A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

COLA II - Radio and Spectroscopic Diagnostics of Nuclear Activity in Galaxies

We present optical spectroscopic observations of 93 galaxies taken from the infra-red selected COLA (Compact Objects in Low Power AGN) sample. The sample spans the range of far-IR luminosities from normal galaxies to LIRGs. Of the galaxies observed, 78 (84%) exhibit emission lines. Using a theoretically-based optical emission-line scheme we classify 15% of the emission-line galaxies as Seyferts, 77% as starbursts, and the rest are either borderline AGN/starburst or show ambiguous characteristics. We find little evidence for an increase in the fraction of AGN in the sample as a function of far-IR luminosity but our sample covers only a small range in infrared luminosity and thus a weak trend may be masked. As a whole the Seyfert galaxies exhibit a small, but significant, radio excess on the radio-FIR correlation compared to the galaxies classified as starbursts. Compact (<0.05'') radio cores are detected in 55% of the Seyfert galaxies, and these galaxies exhibit a significantly larger radio excess than the Seyfert galaxies in which cores were not detected. Our results indicate that there may be two distinct populations of Seyferts, ``radio-excess'' Seyferts, which exhibit extended radio structures and compact radio cores, and ``radio-quiet'' Seyferts, in which the majority of the radio emission can be attributed to star-formation in the host galaxy. No significant difference is seen between the IR and optical spectroscopic properties of Seyferts with and without radio cores. (Abridged)Comment: 24 pages, 4 figures, 6 tables. Accepted for publication in ApJ, February 200

Ownership and control in a competitive industry

We study a differentiated product market in which an investor initially owns a controlling stake in one of two competing firms and may acquire a non-controlling or a controlling stake in a competitor, either directly using her own assets, or indirectly via the controlled firm. While industry profits are maximized within a symmetric two product monopoly, the investor attains this only in exceptional cases. Instead, she sometimes acquires a noncontrolling stake. Or she invests asymmetrically rather than pursuing a full takeover if she acquires a controlling one. Generally, she invests indirectly if she only wants to affect the product market outcome, and directly if acquiring shares is profitable per se. --differentiated products,separation of ownership and control,private benefits of control

Efficacy and safety profiles of manidipine compared with amlodipine: A meta-analysis of head-to-head trials

The aim of this meta-analysis was to compare the efficacy and safety profile of manidipine 20 mg with that of amlodipine 10 mg. A systematic research of quantitative data produced or published between 1995 and 2009 was performed. Head-to-head randomized controlled trials (RCTs) of 12 months minimum duration reporting comparative efficacy (changes in systolic and diastolic blood pressure) and safety (total adverse events and ankle oedema), were included. Four high-quality RCTs, accounting for 838 patients (436 received manidipine and 402 received amlodipine) were included. The effi cacy of manidipine and amlodipine was statistically equivalent: effect size for DBP =−0.08 (p = 0.22) and SBP =−0.01 (p =0.83).The global safety of manidipine was signifi cantly better than amlodipine: the relative risk (RR) for adverse event was 0.69 (0.56 – 0.85), and particularly for ankle oedema RR was 0.35 (0.22 – 0.54). Publication bias was not signifi cant and the robustness of the analyses was good. These data suggest a better efficacy/safety ratio of manidipine over amlodipine

Using LES to Study Reacting Flows and Instabilities in Annular Combustion Chambers

Great prominence is put on the design of aeronautical gas turbines due to increasingly stringent regulations and the need to tackle rising fuel prices. This drive towards innovation has resulted sometimes in new concepts being prone to combustion instabilities. In the particular field of annular combustion chambers, these instabilities often take the form of azimuthal modes. To predict these modes, one must compute the full combustion chamber, which remained out of reach until very recently and the development of massively parallel computers. Since one of the most limiting factors in performing Large Eddy Simulation (LES) of real combustors is estimating the adequate grid, the effects of mesh resolution are investigated by computing full annular LES of a realistic helicopter combustion chamber on three grids, respectively made of 38, 93 and 336 million elements. Results are compared in terms of mean and fluctuating fields. LES captures self-established azimuthal modes. The presence and structure of the modes is discussed. This study therefore highlights the potential of LES for studying combustion instabilities in annular gas turbine combustors

The AO Pediatric Comprehensive Classification of Long Bone Fractures (PCCF).

