Inhibition of a yeast LTR retrotransposon by human APOBEC3 cytidine deaminases

The mammalian APOBEC3 family of cytidine deaminases includes several members that possess potent antiretroviral activity. Human APOBEC3F and APOBEC3G are specifically incorporated into human immunodeficiency virus type 1 (HIV-1) progeny virions in the absence of virion infectivity factor (Vif), where they deaminate deoxycytidine to deoxyuridine on the minus strand of nascent reverse transcripts. Editing of the HIV-1 cDNA leads to its degradation or to G to A hypermutation of the integrated provirus [1-8]. Here, we show that APOBEC3 proteins also restrict the activity of a distantly related long terminal repeat (LTR) retrotransposon. When expressed in the yeast Saccharomyces cerevisiae, human APOBEC3C, APOBEC3F, or APOBEC3G or mouse APOBEC3 potently inhibit replication of the Ty1 LTR retrotransposon. APOBEC3G interacts with Ty1 Gag and is packaged into Ty1 virus-like particles (VLPs) by a mechanism that closely resembles the one it uses to enter HIV-1 virions. Expression of APOBEC3G results in a reduced level of Ty1 cDNA integration and G to A editing of integrated Ty1 cDNA. Our findings indicate that APOBEC3G restricts Ty1 and HIV-1 by similar mechanisms and suggest that the APOBEC3 proteins target a substantially broader spectrum of retroelements than previously appreciated

Indoor free space optics link under the weak turbulence regime: measurements and model validation

This paper is a postprint of a paper submitted to and accepted for publication in [journal] and is subject to Institution of Engineering and Technology Copyright. The copy of record is available at IET Digital LibraryIn this study, the authors present the measurements performed on a free space optics (FSO) communications link using an indoor atmospheric chamber. In particular, the authors have generated several different optical turbulence conditions, demonstrating how even the weak turbulence regime can strongly affect the FSO link performance. The authors have carried out an in-depth analysis of the data collected during the measurements, and calculated the turbulence strength (i.e. scintillation index and Rytov variance) and the important performance metrics (i.e. the Q-factor and bit error rate) to evaluate the FSO link quality. Moreover, the authors have tested, for the first time, an appositely developed temporally-correlated gamma-gamma channel model to generate the temporal irradiance fluctuations observed at the receiver. This has been accomplished by using a complete analysis tool that enables the authors to fully simulate the experimental FSO link. Finally, the authors compare the generated time-series with the collected experimental data, showing a good agreement and thus proving the effectiveness of the model.This work was supported by the European Space Agency under grant no. 5401001020. We are very grateful to Dr. E. Armandillo for enlightening discussions. J. Perez's work was support by Spanish MINECO Juan de la Cierva Fellowship JCI-2012-14805. This research project falls within the frame of COST ICT Action IC1101 - Optical Wireless Communications - An Emerging Technology (OPTICWISE).Pernice, R.; Ando, A.; Cardinale, M.; Curcio, L.; Stivala, S.; Parisi, A.; Busacca, AC.... (2015). Indoor free space optics link under the weak turbulence regime: measurements and model validation. IET Communications. 9(1):62-70. https://doi.org/10.1049/iet-com.2014.0432S627091Tsukamoto, K., Hashimoto, A., Aburakawa, Y., & Matsumoto, M. (2009). The case for free space. IEEE Microwave Magazine, 10(5), 84-92. doi:10.1109/mmm.2009.933086Suriza, A. Z., Md Rafiqul, I., Wajdi, A. K., & Naji, A. W. (2013). Proposed parameters of specific rain attenuation prediction for Free Space Optics link operating in tropical region. Journal of Atmospheric and Solar-Terrestrial Physics, 94, 93-99. doi:10.1016/j.jastp.2012.11.008Nebuloni, R. (2005). Empirical relationships between extinction coefficient and visibility in fog. Applied Optics, 44(18), 3795. doi:10.1364/ao.44.003795García-Zambrana, A., Castillo-Vázquez, C., & Castillo-Vázquez, B. (2011). Outage performance of MIMO FSO links over strong turbulence and misalignment fading channels. Optics Express, 19(14), 13480. doi:10.1364/oe.19.013480Shokrollahi, A. (2006). Raptor codes. IEEE Transactions on Information Theory, 52(6), 2551-2567. doi:10.1109/tit.2006.874390MacKay, D. J. C. (2005). Fountain codes. IEE Proceedings - Communications, 152(6), 1062. doi:10.1049/ip-com:20050237Uysal, M., Jing Li, & Meng Yu. (2006). Error rate performance analysis of coded free-space optical links over gamma-gamma atmospheric turbulence channels. IEEE Transactions on Wireless Communications, 5(6), 1229-1233. doi:10.1109/twc.2006.1638639Tsiftsis, T. A. (2008). Performance of heterodyne wireless optical communication systems over gamma-gamma atmospheric turbulence channels. Electronics Letters, 44(5), 373. doi:10.1049/el:20083028Popoola, W. O., & Ghassemlooy, Z. (2009). BPSK Subcarrier Intensity Modulated Free-Space Optical Communications in Atmospheric Turbulence. Journal of Lightwave Technology, 27(8), 967-973. doi:10.1109/jlt.2008.2004950Nistazakis, H. E., Tsiftsis, T. A., & Tombras, G. S. (2009). Performance analysis of free-space optical communication systems over atmospheric turbulence channels. IET Communications, 3(8), 1402. doi:10.1049/iet-com.2008.0212Bayaki, E., Schober, R., & Mallik, R. (2009). Performance analysis of MIMO free-space optical systems in gamma-gamma fading. IEEE Transactions on Communications, 57(11), 3415-3424. doi:10.1109/tcomm.2009.11.080168Anguita, J. A., Neifeld, M. A., Hildner, B., & Vasic, B. (2010). Rateless Coding on Experimental Temporally Correlated FSO Channels. Journal of Lightwave Technology, 28(7), 990-1002. doi:10.1109/jlt.2010.2040136Andò, A., Mangione, S., Curcio, L., Stivala, S., Garbo, G., Pernice, R., & Busacca, A. C. (2013). Recovery Capabilities of Rateless Codes on Simulated Turbulent Terrestrial Free Space Optics Channel Model. International Journal of Antennas and Propagation, 2013, 1-8. doi:10.1155/2013/692915Ghassemlooy, Z., Le Minh, H., Rajbhandari, S., Perez, J., & Ijaz, M. (2012). Performance Analysis of Ethernet/Fast-Ethernet Free Space Optical Communications in a Controlled Weak Turbulence Condition. Journal of Lightwave Technology, 30(13), 2188-2194. doi:10.1109/jlt.2012.2194271Xiaoming Zhu, & Kahn, J. M. (2002). Free-space optical communication through atmospheric turbulence channels. IEEE Transactions on Communications, 50(8), 1293-1300. doi:10.1109/tcomm.2002.800829Xu, F., Khalighi, A., Caussé, P., & Bourennane, S. (2009). Channel coding and time-diversity for optical wireless links. Optics Express, 17(2), 872. doi:10.1364/oe.17.00087

