TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species

Analysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor-target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription factor-target gene interactions (∼12 million), nucleotide sequences and genomic locations of transcription factor binding sites (∼9 million) for human and six model organisms: mouse, rat, zebrafish, fruit fly, worm and yeast by integrating 10 resources. TFLink provides user-friendly access to data on transcription factor-target gene interactions, interactive network visualizations and transcription factor binding sites, with cross-links to several other databases. Besides containing accurate information on transcription factors, with a clear labelling of the type/volume of the experiments (small-scale or high-throughput), the source database and the original publications, TFLink also provides a wealth of standardized regulatory data available for download in multiple formats. The database offers easy access to high-quality data for wet-lab researchers, supplies data for gene set enrichment analyses and facilitates systems biology and comparative gene regulation studies. Database URL https://tflink.net/

A Search for Dark Higgs Bosons

Recent astrophysical and terrestrial experiments have motivated the proposal of a dark sector with GeV-scale gauge boson force carriers and new Higgs bosons. We present a search for a dark Higgs boson using 516 fb-1 of data collected with the BABAR detector. We do not observe a significant signal and we set 90% confidence level upper limits on the product of the Standard Model-dark sector mixing angle and the dark sector coupling constant.Comment: 7 pages, 5 postscript figures, published version with improved plots for b/w printin

Formation of the ηc\eta_c in Two-Photon Collisions at LEP

The two-photon width $\Gamma_{\gamma\gamma}$ of the $\eta_c$ meson has been measured with the L3 detector at LEP. The $\eta_c$ is studied in the decay modes $\pi^+\pi^-\pi^+\pi^-$, $\pi^+\pi^-$K$^+$K$^-$, K$_s^0$K$^\pm\pi^\mp$, K$^+$K$^-\pi^{0}$, $\pi^+\pi^-\eta$, $\pi^+\pi^-\eta'$, and $\rho^+\rho^-$ using an integrated luminosity of 140 pb$^{-1}$ at $\sqrt{s} \simeq 91$ GeV and of 52 pb$^{-1}$ at $\sqrt{s} \simeq 183$ GeV. The result is $\Gamma_{\gamma\gamma}(\eta_c) = 6.9 \pm 1.7 (stat.) \pm 0.8 (sys.) \pm 2.0$(BR) keV. The $Q^2$ dependence of the $\eta_c$ cross section is studied for $Q^2 < 9$ GeV$^{2}$. It is found to be better described by a Vector Meson Dominance model form factor with a J-pole than with a $\rho$-pole. In addition, a signal of $29 \pm 11$ events is observed at the $\chi_c0$ mass. Upper limits for the two-photon widths of the $\chi_c0$, $\chi_c2$, and $\eta_c'$ are also given

Study of Z Boson Pair Production in e+e- Collisions at LEP at \sqrt{s}=189 GeV

The pair production of Z bosons is studied using the data collected by the L3 detector at LEP in 1998 in e+e- collisions at a centre-of-mass energy of 189 GeV. All the visible final states are considered and the cross section of this process is measured to be 0.74 +0.15 -0.14 (stat.) +/- 0.04 (syst.) pb. Final states containing b quarks are enhanced by a dedicated selection and their production cross section is found to be 0.18 +0.09 -0.07 (stat.) +/- 0.02 (syst.) pb. Both results are in agreement with the Standard Model predictions. Limits on anomalous couplings between neutral gauge bosons are derived from these measurements

Search for Scalar Leptons in e+e- collisions at \sqrt{s}=189 GeV

We report the result of a search for scalar leptons in e+e- collisions at 189 GeV centre-of-mass energy at LEP. No evidence for such particles is found in a data sample of 176 pb^{-1}. Improved upper limits are set on the production cross sections for these new particles. New exclusion contours in the parameter space of the Minimal Supersymmetric Standard Model are derived, as well as new lower limits on the masses of these supersymmetric particles. Under the assumptions of common gaugino and scalar masses at the GUT scale, we set an absolute lower limit on the mass of the lightest scalar electron of 65.5 Ge

Search for Low Scale Gravity Effects in e+e- Collisions at LEP

Recent theories propose that quantum gravity effects may be observable at LEP energies via gravitons that couple to Standard Model particles and propagate into extra spatial dimensions. The associated production of a graviton and a photon is searched for as well as the effects of virtual graviton exchange in the processes: e+e- -> gamma gamma, ZZ, WW, mu mu, tau tau, qq and ee No evidence for this new interaction is found in the data sample collected by the L3 detector at LEP at centre-of-mass energies up to 183 GeV. Limits close to 1 TeV on the scale of this new scenario of quantum gravity are set