Background and purpose - To achieve a common understanding when dealing with long bone fractures in children, the AO Pediatric Comprehensive Classification of Long Bone Fractures (AO PCCF) was introduced in 2007. As part of its final validation, we present the most relevant fracture patterns in the lower extremities of a representative population of children classified according to the PCCF. Patients and methods - We included patients up to the age of 17 who were diagnosed with 1 or more long bone fractures between January 2009 and December 2011 at either of 2 tertiary care university hospitals in Switzerland. Patient charts were retrospectively reviewed. Results - More lower extremity fractures occurred in boys (62%, n = 341). Of 548 fractured long bones in the lower extremity, 25% involved the femur and 75% the lower leg. The older the patients, the more combined fractures of the tibia and fibula were sustained (adolescents: 50%, 61 of 123). Salter-Harris (SH) fracture patterns represented 66% of single epiphyseal fractures (83 of 126). Overall, 74 of the 83 SH patterns occurred in the distal epiphysis. Of all the metaphyseal fractures, 74 of 79 were classified as incomplete or complete. Complete oblique spiral fractures accounted for 57% of diaphyseal fractures (120 of 211). Of all fractures, 7% (40 of 548) were classified in the category "other", including 29 fractures that were identified as toddler's fractures. 5 combined lower leg fractures were reported in the proximal metaphysis, 40 in the diaphysis, 26 in the distal metaphysis, and 8 in the distal epiphysis. Interpretation - The PCCF allows classification of lower extremity fracture patterns in the clinical setting. Re-introduction of a specific code for toddler's fractures in the PCCF should be considered

Pain

Chronic pain (CP) is often accompanied by mental disorders (MDs). However, little is known concerning the long-term effect of MDs, personality traits, and early-life traumatic events (ETEs) on CP course. Accordingly, we aimed to prospectively assess the associations of major depressive disorders (MDDs), anxiety disorders, personality traits, and ETEs with the incidence and the persistence of CP in middle-aged and older community dwellers. Data stemmed from the 3 first follow-up evaluations of CoLaus|PsyCoLaus, a prospective cohort conducted in the general population of Lausanne (Switzerland). Diagnostic criteria for MDs and ETEs were elicited using semistructured interviews. CP and personality traits were assessed by self-rating questionnaires. Follow-up intervals were subdivided into 2 groups: those without (n = 2280) and those with (n = 1841) CP initially. The associations between the psychological variables and the occurrence or persistence of CP 5 years later were assessed using serially adjusted logistic regression models. Higher neuroticism (odds ratio [95% confidence interval] 1.21 [1.08; 1.36]) and extraversion (1.18 [1.06; 1.32]) were associated with higher 5-year CP incidence, whereas current (2.14 [1.34; 3.44]) and remitted MDD (1.29 [1.00; 1.66]) as well as lower extraversion (0.83 [0.74; 0.94]) were associated with persistence of CP. By contrast, ETEs and anxiety disorders were not associated with the incidence or persistence of CP. Our results suggest that personality traits are associated with both CP occurrence and persistence, whereas the MDDs may be more associated with CP persistence. Both personality and MDD are accessible to psychotherapy, and MDD is also accessible to pharmacotherapy. Hence, these therapeutic measures might decrease the risk of CP and its persistence

