Detection of copy number variants in sequencing data.

In this work a program for detection of CNVs in sequencing data based on depth of coverage was implemented in C++ (copyDOC). Single steps in the pipeline, the acquisition of DOC signals in windows, the event calling and merging are implemented using generic programming techniques that enable the future integration of other algorithms in the pipeline. Furthermore, a testing environment was implemented, the copySim platform, which is very useful for testing and evaluation of different algorithms. CopyDOC was successfully applied to synthetic and real data using constant sized windows. Dynamic windows, that adapt according to the local mappability of the sequence, are implemented in the pipeline, but could not be tested in this work. They might be advantageous in datasets that contain uniquely mapped reads. However, CNVs have been shown to be overrepresented in segmental duplications (Nguyen et al. 2006; Cooper et al. 2007) and by a general exclusion of multireads those CNVs might be difficult to ascertain. In the application of copyDOC to a 1000 genomes dataset the overlap of predicted variants was considerable higer using multireads compared to uniquely mapped reads. Thus there is a requirement for tools that can handle multireads. Futher improvements of copyDOC might be done for the CNV calling algorithm and the merging step. For example the program workflow could be tested with a direct comparison of the DOC signals in two datasets via log ratios instead of appling a t-test on DOC signals in the two datasets. CopyDOC and copySim could be used as platform for the implementation and evaluation of futher CNV detection algorithms

Perturbative Corrections to a Sum Rule for the Heavy Quark Kinetic Energy

We calculate the perturbative corrections to order \alpha_s^2\beta_0 to the sum rule derived from the second moment of the time-ordered product of b \to c currents near zero recoil. This sum rule yields a bound on \lambda_1, the expectation value of the b quark kinetic energy operator inside the B meson. The perturbative corrections significantly weaken the bound relative to the tree level result, yielding \lambda_1 < -0.15 GeV^2.Comment: 10 pages revtex, uses FEYNMA

A Consistent Calculation of Heavy Meson Decay Constants and Transition Wave Functions in the Complete HQEFT

Within the complete heavy quark effective field theory (HQEFT), the QCD sum rule approach is used to evaluate the decay constants including 1/m_Q corrections and the Isgur-Wise function and other additional important wave functions concerned at 1/m_Q for the heavy-light mesons. The 1/m_Q corrections to the scaling law f_M \sim F/\sqrt{m_M} are found to be small in HQEFT, which demonstrates again the validity of 1/m_Q expansion in HQEFT. It is also shown that the residual momentum v.k of heavy quark within hadrons does be around the binding energy \bar{\Lambda} of the heavy hadrons. The calculations presented in this paper provide a consistent check on the HQEFT and shows that the HQEFT is more reliable than the usual HQET for describing a slightly off-mass shell heavy quark within hadron as the usual HQET seems to lead to the breakdown of 1/m_Q expansion in evaluating the meson decay constants. It is emphasized that the introduction of the `dressed heavy quark' mass is useful for the heavy-light mesons (Qq) with m_Q >> \bar{\Lambda} >> m_q, while for heavy-heavy bound states (\psi_1\psi_2) with masses m_1, m_2 >> \bar{\Lambda}, like bottom-charm hadrons or similarly for muonium in QED, one needs to treat both particles as heavy effective particles via 1/m_1 and 1/m_2 expansions and redefine the effective bound states and modified `dressed heavy quark' masses within the HQEFT.Comment: 20 pages, revtex, 22 figures, axodraw.sty, two irrelevant figures are moved awa

The emission of energetic electrons from the complex streamer corona adjacent to leader stepping

We here propose a model to capture the complexity of the streamer corona adjacent to leader stepping and relate it to the production of energetic electrons serving as a source of X-rays and $\gamma$-rays, manifesting in terrestrial gamma-ray flashes (TGFs). During its stepping, the leader tip is accompanied by a corona consisting of multitudinous streamers perturbing the air in its vicinity and leaving residual charge behind. We explore the relative importance of air perturbations and preionization on the production of energetic run-away electrons by 2.5D cylindrical Monte Carlo particle simulations of streamers in ambient fields of 16 kV cm$^{-1}$ and 50 kV cm$^{-1}$ at ground pressure. We explore preionization levels between $10^{10}$ m$^{-3}$ and $10^{13}$ m$^{-3}$, channel widths between 0.5 and 1.5 times the original streamer widths and air perturbation levels between 0\% and 50\% of ambient air. We observe that streamers in preionized and perturbed air accelerate more efficiently than in non-ionized and uniform air with air perturbation dominating the streamer acceleration. We find that in unperturbed air preionization levels of $10^{11}$ m$^{-3}$ are sufficient to explain run-away electron rates measured in conjunction with terrestrial gamma-ray flashes. In perturbed air, the production rate of runaway electrons varies from $10^{10}$ s$^{-1}$ to $10^{17}$ s$^{-1}$ with maximum electron energies from some hundreds of eV up to some hundreds of keV in fields above and below the breakdown strength. In the presented simulations the number of runaway electrons matches with the number of energetic electrons measured in alignment with the observations of terrestrial gamma-ray flashes. Conclusively, the complexity of the streamer zone ahead of leader tips allows explaining the emission of energetic electrons and photons from streamer discharges.Comment: 29 pages, 11 figures, 2 table

