ngsLD: evaluating linkage disequilibrium using genotype likelihoods

MOTIVATION: Linkage disequilibrium measures the correlation between genetic loci and is highly informative for association mapping and population genetics. As many studies rely on called genotypes for estimating linkage disequilibrium, their results can be affected by data uncertainty, especially when employing a low read depth sequencing strategy. Furthermore, there is a manifest lack of tools for the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with limited sample sizes. RESULTS: ngsLD addresses these issues by estimating linkage disequilibrium directly from genotype likelihoods in a fast, reliable and user-friendly implementation. This method makes use of the full information available from sequencing data and provides accurate estimates of linkage disequilibrium patterns compared to approaches based on genotype calling. We conducted a case study to investigate how linkage disequilibrium decays over physical distance in two avian species. AVAILABILITY: The methods presented in this work were implemented in C/C and are freely available for non-commercial use from https://github.com/fgvieira/ngsLD

QCD Corrections to K-Kbar Mixing in R-symmetric Supersymmetric Models

The leading-log QCD corrections to K-Kbar mixing in R-symmetric supersymmetric models are computed using effective field theory techniques. The spectrum topology where the gluino is significantly heavier than the squarks is motivated and focused on. It is found that, like in the MSSM, QCD corrections can tighten the kaon mass difference bound by roughly a factor of three. CP violation is also briefly considered, where QCD corrections can constrain phases to be as much as a factor of ten smaller than the uncorrected value.Comment: 11 pages, 11 pdf-figures; updated acknowledgments and references, clarified relationship to Ref[17], clarified CP-violation sectio

Visible Effects of the Hidden Sector

The renormalization of operators responsible for soft supersymmetry breaking is usually calculated by starting at some high scale and including only visible sector interactions in the evolution equations, while ignoring hidden sector interactions. Here we explain why this is correct only for the most trivial structures in the hidden sector, and discuss possible implications. This investigation was prompted by the idea of conformal sequestering. In that framework hidden sector renormalizations by nearly conformal dynamics are critical. In the original models of conformal sequestering it was necessary to impose hidden sector flavor symmetries to achieve the sequestered form. We present models which can evade this requirement and lead to no-scale or anomaly mediated boundary conditions; but the necessary structures do not seem generic. More generally, the ratios of scalar masses to gaugino masses, the $\mu$-term, the $B\mu$-term, $A$-terms, and the gravitino mass can be significantly affected.Comment: 23 pages, no figure

Supersymmetry with a Chargino NLSP and Gravitino LSP

We demonstrate that the lightest chargino can be lighter than the lightest neutralino in supersymmetric models with Dirac gaugino masses as well as within a curious parameter region of the MSSM. Given also a light gravitino, such as from low scale supersymmetry breaking, this mass hierarchy leads to an unusual signal where every superpartner cascades down to a chargino that decays into an on-shell W and a gravitino, possibly with a macroscopic chargino track. We clearly identify the region of parameters where this signal can occur. We find it is generic in the context of the R-symmetric supersymmetric standard model, whereas it essentially only occurs in the MSSM when sign(M1) is not equal to sign(M2) = sign(\mu) and tan(beta) is small. We briefly comment on the search strategies for this signal at the LHC.Comment: 27 pages and 16 figure

Dirac gaugino as leptophilic dark matter

We investigate the leptophilic properties of Dirac gauginos in an R--symmetric N=2 supersymmetric model with extended gauge and Higgs sectors. The annihilation of Dirac gauginos to leptons requires no chirality flip in the final states so that it is not suppressed as in the Majorana case. This implies that it can be sizable enough to explain the positron excess observed by the PAMELA experiment with moderate or no boost factors. When squark masses are heavy, the annihilation of Dirac gauginos to hadrons is controlled by their Higgsino fraction and is driven by the $hZ$ and $W^+W^-$ final states. Moreover, at variance with the Majorana case, Dirac gauginos with a non-vanishing higgsino fraction can also have a vector coupling with the $Z$ gauge boson leading to a sizable spin--independent scattering cross section off nuclei. Saturating the current antiproton limit, we show that Dirac gauginos can leave a signal in direct detection experiments at the level of the sensitivity of dark matter searches at present and in the near future.Comment: 24 pages, 10 figures, typos corrected, final version published on JCA

High-efficiency Bragg grating enhanced on-chip photon-number-resolving detectors

The recent trend towards integration of quantum optics experiments has produced a demand for on-chip single photon detectors with high quantum efficiencies. In previous work we demonstrated integrated photon number resolving detectors for use at telecommunications wavelengths [1], here we outline developments of this design which have enabled improvements in the quantum efficiency, permitting an on-chip detection efficiency of 92% to be obtained in the device of Fig. 1. ..

Direct measurement of the14N(p, γ)15O S factor

The 14(p, γ)15O reaction regulates the rate of energy generation in the stellar CN cycle. Because discrepancies have been found in the analysis and interpretation of previous capture data, we have measured the 14N(p, γ)15O excitation function for energies in the range Eplab = 155-524 keV. Fits of these data using K-matrix theory yield a value for the S factor at zero energy of 1.68 ±0.09(stat) ± 0.16(syst) keVb, which is significantly smaller than the previous result. The corresponding reduction in the stellar reaction rate for 14N(p, γ)15O has a number of interesting consequences, including an impact on estimates for the age of the Galaxy derived from globular clusters

Search for a resonance in the 14N(p, γ)15O reaction at Ep = 127 keV

The 14N(p, γ)15O reaction regulates the energy produced by the CN cycle in main-sequence stars and in red giants. Recently, preliminary evidence was presented for a new resonance in this reaction, which would significantly increase the reaction rate for temperatures near 108 K. We have attempted to confirm this result and find no indication of a resonance near Eplab = 127 keV. Our upper limit on its strength is ω γ≤32 neV (95% C.L.), which is more than 2 orders of magnitude below the previously reported value

R-symmetric gauge mediation

We present a version of Gauge Mediated Supersymmetry Breaking which preserves an R-symmetry - the gauginos are Dirac particles, the A-terms are zero, and there are four Higgs doublets. This offers an alternative way for gauginos to acquire mass in the supersymmetry-breaking models of Intriligator, Seiberg, and Shih. We investigate the possibility of using R-symmetric gauge mediation to realize the spectrum and large sfermion mixing of the model of Kribs, Poppitz, and Weiner.Comment: 26+ pages, 3 figures, BIBTEX; v2 published version: references added, paragraph on spectrum running removed, section added on adjoint scalar masses, clarification of the meaning of Table 3 adde

"Lexis" de Richard Goulet: un programa para la elaboración automática de léxicos de textos griegos y latinos en Macintosh (Apple)

The present paper analyzes Richard Goulet's software «Lexis» as a tool for the design of Greek and Latin texts on Macintosh computers. Because of its comprehensive Greek dictionary, this computer program succeeds in the authomatic lemmatizing of a Greek text in 70-80 per cent of the cases. Obviously, this lemmatization will later be corrected and completed through a comprehensive and user-friendly editing window. This software can also perform other functions, such as generating concordances, indexes of ocurrences, and various search modes. It can also import texts from the Thesaurus Linguae Graecae