SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding

Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SLIQ, a set of simple linear inequalities derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a preprocessing step for any scaffolding algorithm. We tested the SLIQ inequalities on five real data sets ranging in complexity from simple bacterial genomes to complex mammalian genomes and compared the results to the majority voting procedure used by many other scaffolding algorithms. SLIQ predicted the relative positions and orientations of the contigs with high accuracy in all cases and gave more accurate position predictions than majority voting for complex genomes, in particular the human genome. Finally, we present a simple scaffolding algorithm that produces linear scaffolds given a contig digraph. We show that our algorithm is very efficient compared to other scaffolding algorithms while maintaining high accuracy in predicting both contig positions and orientations for real data sets.Comment: 16 pages, 6 figures, 7 table

OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L

OPA1, a dynamin-related guanosine triphosphatase mutated in dominant optic atrophy, is required for the fusion of mitochondria. Proteolytic cleavage by the mitochondrial processing peptidase generates long isoforms from eight messenger RNA (mRNA) splice forms, whereas further cleavages at protease sites S1 and S2 generate short forms. Using OPA1-null cells, we developed a cellular system to study how individual OPA1 splice forms function in mitochondrial fusion. Only mRNA splice forms that generate a long isoform in addition to one or more short isoforms support substantial mitochondrial fusion activity. On their own, long and short OPA1 isoforms have little activity, but, when coexpressed, they functionally complement each other. Loss of mitochondrial membrane potential destabilizes the long isoforms and enhances the cleavage of OPA1 at S1 but not S2. Cleavage at S2 is regulated by the i-AAA protease Yme1L. Our results suggest that mammalian cells have multiple pathways to control mitochondrial fusion through regulation of the spectrum of OPA1 isoforms

Love motels : oriental phenomenon or emergent sector?

This study explores the 'Love Motel' concept by examining the changing attitude of consumers in Taiwan. This will increase knowledge of the sector and define love motels. The literature review charts the development of Taiwanese love motels from a duel origin; American Motels and Japanese 'Love Hotels.' This is followed by an empirical qualitative study consisting of a two-stage collection strategy: focus groups of hospitality and tourism professionals to gather a wide range of opinions on the subject area followed by semi-structured interviews with consumers. The findings split into three interrelated areas: growth of Taiwanese love motels due to more liberal attitudes towards sexual practice; a change in the public perception of motels due to increased standards and an increased satisfaction with the personal consumption experience; these hotels are designed for couples. The empirical element of this study is an exploration of consumer experience in Taiwanese love hotels. Due to the sensitive nature of some of the data that was gathered a qualitative approach has been adopted. The sexual associations with this product appear almost coincidental. If the love motel product is considered in its purest form it is simply a hotel product that provides complete anonymity for its guests. Therefore, despite its application in South East Asia, this hospitality concept has potential to be applied in a variety of guises. The phenomenon of 'Love Hotels' is absent from hospitality management literature; this paper begins to fill that gap by beginning a discussion on this possibly controversial sector

One-way quantum computing with arbitrarily large time-frequency continuous-variable cluster states from a single optical parametric oscillator

One-way quantum computing is experimentally appealing because it requires only local measurements on an entangled resource called a cluster state. Record-size, but non-universal, continuous-variable cluster states were recently demonstrated separately in the time and frequency domains. We propose to combine these approaches into a scalable architecture in which a single optical parametric oscillator and simple interferometer entangle up to ($3\times 10^3$ frequencies) $\times$ (unlimited number of temporal modes) into a new and computationally universal continuous-variable cluster state. We introduce a generalized measurement protocol to enable improved computational performance on this new entanglement resource.Comment: (v4) Consistent with published version; (v3) Fixed typo in arXiv abstract, 14 pages, 8 figures; (v2) Supplemental material incorporated into main text, additional explanations added, results unchanged, 14 pages, 8 figures; (v1) 5 pages (3 figures) + 6 pages (5 figures) of supplemental material; submitted for publicatio

Black hole variability and the star formation-active galactic nucleus connection : do all star-forming galaxies host an active galactic nucleus?

We investigate the effect of active galactic nucleus (AGN) variability on the observed connection between star formation and black hole accretion in extragalactic surveys. Recent studies have reported relatively weak correlations between observed AGN luminosities and the properties of AGN hosts, which has been interpreted to imply that there is no direct connection between AGN activity and star formation. However, AGNs may be expected to vary significantly on a wide range of timescales (from hours to Myr) that are far shorter than the typical timescale for star formation (gsim100 Myr). This variability can have important consequences for observed correlations. We present a simple model in which all star-forming galaxies host an AGN when averaged over ~100 Myr timescales, with long-term average AGN accretion rates that are perfectly correlated with the star formation rate (SFR). We show that reasonable prescriptions for AGN variability reproduce the observed weak correlations between SFR and L AGN in typical AGN host galaxies, as well as the general trends in the observed AGN luminosity functions, merger fractions, and measurements of the average AGN luminosity as a function of SFR. These results imply that there may be a tight connection between AGN activity and SFR over galaxy evolution timescales, and that the apparent similarities in rest-frame colors, merger rates, and clustering of AGNs compared to "inactive" galaxies may be due primarily to AGN variability. The results provide motivation for future deep, wide extragalactic surveys that can measure the distribution of AGN accretion rates as a function of SFR

Conservative Initial Mapping For Multidimensional Simulations of Stellar Explosions

Mapping one-dimensional stellar profiles onto multidimensional grids as initial conditions for hydrodynamics calculations can lead to numerical artifacts, one of the most severe of which is the violation of conservation laws for physical quantities such as energy and mass. Here we introduce a numerical scheme for mapping one-dimensional spherically-symmetric data onto multidimensional meshes so that these physical quantities are conserved. We validate our scheme by porting a realistic 1D Lagrangian stellar profile to the new multidimensional Eulerian hydro code CASTRO. Our results show that all important features in the profiles are reproduced on the new grid and that conservation laws are enforced at all resolutions after mapping.Comment: 7 pages, 5 figures, Proceeding for Conference on Computational Physics (CCP 2011

Carbonic anhydrase, coral calcification and a new model of stable isotope vital effects

The stable isotope compositions of biogenic carbonates have been used for paleoceanographic and paleoclimatic reconstructions for decades, and produced some of the most iconic records in the field. However, we still lack a fully mechanistic understanding of the stable isotope proxies, especially the biological overprint on the environmental signals termed “vital effects”. A ubiquitous feature of stable isotope vital effects in marine calcifying organisms is a strong correlation between δ^(18)O and δ^(13)C in a range of values that are depleted from inorganic calcite/aragonite. Two mechanisms have been proposed to explain this correlation, one based on kinetic isotope effects during CO_2(aq)-HCO_3− inter-conversion, the other based on equilibrium isotope exchange during pH dependent speciation of the dissolved inorganic carbon (DIC) pool. Neither mechanism explains all the stable isotope features observed in biogenic carbonates. Here we present a fully kinetic model of biomineralization and its isotope effects using deep-sea corals as a test organism. A key component of our model is the consideration of the enzyme carbonic anhydrase in catalyzing the CO2(aq)-HCO_3− inter-conversion reactions in the extracellular calcifying fluid (ECF). We find that the amount of carbonic anhydrase not only modulates the carbonate chemistry of the calcifying fluid, but also helps explain the slope of the δ^(18)O-δ^(13)C correlation. Differences in CA activity in the biomineralization process can possibly explain the observed range of δ^(18)O-δ^(13)C slopes in different calcifying organisms. A mechanistic understanding of stable isotope vital effects with numerical models can help us develop better paleoceanographic tracers