Measurement of the tt¯ production cross-section in pp collisions at s√ = 5.02 TeV with the ATLAS detector

The inclusive top-quark pair (tt¯) production cross-section σtt¯ is measured in proton–proton collisions at a centre-of-mass energy s√ = 5.02 TeV, using 257 pb−1 of data collected in 2017 by the ATLAS experiment at the LHC. The tt¯ cross-section is measured in both the dilepton and single-lepton final states of the tt¯ system and then combined. The combination of the two measurements yields σtt¯=67.5±0.9(stat.)±2.3(syst.)±1.1(lumi.)±0.2(beam)pb, where the four uncertainties reflect the limited size of the data sample, experimental and theoretical systematic effects, and imperfect knowledge of both the integrated luminosity and the LHC beam energy, giving a total uncertainty of 3.9%. The result is in agreement with theoretical quantum chromodynamic calculations at next-to-next-to-leading order in the strong coupling constant, including the resummation of next-to-next-to-leading logarithmic soft-gluon terms, and constrains the parton distribution functions of the proton at large Bjorken-x

Evidence for the charge asymmetry in pp → tt¯ production at s√ = 13 TeV with the ATLAS detector

Inclusive and differential measurements of the top–antitop (tt¯) charge asymmetry Att¯C and the leptonic asymmetry Aℓℓ¯C are presented in proton–proton collisions at s√ = 13 TeV recorded by the ATLAS experiment at the CERN Large Hadron Collider. The measurement uses the complete Run 2 dataset, corresponding to an integrated luminosity of 139 fb−1, combines data in the single-lepton and dilepton channels, and employs reconstruction techniques adapted to both the resolved and boosted topologies. A Bayesian unfolding procedure is performed to correct for detector resolution and acceptance effects. The combined inclusive tt¯ charge asymmetry is measured to be Att¯C = 0.0068 ± 0.0015, which differs from zero by 4.7 standard deviations. Differential measurements are performed as a function of the invariant mass, transverse momentum and longitudinal boost of the tt¯ system. Both the inclusive and differential measurements are found to be compatible with the Standard Model predictions, at next-to-next-to-leading order in quantum chromodynamics perturbation theory with next-to-leading-order electroweak corrections. The measurements are interpreted in the framework of the Standard Model effective field theory, placing competitive bounds on several Wilson coefficients

