Stirling material technology

The Stirling engine is an external combustion engine that offers the advantage of high fuel economy, low emissions, low noise, and low vibrations compared to current internal combustion automotive engines. The most critical component from a materials viewpoint is the heater head consisting of the cylinders, heating tubes, and regenerator housing. Materials requirements for the heater head include compatibility with hydrogen, resistance to hydrogen permeation, high temperature oxidation/corrosion resistance, and high temperature creep-rupture and fatigue properties. A materials research and technology program identified the wrought alloys CG-27 and 12RN72 and the cast alloys XF-818, NASAUT 4G-A1, and NASACC-1 as candidate replacements for the cobalt containing alloys used in current prototype engines. It is concluded that manufacture of the engine is feasible from low cost iron-base alloys rather than the cobalt alloys used in prototype engines. Results of research that lead to this conclusion are presented

The new versatile general purpose surface-muon instrument (GPS) based on silicon photomultipliers for μ{\mu}SR measurements on a continuous-wave beam

We report on the design and commissioning of a new spectrometer for muon-spin relaxation/rotation studies installed at the Swiss Muon Source (S$\mu$S) of the Paul Scherrer Institute (PSI, Switzerland). This new instrument is essentially a new design and replaces the old general-purpose surface-muon instrument (GPS) which has been for long the workhorse of the $\mu$SR user facility at PSI. By making use of muon and positron detectors made of plastic scintillators read out by silicon photomultipliers (SiPMs), a time resolution of the complete instrument of about 160 ps (standard deviation) could be achieved. In addition, the absence of light guides, which are needed in traditionally built $\mu$SR instrument to deliver the scintillation light to photomultiplier tubes located outside magnetic fields applied, allowed us to design a compact instrument with a detector set covering an increased solid angle compared to the old GPS.Comment: 11 pages, 11 figure

Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

BackgroundThe recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics.DesignThe Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.ResultsTo demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks.ConclusionsThe IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics

FuGEFlow: data model and markup language for flow cytometry

<p>Abstract</p> <p>Background</p> <p>Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata.</p> <p>Methods</p> <p>We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description.</p> <p>Results</p> <p>The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project.</p> <p>Conclusion</p> <p>We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development.</p

Switching between dynamic states in intermediate-length Josephson junctions

The appearance of zero-field steps (ZFS’s) in the current-voltage characteristics of intermediate-length overlap-geometry Josephson tunnel junctions described by a perturbed sine-Gordon equation (PSGE) is associated with the growth of parametrically excited instabilities of the McCumber background curve (MCB). A linear stability analysis of a McCumber solution of the PSGE in the asymptotic linear region of the MCB and in the absence of magnetic field yields a Hill’s equation which predicts how the number, locations, and widths of the instability regions depend on the junction parameters. A numerical integration of the PSGE in terms of truncated series of time-dependent Fourier spatial modes verifies that the parametrically excited instabilities of the MCB evolve into the fluxon oscillations characteristic of the ZFS’s. An approximate analysis of the Fourier mode equations in the presence of a small magnetic field yields a field-dependent Hill’s equation which predicts that the major effect of such a field is to reduce the widths of the instability regions. Experimental measurements on Nb-NbxOy-Pb junctions of intermediate length, performed at different operating temperatures in order to vary the junction parameters and for various magnetic field values, verify the physical existence of switching from the MCB to the ZFS’s. Good qualitative, and in many cases quantitative, agreement between analytic, numerical, and experimental results is obtained

VO: Vaccine Ontology

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented

Resonant flux motion and I-V -characteristics in frustrated Josephson junctions

We describe the dynamics of fluxons moving in a frustrated Josephson junction with p, d, and f-wave symmetry and calculate the I-V characteristics. The behavior of fluxons is quite distinct in the long and short length junction limit. For long junctions the intrinsic flux is bound at the center and the moving integer fluxon or antifluxon interacts with it only when it approaches the junction's center. For small junctions the intrinsic flux can move as a bunched type fluxon introducing additional steps in the I-V characteristics. Possible realization in quantum computation is presented.Comment: 21 pages, 8 figure

A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. &lt;p/&gt;Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. &lt;p/&gt;Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics