A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data

Motivation: Advances in chromosome conformation capture and next-generation sequencing technologies are enabling genome-wide investigation of dynamic chromatin interactions. For example, Hi-C experiments generate genome-wide contact frequencies between pairs of loci by sequencing DNA segments ligated from loci in close spatial proximity. One essential task in such studies is peak calling, that is, detecting non-random interactions between loci from the two-dimensional contact frequency matrix. Successful fulfillment of this task has many important implications including identifying long-range interactions that assist interpreting a sizable fraction of the results from genome-wide association studies. The task - distinguishing biologically meaningful chromatin interactions from massive numbers of random interactions - poses great challenges both statistically and computationally. Model-based methods to address this challenge are still lacking. In particular, no statistical model exists that takes the underlying dependency structure into consideration. Results: In this paper, we propose a hidden Markov random field (HMRF) based Bayesian method to rigorously model interaction probabilities in the two-dimensional space based on the contact frequency matrix. By borrowing information from neighboring loci pairs, our method demonstrates superior reproducibility and statistical power in both simulation studies and real data analysis

Time-integrated luminosity recorded by the BABAR detector at the PEP-II e+e- collider

This article is the Preprint version of the final published artcile which can be accessed at the link below.We describe a measurement of the time-integrated luminosity of the data collected by the BABAR experiment at the PEP-II asymmetric-energy e+e- collider at the ϒ(4S), ϒ(3S), and ϒ(2S) resonances and in a continuum region below each resonance. We measure the time-integrated luminosity by counting e+e-→e+e- and (for the ϒ(4S) only) e+e-→μ+μ- candidate events, allowing additional photons in the final state. We use data-corrected simulation to determine the cross-sections and reconstruction efficiencies for these processes, as well as the major backgrounds. Due to the large cross-sections of e+e-→e+e- and e+e-→μ+μ-, the statistical uncertainties of the measurement are substantially smaller than the systematic uncertainties. The dominant systematic uncertainties are due to observed differences between data and simulation, as well as uncertainties on the cross-sections. For data collected on the ϒ(3S) and ϒ(2S) resonances, an additional uncertainty arises due to ϒ→e+e-X background. For data collected off the ϒ resonances, we estimate an additional uncertainty due to time dependent efficiency variations, which can affect the short off-resonance runs. The relative uncertainties on the luminosities of the on-resonance (off-resonance) samples are 0.43% (0.43%) for the ϒ(4S), 0.58% (0.72%) for the ϒ(3S), and 0.68% (0.88%) for the ϒ(2S).This work is supported by the US Department of Energy and National Science Foundation, the Natural Sciences and Engineering Research Council (Canada), the Commissariat à l’Energie Atomique and Institut National de Physique Nucléaire et de Physiquedes Particules (France), the Bundesministerium für Bildung und Forschung and Deutsche Forschungsgemeinschaft (Germany), the Istituto Nazionale di Fisica Nucleare (Italy), the Foundation for Fundamental Research on Matter (The Netherlands), the Research Council of Norway, the Ministry of Education and Science of the Russian Federation, Ministerio de Ciencia e Innovación (Spain), and the Science and Technology Facilities Council (United Kingdom). Individuals have received support from the Marie-Curie IEF program (European Union) and the A.P. Sloan Foundation (USA)

Measurement of the B0-anti-B0-Oscillation Frequency with Inclusive Dilepton Events

The $B^0$-$\bar B^0$ oscillation frequency has been measured with a sample of 23 million \B\bar B pairs collected with the BABAR detector at the PEP-II asymmetric B Factory at SLAC. In this sample, we select events in which both B mesons decay semileptonically and use the charge of the leptons to identify the flavor of each B meson. A simultaneous fit to the decay time difference distributions for opposite- and same-sign dilepton events gives $\Delta m_d = 0.493 \pm 0.012{(stat)}\pm 0.009{(syst)}$ ps$^{-1}$.Comment: 7 pages, 1 figure, submitted to Physical Review Letter

The first Hubble diagram and cosmological constraints using superluminous supernovae

