Ontology Summit 2008 Communiqué: Towards an open ontology repository

Each annual Ontology Summit initiative makes a statement appropriate to each Summits theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies

Pairing interactions and pairing mechanism in high temperature copper oxide superconductors

The polaron binding energy E_{p} in undoped parent cuprates has been determined to be about 1.0 eV from the unconventional oxygen-isotope effect on the antiferromagnetic ordering temperature. The deduced value of E_{p} is in quantitative agreement with that estimated from independent optical data and that estimated theoretically from the measured dielectric constants. The substantial oxygen-isotope effect on the in-plane supercarrier mass observed in optimally doped cuprates suggests that polarons are bound into the Cooper pairs. We also identify the phonon modes that are strongly coupled to conduction electrons from the angle-resolved photoemission spectroscopy, tunneling spectra, and optical data. We consistently show that there is a very strong electron-phonon coupling feature at a phonon energy of about 20 meV along the antinodal direction and that this coupling becomes weaker towards the diagonal direction. We further show that high-temperature superconductivity in cuprates is caused by strong electron-phonon coupling, polaronic effect, and significant coupling with 2 eV Cu-O charge transfer fluctuation.Comment: 11 pages, 7 figure

Flagellum Pumping Efficacy in Shear-Thinning Viscoelastic Fluids

Microorganism motility often takes place within complex, viscoelastic fluid environments, e.g., sperm in cervicovaginal mucus and bacteria in biofilms. In such complex fluids, strains and stresses generated by the microorganism are stored and relax across a spectrum of length and time scales and the complex fluid can be driven out of its linear response regime. Phenomena not possible in viscous media thereby arise from feedback between the "swimmer" and the complex fluid, making swimming efficiency co-dependent on the propulsion mechanism and fluid properties. Here we parameterize a flagellar motor and filament properties together with elastic relaxation and nonlinear shear-thinning properties of the fluid in a computational immersed boundary model. We then explore swimming efficiency over this parameter space. One exemplary insight is that motor efficiency (measured by the volumetric flow rate) can be boosted vs.\ degraded by moderate vs.\ strong shear-thinning of the viscoelastic environment.Comment: 15 pages, 8 figure

Manufacturing knowledge sharing in PLM: a progression towards the use of heavy weight ontologies

The drive to maximize the potential benefits of decision support systems continues to increase as industry is continually driven by the competitive needs of operating in dynamic global environments. The more extensive information support tools which are becoming available in the PLM world appear to have great potential but require a substantial overhead in their configuration. However, sharing information and knowledge in cross-disciplinary teams and across system and company boundaries is not straightforward and there is a clear need for more effective frameworks for information and knowledge sharing if new product development processes are to have effective ICT support. This paper presents a view of the current status of manufacturing information sharing using light-weight ontologies and goes on to discuss the potential for heavyweight ontological engineering approaches such as the Process Specification Language (PSL). It explains why such languages are needed and how they provide an important step towards process knowledge sharing. Machining examples are used to illustrate how PSL provides a rigorous basis for process knowledge sharing and subsequently to illustrate the value of linking foundation and domain ontologies to provide a basis for multi-context knowledge sharing

Application of the scattering rate sum-rule to the interplane optical conductivity of high temperature superconductors: pseudogap and bi-layer effects

We use a recently proposed model of the interplane conductivity of high temperature superconductors to investigate the `scattering rate sum-rule' introduced by Basov and co-workers. We present a new derivation of the sum-rule. The quantal and thermal fluctuations of the order parameter which have been argued to produce the observed pseudogap behavior are shown to increase the total integrated `scattering rate' but may either increase or decrease the `quasiparticle' contribution from frequencies greater than twice the superconducting gap.Comment: 4 pages, 5 figures, revise

Healthcare provider-led interventions to support medication adherence following ACS:a meta-analysis

The efficiency with which the anaerobic fungi (phylum Neocallimastigomycota) degrade plant biomass is well-recognized and in recent years has received renewed interest. To further understand the biological mechanisms that are utilized by the rumen anaerobic fungi to break down lignocellulose, we have used a transcriptomic approach to examine carbohydrate digestion by Neocallimastix frontalis, Piromyces rhizinflata, Orpinomyces joyonii, and Anaeromyces mucronatus cultured on several carbon sources. The number of predicted unique transcripts ranged from 6,633 to 12,751. Pfam domains were identified in 62–70% of the fungal proteins and were linked to gene ontology terms to infer the biological function of the transcripts. Most of the predicted functions are consistent across species suggesting a similar overall strategy evolved for successful colonization of the rumen. However, the presence of differential profiles in enzyme classes suggests that there may be also be niche specialization. All fungal species were found to express an extensive array of transcripts encoding carbohydrate active enzymes (CAZymes) ranging from 8.3 to 11.3% of the transcriptome. CAZyme families involved in hemicellulose digestion were the most abundant across all four fungi. This study provides additional insight into how anaerobic fungi have evolved to become specialists at breaking down the plant cell wall in the complex and, strictly anaerobic rumen ecosystem

C-axis optical properties of high Tc cuprates

A review is given of the experimental status of the interlayer coupling energy in the cuprates. A second c-axis plasmon is identified in the double layer compound Y123 for various dopings. The anomalous transport properties along the c-direction and in the planar directions are compared to model calculations based on strongly anisotropic scattering. An excellent description of the optical data at optimal doping is obtained if an anomalously large anisotropy of the scattering rate between cold spots and hot spots is assumed. This raises questions as to the physical meaning of these parameters.Comment: 4 pages, LaTeX, espcrc2.sty, 3 figures in encapsulated postscript forma

Superconductivity, phase fluctuations and the c-axis conductivity of bilayer high temperature superconductors

We present a theory of the interplane conductivity of bilayer high temperature superconductors, focusing on the effect of quantal and thermal fluctuations on the oscillator strengths of the superfluid stiffness and the bilayer plasmon. We find that the opening of the superconducting gap and establishment of superconducting phase coherence each lead to redistribution of spectral weight over wide energy scales. The factor-of-two relation between the superfluid stiffness and the change below $T_c$ in the oscillator strength of the absorptive part of the conductivity previously derived for single-layer systems, is found to be substantially modified in bilayer systems.Comment: 11 pages, 14 figure

Orbital Wave and its Observation in Orbital Ordered Titanates and Vanadates

We present a theory of the collective orbital excitation termed orbital wave in perovskite titanates and vanadates with the triply degenerate $t_{2g}$ orbitals. The dispersion relations of the orbital waves for the orbital ordered LaVO$_3$, YVO$_3$ and YTiO$_3$ are examined in the effective spin-orbital coupled Hamiltonians associated with the Jahn-Teller type couplings. We propose possible scattering processes for the Raman and inelastic neutron scatterings from the orbital wave and calculate the scattering spectra for titanates and vanadates. It is found that both the excitation spectra and the observation methods of the orbital wave are distinct qualitatively from those for the $e_g$ orbital ordered systems.Comment: 9 pages, 7 figure