A divergent heritage for complex organics in Isheyevo lithic clasts

Primitive meteorites are samples of asteroidal bodies that contain a high proportion of chemically complex organic matter (COM) including prebiotic molecules such as amino acids, which are thought to have been delivered to Earth via impacts during the early history of the Solar System. Thus, understanding the origin of COM, including their formation pathway(s) and environment(s), is critical to elucidate the origin of life on Earth as well as assessing the potential habitability of exoplanetary systems. The Isheyevo CH/CBb carbonaceous chondrite contains chondritic lithic clasts with variable enrichments in 15N believed to be of outer Solar System origin. Using transmission electron microscopy (TEM-EELS) and in situ isotope analyses (SIMS and NanoSIMS), we report on the structure of the organic matter as well as the bulk H and N isotope composition of Isheyevo lithic clasts. These data are complemented by electron microprobe analyses of the clast mineral chemistry and bulk Mg and Cr isotopes obtained by inductively coupled plasma and thermal ionization mass spectrometry, respectively (MC-ICPMS and TIMS). Weakly hydrated (A) clasts largely consist of Mg-rich anhydrous silicates with local hydrated veins composed of phyllosilicates, magnetite and globular and diffuse organic matter. Extensively hydrated clasts (H) are thoroughly hydrated and contain Fe-sulfides, sometimes clustered with organic matter, as well as magnetite and carbonates embedded in a phyllosilicate matrix. The A-clasts are characterized by a more 15N-rich bulk nitrogen isotope composition (δ15N = 200–650‰) relative to H-clasts (δ15N = 50–180‰) and contain extremely 15N-rich domains with δ15N 15N-rich domains show that the lithic clast diffuse organic matter is typically more 15N-rich than globular organic matter. The correlated δ15N values and C/N ratios of nanoglobules require the existence of multiple organic components, in agreement with the H isotope data. The combined H and N isotope data suggest that the organic precursors of the lithic clasts are defined by an extremely 15N-poor (similar to solar) and D-rich component for H-clasts, and a moderately 15N-rich and D-rich component for A-clasts. In contrast, the composition of the putative fluids is inferred to include D-poor but moderately to extremely 15N-rich H- and N-bearing components. The variable 15N enrichments in H- and A-clasts are associated with structural differences in the N bonding environments of their diffuse organic matter, which are dominated by amine groups in H-clasts and nitrile functional groups in A-clasts. We suggest that the isotopically divergent organic precursors in Isheyevo clasts may be similar to organic moieties in carbonaceous chondrites (CI, CM, CR) and thermally recalcitrant organic compounds in ordinary chondrites, respectively. The altering fluids, which are inferred to cause the 15N enrichments observed in the clasts, may be the result of accretion of variable abundances of NH3 and HCN ices. Finally, using bulk Mg and Cr isotope composition of clasts, we speculate on the accretion regions of the various primitive chondrites and components and the origin of the Solar System’s N and H isotope variability

Optimal Homogenization of Perfusion Flows in Microfluidic Bio-Reactors: A Numerical Study

In recent years, the interest in small-scale bio-reactors has increased dramatically. To ensure homogeneous conditions within the complete area of perfused microfluidic bio-reactors, we develop a general design of a continually feed bio-reactor with uniform perfusion flow. This is achieved by introducing a specific type of perfusion inlet to the reaction area. The geometry of these inlets are found using the methods of topology optimization and shape optimization. The results are compared with two different analytic models, from which a general parametric description of the design is obtained and tested numerically. Such a parametric description will generally be beneficial for the design of a broad range of microfluidic bioreactors used for, e.g., cell culturing and analysis and in feeding bio-arrays

Discovery of VHE gamma-rays from the high-frequency-peaked BL Lac object RGB J0152+017

Aims: The BL Lac object RGB J0152+017 (z=0.080) was predicted to be a very high-energy (VHE; > 100 GeV) gamma-ray source, due to its high X-ray and radio fluxes. Our aim is to understand the radiative processes by investigating the observed emission and its production mechanism using the High Energy Stereoscopic System (H.E.S.S.) experiment. Methods: We report recent observations of the BL Lac source RGB J0152+017 made in late October and November 2007 with the H.E.S.S. array consisting of four imaging atmospheric Cherenkov telescopes. Contemporaneous observations were made in X-rays by the Swift and RXTE satellites, in the optical band with the ATOM telescope, and in the radio band with the Nancay Radio Telescope. Results: A signal of 173 gamma-ray photons corresponding to a statistical significance of 6.6 sigma was found in the data. The energy spectrum of the source can be described by a powerlaw with a spectral index of 2.95+/-0.36stat+/-0.20syst. The integral flux above 300 GeV corresponds to ~2% of the flux of the Crab nebula. The source spectral energy distribution (SED) can be described using a two-component non-thermal synchrotron self-Compton (SSC) leptonic model, except in the optical band, which is dominated by a thermal host galaxy component. The parameters that are found are very close to those found in similar SSC studies in TeV blazars. Conclusions: RGB J0152+017 is discovered as a source of VHE gamma-rays by H.E.S.S. The location of its synchrotron peak, as derived from the SED in Swift data, allows clearly classification it as a high-frequency-peaked BL Lac (HBL).Comment: Accepted for publication in A&A Letters (5 pages, 4 figures