This paper has gone through internal review by the DES collaboration. It has Fermilab preprint number 19-115-AE and DES publication number 13387. We acknowledge support from EU/FP7- ERC grant 615929. RCN would like to acknowledge support from STFC grant ST/N000688/1 and the Faculty of Technology at the University of Portsmouth. LG was funded by the European Union’s Horizon 2020 Framework Programme under the Marie Skłodowska- Curie grant agreement no. 839090. This work has been partially supported by the Spanish grant PGC2018-095317-B-C21 within the European Funds for Regional Development (FEDER). Funding for the DES Projects has been provided by the U.S. Department of Energy, the U.S. National Science Foundation, the Ministry of Science and Education of Spain, the Science and Technology Facilities Council of the United Kingdom, the Higher Education Funding Council for England, the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, the Kavli Institute of Cosmological Physics at the University of Chicago, the Center for Cosmology and Astro-Particle Physics at the Ohio State University, the Mitchell Institute for Fundamental Physics and Astronomy at Texas A&M University, Financiadora de Estudos e Projetos, Fundac¸ ˜ao Carlos Chagas Filho de Amparo `a Pesquisa do Estado do Rio de Janeiro, Conselho Nacional de Desenvolvimento Cient´ıfico e Tecnol´ogico and the Minist´erio da Ciˆencia, Tecnologia e Inovac¸ ˜ao, the Deutsche Forschungsgemeinschaft, and the Collaborating Institutions in the Dark Energy Survey. The Collaborating Institutions are Argonne National Laboratory, the University of California at Santa Cruz, the University of Cambridge, Centro de Investigaciones Energ´eticas, Medioambientales y Tecnol ´ogicas-Madrid, the University of Chicago, University College London, the DES-Brazil Consortium, the University of Edinburgh, the Eidgen¨ossische Technische Hochschule (ETH) Z¨urich, Fermi NationalAccelerator Laboratory, theUniversity of Illinois atUrbana- Champaign, the Institut de Ci`encies de l’Espai (IEEC/CSIC), the Institut de F´ısica d’Altes Energies, Lawrence Berkeley National Laboratory, the Ludwig-Maximilians Universit¨at M¨unchen and the associated Excellence Cluster Universe, the University of Michigan, the National Optical Astronomy Observatory, the University of Nottingham, The Ohio State University, the University of Pennsylvania, the University of Portsmouth, SLAC National Accelerator Laboratory, Stanford University, the University of Sussex, Texas A&M University, and the OzDES Membership Consortium. Based in part on observations at Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, which is operated by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. The DES data management system is supported by the National Science Foundation under grant numbers AST-1138766 and AST-1536171. The DES participants from Spanish institutions are partially supported by MINECO under grants AYA2015- 71825, ESP2015-66861, FPA2015-68048, SEV-2016-0588, SEV- 2016-0597, and MDM-2015-0509, some of which include ERDF funds from the European Union. IFAE is partially funded by the CERCA program of the Generalitat de Catalunya. Research leading to these results has received funding from the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013) including ERC grant agreements 240672, 291329, and 306478.We acknowledge support from the Australian Research Council Centre of Excellence for All-skyAstrophysics (CAASTRO), through project number CE110001020, and the Brazilian Instituto Nacional de Ciˆencia e Tecnologia (INCT) e-Universe (CNPq grant 465376/2014-2). This paper has been authored by Fermi Research Alliance, LLC under Contract No.DE-AC02-07CH11359 with theU.S.Department of Energy, Office of Science, Office of High Energy Physics. The United States Government retains and the publisher, by accepting the paper for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this paper, or allow others to do so, for United States Government purposes.We present the first Hubble diagram of superluminous supernovae (SLSNe) out to a redshift of two, together with constraints on the matter density, M, and the dark energy equation-of-state parameter, w(≡p/ρ). We build a sample of 20 cosmologically useful SLSNe I based on light curve and spectroscopy quality cuts. We confirm the robustness of the peak–decline SLSN I standardization relation with a larger data set and improved fitting techniques than previous works. We then solve the SLSN model based on the above standardization via minimization of the χ2 computed from a covariance matrix that includes statistical and systematic uncertainties. For a spatially flat cold dark matter ( CDM) cosmological model, we find M = 0.38+0.24 −0.19, with an rms of 0.27 mag for the residuals of the distance moduli. For a w0waCDM cosmological model, the addition of SLSNe I to a ‘baseline’ measurement consisting of Planck temperature together with Type Ia supernovae, results in a small improvement in the constraints of w0 and wa of 4 per cent.We present simulations of future surveys with 868 and 492 SLSNe I (depending on the configuration used) and show that such a sample can deliver cosmological constraints in a flat CDM model with the same precision (considering only statistical uncertainties) as current surveys that use Type Ia supernovae, while providing a factor of 2–3 improvement in the precision of the constraints on the time variation of dark energy, w0 and wa. This paper represents the proof of concept for superluminous supernova cosmology, and demonstrates they can provide an independent test of cosmology in the high-redshift (z > 1) universe.EU/FP7-ERC grant 615929STFC grant ST/N000688/1Faculty of Technology at the University of PortsmouthEuropean Union’s Horizon 2020 Framework Programme under the Marie Skłodowska- Curie grant agreement no. 839090Spanish grant PGC2018-095317-B-C21 within the European Funds for Regional Development (FEDER)U.S. Department of EnergyU.S. National Science FoundationMinistry of Science and Education of SpainScience and Technology Facilities Council of the United KingdomHigher Education Funding Council for EnglandNational Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign,Kavli Institute of Cosmological Physics at the University of ChicagoCenter for Cosmology and Astro-Particle Physics at the Ohio State UniversityMitchell Institute for Fundamental Physics and Astronomy at Texas A&M University, Financiadora de Estudos e Projetos, Fundacão Carlos Chagas Filho de Amparo `a Pesquisa do Estado do Rio de Janeiro, Conselho Nacional de Desenvolvimento Científico e Tecnológico and the Ministério da Ciencia, Tecnologia e InovacãoDeutsche ForschungsgemeinschaftCollaborating Institutions in the Dark Energy Survey.National Science Foundation under grant numbers AST-1138766 and AST-1536171.T MINECO under grants AYA2015- 71825, ESP2015-66861, FPA2015-68048, SEV-2016-0588, SEV- 2016-0597, and MDM-2015-0509, some of which include ERDF funds from the European Union.CERCA program of the Generalitat de Catalunya.European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013) including ERC grant agreements 240672, 291329, and 306478.Australian Research Council Centre of Excellence for All-skyAstrophysics (CAASTRO), through project number CE110001020Brazilian Instituto Nacional de Ciˆencia e Tecnologia (INCT) e-Universe (CNPq grant 465376/2014-2)Fermi Research Alliance, LLC under Contract No.DE-AC02-07CH11359 with theU.S.Department of Energy, Office of Science, Office of High Energy Physic

First cosmology results using SNe Ia from the dark energy survey: analysis, systematic uncertainties, and validation

International audienceWe present the analysis underpinning the measurement of cosmological parameters from 207 spectroscopically classified type Ia supernovae (SNe Ia) from the first three years of the Dark Energy Survey Supernova Program (DES-SN), spanning a redshift range of 0.01

First cosmology results using type Ia supernovae from the Dark Energy Survey: constraints on cosmological parameters

We present the first cosmological parameter constraints using measurements of type Ia supernovae (SNe Ia) from the Dark Energy Survey Supernova Program (DES-SN). The analysis uses a subsample of 207 spectroscopically confirmed SNe Ia from the first three years of DES-SN, combined with a low-redshift sample of 122 SNe from the literature. Our "DES-SN3YR" result from these 329 SNe Ia is based on a series of companion analyses and improvements covering SN Ia discovery, spectroscopic selection, photometry, calibration, distance bias corrections, and evaluation of systematic uncertainties. For a flat LCDM model we find a matter density Omega_m = 0.331 +_ 0.038. For a flat wCDM model, and combining our SN Ia constraints with those from the cosmic microwave background (CMB), we find a dark energy equation of state w = -0.978 +_ 0.059, and Omega_m = 0.321 +_ 0.018. For a flat w0waCDM model, and combining probes from SN Ia, CMB and baryon acoustic oscillations, we find w0 = -0.885 +_ 0.114 and wa = -0.387 +_ 0.430. These results are in agreement with a cosmological constant and with previous constraints using SNe Ia (Pantheon, JLA)

Observation of the baryonic decay B \uaf 0 \u2192 \u39bc+ p \uaf K-K+

We report the observation of the baryonic decay B\uaf0\u2192\u39bc+p\uafK-K+ using a data sample of 471 7106 BB\uaf pairs produced in e+e- annihilations at s=10.58GeV. This data sample was recorded with the BABAR detector at the PEP-II storage ring at SLAC. We find B(B\uaf0\u2192\u39bc+p\uafK-K+)=(2.5\ub10.4(stat)\ub10.2(syst)\ub10.6B(\u39bc+)) 710-5, where the uncertainties are statistical, systematic, and due to the uncertainty of the \u39bc+\u2192pK-\u3c0+ branching fraction, respectively. The result has a significance corresponding to 5.0 standard deviations, including all uncertainties. For the resonant decay B\uaf0\u2192\u39bc+p\uaf\u3c6, we determine the upper limit B(B\uaf0\u2192\u39bc+p\uaf\u3c6)<1.2 710-5 at 90% confidence level

Search for Darkonium in e+e- Collisions

Collider searches for dark sectors, new particles interacting only feebly with ordinary matter, have largely focused on identifying signatures of new mediators, leaving much of dark sector structures unexplored. In particular, the existence of dark matter bound states (darkonia) remains to be investigated. This possibility could arise in a simple model in which a dark photon (A0 ) is light enough to generate an attractive force between dark fermions. We report herein a search for a JPC ¼ 1−− darkonium state, the ϒD, produced in the reaction eþe− → γϒD, ϒD → A0 A0 A0 , where the dark photons subsequently decay into pairs of leptons or pions, using 514 fb−1 of data collected with the BABAR detector. No significant signal is observed, and we set bounds on the γ − A0 kinetic mixing as a function of the dark sector coupling constant for 0.001 < mA0 < 3.16 GeV and 0.05 < mϒD < 9.5 GeV.publishedVersio

Cosmic-ray positron fraction measurement from 1 to 30 GeV with AMS-01

A measurement of the cosmic ray positron fraction e+/(e+ + e-) in the energy range of 1-30 GeV is presented. The measurement is based on data taken by the AMS-01 experiment during its 10 day Space Shuttle flight in June 1998. A proton background suppression on the order of 10^6 is reached by identifying converted bremsstrahlung photons emitted from positrons