SANA NetGO: A combinatorial approach to using Gene Ontology (GO) terms to score network alignments

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment are not isolated: each pairing is implicitly dependent upon every other pairing via the alignment itself. Current methods fail to take into account the frequency of GO terms across the networks, and attempt to account for common GO terms in an ad hoc fashion by imposing arbitrary rules on when to "allow" GO terms based on their location in the GO hierarchy, rather than using readily available frequency information in the PPI networks themselves. Here we develop a new measure, NetGO, that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without requiring arbitrary cutoffs. In particular, NetGO down-weights the score of frequent GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO by creating alignments of predetermined quality based on homologous pairs of nodes and show that NetGO correlates with alignment quality much better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measures--a feature not shared with existing GO-based network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job than existing measures at separating good alignments from bad ones

Deriving real-time action systems with multiple time bands using algebraic reasoning

The verify-while-develop paradigm allows one to incrementally develop programs from their specifications using a series of calculations against the remaining proof obligations. This paper presents a derivation method for real-time systems with realistic constraints on their behaviour. We develop a high-level interval-based logic that provides flexibility in an implementation, yet allows algebraic reasoning over multiple granularities and sampling multiple sensors with delay. The semantics of an action system is given in terms of interval predicates and algebraic operators to unify the logics for an action system and its properties, which in turn simplifies the calculations and derivations

Scalable Automated Detection of Spiral Galaxy Arm Segments

Given an approximately centered image of a spiral galaxy, we describe an entirely automated method that finds, centers, and sizes the galaxy and then automatically extracts structural information about the spiral arms. For each arm segment found, we list the pixels in that segment and perform a least-squares fit of a logarithmic spiral arc to the pixels in the segment. The algorithm takes about 1 minute per galaxy, and can easily be scaled using parallelism. We have run it on all ~644,000 Sloan objects classified as "galaxy" and large enough to observe some structure. Our algorithm is stable in the sense that the statistics across a large sample of galaxies vary smoothly based on algorithmic parameters, although results for individual galaxies can sometimes vary in a non-smooth but easily understood manner. We find a very good correlation between our quantitative description of spiral structure and the qualitative description provided by humans via Galaxy Zoo. In addition, we find that pitch angle often varies significantly segment-to-segment in a single spiral galaxy, making it difficult to define "the" pitch angle for a single galaxy. Finally, we point out how complex arm structure (even of long arms) can lead to ambiguity in defining what an "arm" is, leading us to prefer the term "arm segments".Comment: 4 pages (twocolumn),5 figures, 2 tables. Submitted to ApJ. Letter

Illuminance and luminance distributions of a prototype ambient illumination system for Space Station Freedom

Preliminary results of research conducted in the late 1970's indicate that perceptual qualities of an enclosure can be influenced by the distribution of illumination within the enclosure. Subjective impressions such as spaciousness, perceptual clarity, and relaxation or tenseness, among others, appear to be related to different combinations of surface luminance. A prototype indirect ambient illumination system was developed which will allow crew members to alter surface luminance distributions within an enclosed module, thus modifying perceptual cues to match crew preferences. A traditional lensed direct lighting system was compared to the prototype utilizing the full-scale mockup of Space Station Freedom developed by Marshall Space Flight Center. The direct lensed system was installed in the habitation module with the indirect prototype deployed in the U.S. laboratory module. Analysis centered on the illuminance and luminance distributions resultant from these systems and the implications of various luminaire spacing options. All test configurations were evaluated for compliance with NASA Standard 3000, Man-System Integration Standards

Is airline price dispersion the result of careful planning or competitive forces?

Airlines ; Competition ; Prices

The cD galaxy in Abell cluster 1775

Over the last 20 years, a number of workers have studied the multiple nuclei cD galaxy in the rich Abell cluster 1775, trying to discover its nature. In all the cases though, very little has been published concerning its morphology. The majority of arguments about the nature of this object have been based on the relative radial velocities of the 2 components with each other and with the other galaxies in the cluster, or its radio morphology. Very little work has been done on the optical morphology. To rectify that lack of data, the authors have obtained charge coupled device (CCD) images of the cD. The authors find from the CCD data that the cD is unlikely to be a bound object and that there is strong evidence for a collision

In situ generation of Mes2Mg as a non-nucleophilic carbon-centred base reagent for the efficient one-pot conversion of ketones to silyl enol ethers

Treatment of commercially available MesMgBr with 1,4-dioxane produces the key Mes2Mg reagent in situ which then mediates the deprotonation of ketones to deliver trimethylsilyl enol ethers, at readily accessible temperatures and without any nucleophilic addition, in an expedient and high yielding one-pot process