Charged hadron multiplicity fluctuations in Au+Au and Cu+Cu collisions from sqrt(s_NN) = 22.5 to 200 GeV

A comprehensive survey of event-by-event fluctuations of charged hadron multiplicity in relativistic heavy ions is presented. The survey covers Au+Au collisions at sqrt(s_NN) = 62.4 and 200 GeV, and Cu+Cu collisions sqrt(s_NN) = 22.5, 62.4, and 200 GeV. Fluctuations are measured as a function of collision centrality, transverse momentum range, and charge sign. After correcting for non-dynamical fluctuations due to fluctuations in the collision geometry within a centrality bin, the remaining dynamical fluctuations expressed as the variance normalized by the mean tend to decrease with increasing centrality. The dynamical fluctuations are consistent with or below the expectation from a superposition of participant nucleon-nucleon collisions based upon p+p data, indicating that this dataset does not exhibit evidence of critical behavior in terms of the compressibility of the system. An analysis of Negative Binomial Distribution fits to the multiplicity distributions demonstrates that the heavy ion data exhibit weak clustering properties.Comment: 464 authors from 60 institutions, 17 pages, 12 figures, 1 table. Submitted to Physical Review C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Evidence for the exclusive decay Bc+- to J/psi pi+- and measurement of the mass of the Bc meson

We report first evidence for a fully reconstructed decay mode of the B_c^{\pm} meson in the channel B_c^{\pm} \to J/psi \pi^{\pm}, with J/psi \to mu^+mu^-. The analysis is based on an integrated luminosity of 360 pb$^{-1} in p\bar{p} collisions at 1.96 TeV center of mass energy collected by the Collider Detector at Fermilab. We observe 14.6 \pm 4.6 signal events with a background of 7.1 \pm 0.9 events, and a fit to the J/psi pi^{\pm} mass spectrum yields a B_c^{\pm} mass of 6285.7 \pm 5.3(stat) \pm 1.2(syst) MeV/c^2. The probability of a peak of this magnitude occurring by random fluctuation in the search region is estimated as 0.012%.Comment: 7 pages, 3 figures. Version 3, accepted by PR

Top quark mass measurement using the template method at CDF

We present a measurement of the top quark mass in the lepton+jets and dilepton channels of $t\bar{t}$ decays using the template method. The data sample corresponds to an integrated luminosity of 5.6 fb$^{-1}$ of $p\bar{p}$ collisions at Tevatron with $\sqrt{s}=1.96$ TeV, collected with the CDF II detector. The measurement is performed by constructing templates of three kinematic variables in the lepton+jets and two kinematic variables in the dilepton channel. The variables are two reconstructed top quark masses from different jets-to-quarks combinations and the invariant mass of two jets from the $W$ decay in the lepton+jets channel, and a reconstructed top quark mass and $m_{T2}$, a variable related to the transverse mass in events with two missing particles, in the dilepton channel. The simultaneous fit of the templates from signal and background events in the lepton+jets and dilepton channels to the data yields a measured top quark mass of $M_{top} = 172.1 \pm 1.1(stat) \pm 0.9(syst).$Comment: submitted to Phys. Rev.

Cold Nuclear Matter Effects on J/Psi as Constrained by Deuteron-Gold Measurements at sqrt(s_NN) = 200 GeV

We present a new analysis of J/psi production yields in deuteron-gold collisions at sqrt(s_NN) = 200 GeV using data taken by the PHENIX experiment in 2003 and previously published in [S.S. Adler et al., Phys. Rev. Lett 96, 012304 (2006)]. The high statistics proton-proton J/psi data taken in 2005 is used to improve the baseline measurement and thus construct updated cold nuclear matter modification factors R_dAu. A suppression of J/psi in cold nuclear matter is observed as one goes forward in rapidity (in the deuteron-going direction), corresponding to a region more sensitive to initial state low-x gluons in the gold nucleus. The measured nuclear modification factors are compared to theoretical calculations of nuclear shadowing to which a J/psi (or precursor) break-up cross-section is added. Breakup cross sections of sigma_breakup = 2.8^[+1.7_-1.4] (2.2^[+1.6_-1.5]) mb are obtained by fitting these calculations to the data using two different models of nuclear shadowing. These breakup cross section values are consistent within large uncertainties with the 4.2 +/- 0.5 mb determined at lower collision energies. Projecting this range of cold nuclear matter effects to copper-copper and gold-gold collisions reveals that the current constraints are not sufficient to firmly quantify the additional hot nuclear matter effect.Comment: 453 authors from 59 institutions, 15 pages, 13 figures, 5 tables. Submitted to Physical Review C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm