The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

<p>Abstract</p> <p>Background</p> <p>Enormous molecular sequence data have been accumulated over the past several years and are still exponentially growing with the use of faster and cheaper sequencing techniques. There is high and widespread interest in using these data for phylogenetic analyses. However, the amount of data that one can retrieve from public sequence repositories is virtually impossible to tame without dedicated software that automates processes. Here we present a novel bioinformatics pipeline for downloading, formatting, filtering and analyzing public sequence data deposited in GenBank. It combines some well-established programs with numerous newly developed software tools (available at <url>http://software.zfmk.de/</url>).</p> <p>Results</p> <p>We used the bioinformatics pipeline to investigate the phylogeny of the megadiverse insect order Hymenoptera (sawflies, bees, wasps and ants) by retrieving and processing more than 120,000 sequences and by selecting subsets under the criteria of compositional homogeneity and defined levels of density and overlap. Tree reconstruction was done with a partitioned maximum likelihood analysis from a supermatrix with more than 80,000 sites and more than 1,100 species. In the inferred tree, consistent with previous studies, "Symphyta" is paraphyletic. Within Apocrita, our analysis suggests a topology of Stephanoidea + (Ichneumonoidea + (Proctotrupomorpha + (Evanioidea + Aculeata))). Despite the huge amount of data, we identified several persistent problems in the Hymenoptera tree. Data coverage is still extremely low, and additional data have to be collected to reliably infer the phylogeny of Hymenoptera.</p> <p>Conclusions</p> <p>While we applied our bioinformatics pipeline to Hymenoptera, we designed the approach to be as general as possible. With this pipeline, it is possible to produce phylogenetic trees for any taxonomic group and to monitor new data and tree robustness in a taxon of interest. It therefore has great potential to meet the challenges of the phylogenomic era and to deepen our understanding of the tree of life.</p

Measurement of the Omega_c Lifetime

We present the measurement of the lifetime of the Omega_c we have performed using three independent data samples from two different decay modes. Using a Sigma- beam of 340 GeV/c we have obtained clean signals for the Omega_c decaying into Xi- K- pi+ pi+ and Omega- pi+ pi- pi+, avoiding topological cuts normally used in charm analysis. The short but measurable lifetime of the Omega_c is demonstrated by a clear enhancement of the signals at short but finite decay lengths. Using a continuous maximum likelihood method we determined the lifetime to be tau(Omega_c) = 55 +13-11(stat) +18-23(syst) fs. This makes the Omega_c the shortest living weakly decaying particle observed so far. The short value of the lifetime confirms the predicted pattern of the charmed baryon lifetimes and demonstrates that the strong interaction plays a vital role in the lifetimes of charmed hadrons.Comment: 15 pages, including 7 figures; gzipped, uuencoded postscrip

Search for the exotic Ξ−−(1860)\Xi^{--}(1860) Resonance in 340GeV/c Σ−\Sigma^--Nucleus Interactions

We report on a high statistics search for the $\Xi^{--}(1860)$ resonance in $\Sigma^-$-nucleus collisions at 340GeV/c. No evidence for this resonance is found in our data sample which contains 676000 $\Xi^-$ candidates above background. For the decay channel $\Xi^{--}(1860) \to \Xi^-\pi^-$ and the kinematic range 0.15$<x_F<$0.9 we find a 3$\sigma$ upper limit for the production cross section of 3.1 and 3.5 $\mu$b per nucleon for reactions with carbon and copper, respectively.Comment: 5 pages, 4 figures, modification of ref. 43 and 4

Results and perspectives of the solar axion search with the CAST experiment

The status of the solar axion search with the CERN Axion Solar Telescope (CAST) will be presented. Recent results obtained by the use of $^3$He as a buffer gas has allowed us to extend our sensitivity to higher axion masses than our previous measurements with $^4$He. With about 1 h of data taking at each of 252 different pressure settings we have scanned the axion mass range 0.39 eV$\le m_{a} \le$ 0.64 eV. From the absence of an excess of x rays when the magnet was pointing to the Sun we set a typical upper limit on the axion-photon coupling of g$_{a\gamma} \le 2.3\times 10^{-10}$ GeV$^{-1}$ at 95% C.L., the exact value depending on the pressure setting. CAST published results represent the best experimental limit on the photon couplings to axions and other similar exotic particles dubbed WISPs (Weakly Interacting Slim Particles) in the considered mass range and for the first time the limit enters the region favored by QCD axion models. Preliminary sensitivities for axion masses up to 1.16 eV will also be shown reaching mean upper limits on the axion-photon coupling of g$_{a\gamma} \le 3.5\times 10^{-10}$ GeV$^{-1}$ at 95% C.L. Expected sensibilities for the extension of the CAST program up to 2014 will be presented. Moreover long term options for a new helioscope experiment will be evoked.Comment: 4 pages, 2 pages, to appear in the proceedings of the 24th Rencontres de Blois V2 A few affiliations were not corrected in previous version V3 Author adde