Search for heavy resonances decaying into a Z or W boson and a Higgs boson in final states with leptons and b-jets in 139 fb−1 of pp collisions at s√ = 13 TeV with the ATLAS detector

This article presents a search for new resonances decaying into a Z or W boson and a 125 GeV Higgs boson h, and it targets the νν¯¯¯bb¯¯, ℓ+ℓ−bb¯¯, or ℓ±νbb¯¯ final states, where ℓ = e or μ, in proton-proton collisions at s√ = 13 TeV. The data used correspond to a total integrated luminosity of 139 fb−1 collected by the ATLAS detector during Run 2 of the LHC at CERN. The search is conducted by examining the reconstructed invariant or transverse mass distributions of Zh or Wh candidates for evidence of a localised excess in the mass range from 220 GeV to 5 TeV. No significant excess is observed and 95% confidence-level upper limits between 1.3 pb and 0.3 fb are placed on the production cross section times branching fraction of neutral and charged spin-1 resonances and CP-odd scalar bosons. These limits are converted into constraints on the parameter space of the Heavy Vector Triplet model and the two-Higgs-doublet model

Measurements of Zγ+jets differential cross sections in pp collisions at s√ = 13 TeV with the ATLAS detector

Differential cross-section measurements of Zγ production in association with hadronic jets are presented, using the full 139 fb−1 dataset of s√ = 13 TeV proton–proton collisions collected by the ATLAS detector during Run 2 of the LHC. Distributions are measured using events in which the Z boson decays leptonically and the photon is usually radiated from an initial-state quark. Measurements are made in both one and two observables, including those sensitive to the hard scattering in the event and others which probe additional soft and collinear radiation. Different Standard Model predictions, from both parton-shower Monte Carlo simulation and fixed-order QCD calculations, are compared with the measurements. In general, good agreement is observed between data and predictions from MATRIX and MiNNLOPS, as well as next-to-leading-order predictions from MADGRAPH5_AMC@NLO and SHERPA

Search for third-generation vector-like leptons in pp collisions at s√ = 13 TeV with the ATLAS detector

A search for vector-like leptons in multilepton (two, three, or four-or-more electrons plus muons) final states with zero or more hadronic τ-lepton decays is presented. The search is performed using a dataset corresponding to an integrated luminosity of 139 fb−1 of proton-proton collisions at a centre-of-mass energy of 13 TeV recorded by the ATLAS detector at the LHC. To maximize the separation of signal and background, a machine-learning classifier is used. No excess of events is observed beyond the Standard Model expectation. Using a doublet vector-like lepton model, vector-like leptons coupling to third-generation Standard Model leptons are excluded in the mass range from 130 GeV to 900 GeV at the 95% confidence level, while the highest excluded mass is expected to be 970 GeV

Measurement of electroweak Z(νν) γjj production and limits on anomalous quartic gauge couplings in pp collisions at s√ = 13 TeV with the ATLAS detector

The electroweak production of Z(νν¯¯¯)γ in association with two jets is studied in a regime with a photon of high transverse momentum above 150 GeV using proton–proton collisions at a centre-of-mass energy of 13 TeV at the Large Hadron Collider. The analysis uses a data sample with an integrated luminosity of 139 fb−1 collected by the ATLAS detector during the 2015–2018 LHC data-taking period. This process is an important probe of the electroweak symmetry breaking mechanism in the Standard Model and is sensitive to quartic gauge boson couplings via vector-boson scattering. The fiducial Z(νν¯¯¯)γjj cross section for electroweak production is measured to be 0.77+0.34−0.30 fb and is consistent with the Standard Model prediction. Evidence of electroweak Z(νν¯¯¯)γjj production is found with an observed significance of 3.2σ for the background-only hypothesis, compared with an expected significance of 3.7σ. The combination of this result with the previously published ATLAS observation of electroweak Z(νν¯¯¯)γjj production yields an observed (expected) signal significance of 6.3σ (6.6σ). Limits on anomalous quartic gauge boson couplings are obtained in the framework of effective field theory with dimension-8 operators