A Computational Method for the Rate Estimation of Evolutionary Transpositions

Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as transpositions, they are rarely observed and believed to constitute only a small fraction of genome rearrangements happening in the course of evolution. The analysis of transpositions is further obfuscated by intractability of the underlying computational problems. We propose a computational method for estimating the rate of transpositions in evolutionary scenarios between genomes. We applied our method to a set of mammalian genomes and estimated the transpositions rate in mammalian evolution to be around 0.26.Comment: Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), 2015. (to appear

The stability of modified gravity models

Conditions for the existence and stability of de Sitter space in modified gravity are derived by considering inhomogeneous perturbations in a gauge-invariant formalism. The stability condition coincides with the corresponding condition for stability with respect to homogeneous perturbations, while this is not the case in scalar-tensor gravity. The stability criterion is applied to various modified gravity models of the early and the present universe.Comment: 22 pages, LaTeX, to appear in Phys. Rev.

Rate of photon production from hot hadronic matter

Thermal photon emission rates from hot hadronic matter are studied to order $e^{2}g^{4}$, where $g$ indicates a strong-interaction coupling constant. Radiative decay of mesons, Compton and annihilation processes for hadrons, and bremsstrahlung reactions are all considered. Compared to the standard rates from the literature, one finds two orders of magnitude increase for low photon energies stemming mainly from bremsstrahlung and then a modest increase (factor of 2) for intermediate and high energy photons owing to radiative decays for a variety of mesons and from other reactions involving strangeness. These results could have important consequences for electromagnetic radiation studies at RHIC.Comment: 5 pages LaTeX, 4 Postscript figure

The state of Denmark: what voters can tell us about the future of the Danish ideal

Denmark is often held up as an ideal society with a well-functioning welfare state, low levels of corruption, and high levels of social and political stability. But behind this perception, the country is facing up to a number of important challenges. Drawing on a new book, Rune Stubager, Kasper M. Hansen, Michael S. Lewis-Beck and Richard Nadeau explain how voters have responded to key macrosocial challenges since the 1970s and assess where this leaves the future of the Danish ideal

TRIDENT: an Infrared Differential Imaging Camera Optimized for the Detection of Methanated Substellar Companions

A near-infrared camera in use at the Canada-France-Hawaii Telescope (CFHT) and at the 1.6-m telescope of the Observatoire du Mont-Megantic is described. The camera is based on a Hawaii-1 1024x1024 HgCdTe array detector. Its main feature is to acquire three simultaneous images at three wavelengths across the methane absorption bandhead at 1.6 microns, enabling, in theory, an accurate subtraction of the stellar point spread function (PSF) and the detection of faint close methanated companions. The instrument has no coronagraph and features fast data acquisition, yielding high observing efficiency on bright stars. The performance of the instrument is described, and it is illustrated by laboratory tests and CFHT observations of the nearby stars GL526, Ups And and Chi And. TRIDENT can detect (6 sigma) a methanated companion with delta H = 9.5 at 0.5" separation from the star in one hour of observing time. Non-common path aberrations and amplitude modulation differences between the three optical paths are likely to be the limiting factors preventing further PSF attenuation. Instrument rotation and reference star subtraction improve the detection limit by a factor of 2 and 4 respectively. A PSF noise attenuation model is presented to estimate the non-common path wavefront difference effect on PSF subtraction performance.Comment: 41 pages, 16 figures, accepted for publication in PAS

Management of Occupational Manganism: Consensus of an Experts' Panel

Studies and Research Projects / Report R-417, Montréal, IRSST http://www.irsst.qc.ca/en/_publicationirsst_100134.html (Lucchini R was a member of the Expert Panel

The Exact Evolution Equation of the Curvature Perturbation for Closed Universe

As is well known, the exact evolution equation of the curvature perturbation plays a very important role in investigation of the inflation power spectrum of the flat universe. However, its corresponding exact extension for the non-flat universes has not yet been given out clearly. The interest in the non-flat, specially closed, universes is being aroused recently. The need of this extension is pressing. We start with most elementary physical consideration and obtain finally this exact evolution equation of the curvature perturbation for the non-flat universes, as well as the evolutionary controlling parameter and the exact expression of the variable mass in this equation. We approximately do a primitive and immature analysis on the power spectrum of non-flat universes. This analysis shows that this exact evolution equation of the curvature perturbation for the non-flat universes is very complicated, and we need to do a lot of numerical and analytic work for this new equation in future in order to judge whether the universe is flat or closed by comparison between theories and observations.Comment: 10 pages, no figures, Late

Word Embeddings for Entity-annotated Texts

Learned vector representations of words are useful tools for many information retrieval and natural language processing tasks due to their ability to capture lexical semantics. However, while many such tasks involve or even rely on named entities as central components, popular word embedding models have so far failed to include entities as first-class citizens. While it seems intuitive that annotating named entities in the training corpus should result in more intelligent word features for downstream tasks, performance issues arise when popular embedding approaches are naively applied to entity annotated corpora. Not only are the resulting entity embeddings less useful than expected, but one also finds that the performance of the non-entity word embeddings degrades in comparison to those trained on the raw, unannotated corpus. In this paper, we investigate approaches to jointly train word and entity embeddings on a large corpus with automatically annotated and linked entities. We discuss two distinct approaches to the generation of such embeddings, namely the training of state-of-the-art embeddings on raw-text and annotated versions of the corpus, as well as node embeddings of a co-occurrence graph representation of the annotated corpus. We compare the performance of annotated embeddings and classical word embeddings on a variety of word similarity, analogy, and clustering evaluation tasks, and investigate their performance in entity-specific tasks. Our findings show that it takes more than training popular word embedding models on an annotated corpus to create entity embeddings with acceptable performance on common test cases. Based on these results, we discuss how and when node embeddings of the co-occurrence graph representation of the text can restore the performance.Comment: This paper is accepted in 41st European Conference on Information Retrieva