized to fit the needs of different scenarios. Ontology Recommender 2.0 combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available.Comment: 29 pages, 8 figures, 11 table

Pre-exposure Immunoprophylaxis by Genetically Encoded DMAb anti-OspA Human Monoclonal Antibody to Prevent Lyme Disease

Tick transmission of Borrelia spirochetes to humans results in significant morbidity from Lyme disease. Animal studies have demonstrated that transmission of Borrelia from tick vector to the mammalian host can be blocked by antibodies against outer surface protein A (OspA). We have recently developed borreliacidal human IgG1 monoclonal antibodies (HuMabs) directed against OspA. HuMab 319-44 was borreliacidal against B. burgdorferi (IC50Borreliatransmission after a single dose of 2 mg/kg administered on the day of tick challenge. Since passively administered IgG1 antibodies do not have a sufficient half-life to provide protection for the 6-7 month peak risk period, we investigated a novel approach of vector-mediated gene transfer of HuMabs that could potentially provide protection against Lyme disease during the seasonal risk period. A modified HuMab, 319-44 mod, expressed by a synthetic DNA plasmid (DMAb) was optimized and characterized in in vitro OspA binding and bactericidal assays. To assess in vivo protection, mice were administered a single DMAb injection into the quadriceps followed by electroporation. The mice were then challenged by B. burgdorferi-infected nymphs. Tissue samples were monitored by dark-field microscopy for spirochete growth. Serum samples were analyzed by ELISA to determine antibody concentrations. The modified 319-44 DMAb maintained in vitro biological activity comparable to the un-modified wild type antibody, and formulation-based delivery of DMAb resulted in long-term expression. This led to effective pre-exposure prophylaxis preventing transmission of spirochetes in 80% of mice in the murine model of tick-transmitted Lyme disease. These studies represent the first demonstration of employing DNA transfer as a rapid, novel delivery system for biologically relevant functional full-length HuMAbs in an in vivo animal model and provide support for such an approach for pre-exposure immunoprophylaxis to prevent Lyme disease

Interfacial characteristics and microstructural evolution of ceramics exposed to high temperature sand laden combustion environments

Sand laden combustion environments are a current challenge plaguing ceramic thermal barrier coatings (TBCs) and environmental barrier coatings (EBCs) on metallic and emerging ceramic matrix composite (CMC) turbomachinery components. Exposure of thermal and environmental barrier coatings on ceramic matrix composites to environmental particulate laden deteriorates the ceramic structure via chemical reactions and infiltration into pore structures. The challenge of environmental particulates, collectively referred to as calcium-magnesium-aluminosilicate (CMAS), is expected to be exacerbated in future components that utilize ceramic matric composites (CMCs), since the higher operating temperatures will accelerate particulate melting, infiltration, and diffusion kinetics. This study first presents efforts at ARL to develop sandphobic coatings resistant to CMAS infiltration and deposition. The results of a recent full scale sand ingestion engine test used to evaluate several ARL layered and blended coating compositions are presented. The study also includes the evaluation of interactions of CMAS plasma sprayed environmental barrier coatings and HfO2-Si bond coats on SiC/SiC CMCs in rig simulated engine test conditions. The focus is on the microstructural evolution of the coatings and the interfacial characteristics between the TBCs and EBCs and CMAS. Interfaces between coating constituents are also of interest in order to tailor coatings with superior thermal, structural, and chemical characteristics. Controlled studies on YSZ-based ceramic compacts are also performed in order to gain a more fundamental understanding of the effect of porosity on infiltration kinetics, as well as the nature of interfaces and interfacial products wrought by CMAS infiltration into YSZ ceramic grain boundaries. These model studies on YSZ are conducted by immersing the ceramic compacts into AFRL-02 sand and exposing the system to temperatures of up to 1300 °C. X-ray diffraction, scanning electron microscopy, transmission electron microscopy, electron back scattered diffraction, and focused ion beam (milling and imaging) are utilized for microstructural and interfacial characterization of the CMAS reacted thermal and environmental barrier coating systems

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach

High Temperature Ceramic Microstructure and Interface Evolution during Exposure to Particulate Laden Combustion Flows in Gas Turbine Engines

Objective: To innovate sandphobic coating and surface modification for high temperature turbine blades to resist sand glaze build-up and related Calcia-Magnesia-Alumina-Silicate (CMAS) attack on Thermal/Environmental Barrier Coatings (T/EBCs)

Submicron and Nanometer Structures Technology and Research

Contains reports on twenty research projects and a list of publications.Defense Advanced Research Projects Agency Contract N00019-92-K-0021Joint Services Electronics Program Contract DAAL03-92-C-0001National Science Foundation Grant ECS 90-16437U.S. Army Research Office Grant DAAL03-92-G-0291IBM CorporationU.S. Air Force - Office of Scientific Research Grant F49620-92-J-0064National Science Foundation Grant DMR 87-19217National Science Foundation Grant DMR 90-22933Defense Advanced Research Projects Agency Consortium for Superconducting ElectronicsNational Aeronautics and Space Administration Contract NAS8-36748National Aeronautics and Space Administration Grant NAGW-200

Submicron and Nanometer Structures Technology and Research

Contains reports on sixteen research projects and a list of publications.Joint Services Electronics Program Contract DAAL03-89-C-0001Joint Services Electronics Program Contract DAAL03-92-C-0001National Science Foundation Grant ECS 90-16437Semiconductor Research Corporation Contract 90-SP-080U.S. Navy - Naval Research Laboratory Contract N00014-90-K-2018IBM CorporationU.S. Air Force - Office of Scientific Research Grant F49620-92-J-0064National Science Foundation Grant DMR 87-19217National Science Foundation Grant DMR 90-22933National Aeronautics and Space Administration Contract NAS8-36748National Aeronautics and Space Administration Grant NAGW-2003National Science Foundation Grant DMR 90-01698Spire Corporatio

Adoption of BioPortal's Ontology Registry Software: The Emerging OntoPortal Community

Poster sessionInternational audienceA key BioPortal deliverable has been the Virtual Appliance, which any community can deploy to create their own repository of ontologies and vocabularies. Adoption of the Virtual Appliance has increased significantly, with many developers, operators, and end users adopting and improving the code. We now present this software stack as OntoPortal, and release it as the OntoPortal Virtual Appliance