A Comment on the Extractions of V_{ub} from Radiative Decays

We present a model independent closed form expression for |V_{ub}|^2/|V_{tb} V_{ts}^*|^2, which includes the resummation of large endpoint logarithms as well as the interference effects from the operators $O_2$ and $O_8$. We demonstrate that the method to extract |V_{ub}| presented by the authors in hep-ph/9909404, and modified in this letter to include interference effects, is not just a refinement of the method introduced in hep-ph/9312311. We also discuss the model dependence of the latter proposal. Furthermore, we show that the resummation is not negligible and that the Landau pole does not introduce any significant uncertainties.Comment: 10 pages, 3 figures; one figure added, one reference added, expanded discussion

Psychedelic intimacy: altered states of consciousness in romantic relationships

Objective: Engaging in practices of intimacy meant to develop and sustain intimacy can be beneficial for couples. Psychoactive substances such as 3,4-Methylenedioxymethamphetamine (MDMA) have shown to facilitate bonding within couples and it is hypothesised that classic psychedelics, due to their property to increase prosocial behaviours, can similarly promote interactional intimacy. This study explores shared experiences of altered states of consciousness within romantic couples and their impact on intimacy in relationships. Participants: Twelve participants (six couples) between 19 and 29 years of age who had used psychedelics with their current partner were recruited. Method: Qualitative data was gathered via simultaneous interviews with both members of a couple. The semi-structured interviews featured an in-depth exploration of multiple shared psychedelic experiences. Reflexive thematic analysis was employed to analyse the resulting transcripts. Results: Three themes with subsequent subthemes were identified, portraying couples’ experiences during psychedelic-induced altered states of consciousness: navigating anxiety (subthemes: novelty, preparation, shifting environment, and calming presence), reshaping practices (subthemes: excessive worrying, spirited discussions, and straight talking), and encountering bliss (subthemes: meeting the unexpected, the beauty around us, leaving the everyday behind, and breaking through). Conclusions: Couples’ experiences with classic psychedelics align with criteria for interactional intimacy (i.e., self-exposure, positive involvement, and shared understanding), but their distinct nature warrants a novel definition of psychedelic intimacy. The unique pair bonding during shared psychedelic experiences could be utilized by psychedelic-assisted couples therapy

Determining the Weak Phase γ\gamma in the Presence of Rescattering

We suggest a new technique to determine the CKM phase $\gamma$ {\em without} neglecting the (soft) final state rescattering effects. We use (time integrated) $B$ meson decay rates to $\pi$'s and $K$'s. A set of 5 $\Delta S = 0$ (or 1 $\Delta S =0$ and 4 $\Delta S= 1$) decay rates is used to compute the strong phases and magnitudes of the tree level and penguin contributions as functions of $\gamma$. These are used to {\em predict} a $\Delta S = 1$ $(\Delta S = 0) B_{d/s}$ decay rate as a function of $\gamma$ (using SU(3) symmetry). The measurement of this decay rate then gives $\gamma$. We illustrate this technique using different cases. Most of the decay modes we use are expected to be accessible at the B-factories (e^+ e^- or hadron machines).Comment: LaTeX file, 15 pages including 2 figures. Replacing an earlier version. In version 4, we have corrected some typographic errors. We have also clarified which decay modes require external tagging and have changed/added some comment

Scale Setting for αs\alpha_s Beyond Leading Order

We present a general procedure for applying the scale-setting prescription of Brodsky, Lepage and Mackenzie to higher orders in the strong coupling constant \alphas. In particular, we show how to apply this prescription when the leading coefficient or coefficients in a series in \alphas are anomalously small. We give a general method for computing an optimum scale numerically, within dimensional regularization, and in cases when the coefficients of a series are known. We find significant corrections to the scales for $R_{e^+ e^-}$, $\Gamma(B \to X_u e \bar{\nu})$, $\Gamma(t \to b W)$, and the ratios of the quark pole to \MSbar and lattice bare masses.Comment: Lattice 2000 (Perturbation Theory), 5 pages, 7 figures, LaTe

Bounds on R-parity violating supersymmetric couplings from leptonic and semi-leptonic meson decays

We present a comprehensive update of the bounds on R-Parity violating supersymmetric couplings from lepton-flavour- and lepton-number-violating decay processes. We consider tau and mu decays as well as leptonic and semi-leptonic decays of mesons. We present several new bounds resulting from tau, eta and Kaon decays and correct some results in the literature concerning B-meson decays.Comment: 30 pages; changed title, updated some bounds from the literature from different references, added reference

SU(3) Predictions of B→PPB\to PP Decays in the Standard Model

With SU(3) symmetry one only needs 13 hadronic parameters to describe $B\to PP$ decays in the Standard Model. When annihilation contributions are neglected, only 7 hadronic parameters are needed. These parameters can be determined from existing experimental data and some unmeasured branching ratios and CP asymmetries of the type $B\to PP$ can be predicted. In this talk we present SU(3) predictions of branching ratios and CP asymmetries for $B\to PP$ decays in the Standard Model.Comment: 4 pages, no figure. Talk present at the 5th International Conference on Hyperons, Charm and Beauty Hadrons, Vancouver, June 200