Fast photon detection for the COMPASS RICH detector

The COMPASS experiment at the SPS accelerator at CERN uses a large scale Ring Imaging CHerenkov detector (RICH) to identify pions, kaons and protons in a wide momentum range. For the data taking in 2006, the COMPASS RICH has been upgraded in the central photon detection area (25% of the surface) with a new technology to detect Cherenkov photons at very high count rates of several 10^6 per second and channel and a new dead-time free read-out system, which allows trigger rates up to 100 kHz. The Cherenkov photons are detected by an array of 576 visible and ultra-violet sensitive multi-anode photomultipliers with 16 channels each. The upgraded detector showed an excellent performance during the 2006 data taking.Comment: Proceeding of the IPRD06 conference (Siena, Okt. 06

Fast Photon Detection for Particle Identification with COMPASS RICH-1

Particle identification at high rates is an important challenge for many current and future high-energy physics experiments. The upgrade of the COMPASS RICH-1 detector requires a new technique for Cherenkov photon detection at count rates of several $10^6$ per channel in the central detector region, and a read-out system allowing for trigger rates of up to 100 kHz. To cope with these requirements, the photon detectors in the central region have been replaced with the detection system described in this paper. In the peripheral regions, the existing multi-wire proportional chambers with CsI photocathode are now read out via a new system employing APV pre-amplifiers and flash ADC chips. The new detection system consists of multi-anode photomultiplier tubes (MAPMT) and fast read-out electronics based on the MAD4 discriminator and the F1-TDC chip. The RICH-1 is in operation in its upgraded version for the 2006 CERN SPS run. We present the photon detection design, constructive aspects and the first Cherenkov light in the detector.Comment: Proceedings of the Imaging 2006 conference, Stockholm, Sweden, 27-30 June 2006, 5 pages, 6 figures, to appear in NIM A; corrected typo in caption of Fig.

Solar axion search with the CAST experiment

The CAST (CERN Axion Solar Telescope) experiment is searching for solar axions by their conversion into photons inside the magnet pipe of an LHC dipole. The analysis of the data recorded during the first phase of the experiment with vacuum in the magnet pipes has resulted in the most restrictive experimental limit on the coupling constant of axions to photons. In the second phase, CAST is operating with a buffer gas inside the magnet pipes in order to extent the sensitivity of the experiment to higher axion masses. We will present the first results on the $^{4}{\rm He}$ data taking as well as the system upgrades that have been operated in the last year in order to adapt the experiment for the $^{3}{\rm He}$ data taking. Expected sensitivities on the coupling constant of axions to photons will be given for the recent $^{3}{\rm He}$ run just started in March 2008.Comment: Proceedings of the ICHEP 2008 conferenc

First results from the CERN Axion Solar Telescope (CAST)

Hypothetical axion-like particles with a two-photon interaction would be produced in the Sun by the Primakoff process. In a laboratory magnetic field (``axion helioscope'') they would be transformed into X-rays with energies of a few keV. Using a decommissioned LHC test magnet, CAST has been running for about 6 months during 2003. The first results from the analysis of these data are presented here. No signal above background was observed, implying an upper limit to the axion-photon coupling < 1.16 10^{-10} GeV^-1 at 95% CL for m_a <~0.02 eV. This limit is comparable to the limit from stellar energy-loss arguments and considerably more restrictive than any previous experiment in this axion mass range.Comment: 4 pages, accepted by PRL. Final version after the referees comment

Prospects for the CERN Axion Solar Telescope Sensitivity to 14.4 keV Axions

The CERN Axion Solar Telescope (CAST) is searching for solar axions using the 9.0 T strong and 9.26 m long transverse magnetic field of a twin aperture LHC test magnet, where axions could be converted into X-rays via reverse Primakoff process. Here we explore the potential of CAST to search for 14.4 keV axions that could be emitted from the Sun in M1 nuclear transition between the first, thermally excited state, and the ground state of 57Fe nuclide. Calculations of the expected signals, with respect to the axion-photon coupling, axion-nucleon coupling and axion mass, are presented in comparison with the experimental sensitivity.Comment: 4 pages, 1 figure. Submitted to Nucl. Instr. and Meth.

The Fast Read-out System for the MAPMTs of COMPASS RICH-1

A fast readout system for the upgrade of the COMPASS RICH detector has been developed and successfully used for data taking in 2006 and 2007. The new readout system for the multi-anode PMTs in the central part of the photon detector of the RICH is based on the high-sensitivity MAD4 preamplifier-discriminator and the dead-time free F1-TDC chip characterized by high-resolution. The readout electronics has been designed taking into account the high photon flux in the central part of the detector and the requirement to run at high trigger rates of up to 100 kHz with negligible dead-time. The system is designed as a very compact setup and is mounted directly behind the multi-anode photomultipliers. The data are digitized on the frontend boards and transferred via optical links to the readout system. The read-out electronics system is described in detail together with its measured performances.Comment: Proceeding of RICH2007 Conference, Trieste, Oct. 2007. v2: minor change