Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Health effects of home energy efficiency interventions in England: a modelling study

Objective: To assess potential public health impacts of changes to indoor air quality and temperature due to energy efficiency retrofits in English dwellings to meet 2030 carbon reduction targets. Design: Health impact modelling study. Setting: England. Participants: English household population. Intervention: Three retrofit scenarios were modelled: (1) fabric and ventilation retrofits installed assuming building regulations are met. (2) As with scenario (1) but with additional ventilation for homes at risk of poor ventilation. (3) As with scenario (1) but with no additional ventilation to illustrate the potential risk of weak regulations and non-compliance. Main Outcome: Primary outcomes were changes in quality adjusted life years (QALYs) over 50 years from cardiorespiratory diseases, lung cancer, asthma and common mental disorders due to changes in indoor air pollutants, including: second-hand tobacco smoke, PM2.5 from indoor and outdoor sources, radon, mould, and indoor winter temperatures. Results: The modelling study estimates showed that scenario (1) resulted in positive effects on net mortality and morbidity of 2,241 (95% credible intervals (CI) 2,085 to 2,397) QALYs per 10,000 persons over 50 years due to improved temperatures and reduced exposure to indoor pollutants, despite an increase in exposure to outdoor–generated PM2.5. Scenario (2) resulted in a negative impact of -728 (95% CI -864 to -592) QALYs per 10,000 persons over 50 years due to an overall increase in indoor pollutant exposures. Scenario (3) resulted in -539 (95% CI -678 to -399) QALYs per 10,000 persons over 50 years due to an increase in indoor exposures despite targeting. Conclusions: If properly implemented alongside ventilation, energy efficiency retrofits in housing can improve health by reducing exposure to cold and air pollutants. Maximising the health benefits requires careful understanding of the balance of changes in pollutant exposures, highlighting the importance of ventilation to mitigate the risk of poor indoor air quality

Strength distribution of repeatedly broken chains

We determine the probability distribution of the breaking strength for chains of N links, which have been produced by repeatedly breaking a very long chain.Comment: 4 pages, 1 figur

Critical issues in ionospheric data quality and implications for scientific studies

Ionospheric data are valuable records of the behavior of the ionosphere, solar activity, and the entire Sun-Earth system. The data are critical for both societally important services and scientific investigations of upper atmospheric variability. This work investigates some of the difficulties and pitfalls in maintaining long-term records of geophysical measurements. This investigation focuses on the ionospheric parameters contained in the historical data sets within the National Oceanic and Atmospheric Administration National Geophysical Data Center and Space Physics Interactive Data Resource databases. These archives include data from approximately 100 ionosonde stations worldwide, beginning in the early 1940s. Our study focuses on the quality and consistency of ionosonde data accessible via the primary Space Physics Interactive Data Resource node located within the National Oceanic and Atmospheric Administration National Geophysical Data Center and the World Data Center for Solar-Terrestrial Physics located in Boulder, Colorado. We find that, although the Space Physics Interactive Data Resource archives contained an impressive amount of high-quality data, specific problems existed involving missing and noncontiguous data sets, long-term variations or changes in methodologies and analysis procedures used, and incomplete documentation. The important lessons learned from this investigation are that the data incorporated into an archive must have clear traceability back to the primary source, including scientific validation by the contributors, and that the historical records must have associated metadata that describe relevant nuances in the observations. Although this report only focuses on historical ionosonde data in National Oceanic and Atmospheric Administration databases, we feel that these findings have general applicability to environmental scientists interested in using long-term geophysical data sets for climate and global change research.Peer ReviewedPostprint (published version

The Quantum-Classical Crossover in the Adiabatic Response of Chaotic Systems

The autocorrelation function of the force acting on a slow classical system, resulting from interaction with a fast quantum system is calculated following Berry-Robbins and Jarzynski within the leading order correction to the adiabatic approximation. The time integral of the autocorrelation function is proportional to the rate of dissipation. The fast quantum system is assumed to be chaotic in the classical limit for each configuration of the slow system. An analytic formula is obtained for the finite time integral of the correlation function, in the framework of random matrix theory (RMT), for a specific dependence on the adiabatically varying parameter. Extension to a wider class of RMT models is discussed. For the Gaussian unitary and symplectic ensembles for long times the time integral of the correlation function vanishes or falls off as a Gaussian with a characteristic time that is proportional to the Heisenberg time, depending on the details of the model. The fall off is inversely proportional to time for the Gaussian orthogonal ensemble. The correlation function is found to be dominated by the nearest neighbor level spacings. It was calculated for a variety of nearest neighbor level spacing distributions, including ones that do not originate from RMT ensembles. The various approximate formulas obtained are tested numerically in RMT. The results shed light on the quantum to classical crossover for chaotic systems. The implications on the possibility to experimentally observe deterministic friction are discussed.Comment: 26 pages, including 6 figure

Magnetic Dipole Absorption of Radiation in Small Conducting Particles

We give a theoretical treatment of magnetic dipole absorption of electromagnetic radiation in small conducting particles, at photon energies which are large compared to the single particle level spacing, and small compared to the plasma frequency. We discuss both diffusive and ballistic electron dynamics for particles of arbitrary shape. The conductivity becomes non-local when the frequency is smaller than the frequency \omega_c characterising the transit of electrons from one side of the particle to the other, but in the diffusive case \omega_c plays no role in determining the absorption coefficient. In the ballistic case, the absorption coefficient is proportional to \omega^2 for \omega << \omega_c, but is a decreasing function of \omega for \omega >> \omega_c.Comment: 25 pages of plain TeX, 2 postscipt figure

Wall turbulence control

A variety of wall turbulence control devices which were experimentally investigated are discussed; these include devices for burst control, alteration of outer flow structures, large eddy substitution, increased heat transfer efficiency, and reduction of wall pressure fluctuations. Control of pre-burst flow was demonstrated with a single, traveling surface depression which is phase-locked to elements of the burst production process. Another approach to wall turbulence control is to interfere with the outer layer coherent structures. A device in the outer part of a boundary layer was shown to suppress turbulence and reduce drag by opposing both the mean and unsteady vorticity in the boundary layer. Large eddy substitution is a method in which streamline curvature is introduced into the boundary layer in the form of streamwise vortices. Riblets, which were already shown to reduce turbulent drag, were also shown to exhibit superior heat transfer characteristics. Heat transfer efficiency as measured by the Reynolds Analogy Factor was shown to be as much as 36 percent greater than a smooth flat plate in a turbulent boundary layer. Large Eddy Break-Up (LEBU) which are also known to reduce turbulent drag were shown to reduce turbulent wall pressure fluctuation

Band Distributions for Quantum Chaos on the Torus

Band distributions (BDs) are introduced describing quantization in a toral phase space. A BD is the uniform average of an eigenstate phase-space probability distribution over a band of toral boundary conditions. A general explicit expression for the Wigner BD is obtained. It is shown that the Wigner functions for {\em all} of the band eigenstates can be reproduced from the Wigner BD. Also, BDs are shown to be closer to classical distributions than eigenstate distributions. Generalized BDs, associated with sets of adjacent bands, are used to extend in a natural way the Chern-index characterization of the classical-quantum correspondence on the torus to arbitrary rational values of the scaled Planck constant.Comment: 12 REVTEX page