ART: A machine learning Automated Recommendation Tool for synthetic biology

Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, and fatty acids. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing

Measurement of VH, H → b b ¯ production as a function of the vector-boson transverse momentum in 13 TeV pp collisions with the ATLAS detector

Cross-sections of associated production of a Higgs boson decaying into bottom-quark pairs and an electroweak gauge boson, W or Z, decaying into leptons are measured as a function of the gauge boson transverse momentum. The measurements are performed in kinematic fiducial volumes defined in the `simplified template cross-section' framework. The results are obtained using 79.8 fb-1 of proton-proton collisions recorded by the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 13 TeV. All measurements are found to be in agreement with the Standard Model predictions, and limits are set on the parameters of an effective Lagrangian sensitive to modifications of the Higgs boson couplings to the electroweak gauge bosons

Combined measurements of Higgs boson production and decay using up to 80 fb⁻¹ of proton-proton collision data at \sqrts= 13 TeV collected with the ATLAS experiment

Combined measurements of Higgs boson production cross sections and branching fractions are presented. The combination is based on the analyses of the Higgs boson decay modes H→γγ, ZZ∗, WW∗, ττ, b¯b, μμ, searches for decays into invisible final states, and on measurements of off-shell Higgs boson production. Up to 79.8  fb−1 of proton–proton collision data collected at √s=13  TeV with the ATLAS detector are used. Results are presented for the gluon–gluon fusion and vector-boson fusion processes, and for associated production with vector bosons or top-quarks. The global signal strength is determined to be μ=1.11+0.09−0.08. The combined measurement yields an observed (expected) significance for the vector-boson fusion production process of 6.5σ (5.3σ). Measurements in kinematic regions defined within the simplified template cross section framework are also shown. The results are interpreted in terms of modifiers applied to the Standard Model couplings of the Higgs boson to other particles, and are used to set exclusion limits on parameters in two-Higgs-doublet models and in the simplified minimal supersymmetric Standard Model. No significant deviations from Standard Model predictions are observed

Measurement of the inclusive isolated-photon cross section at √s = 13 TeV using fb⁻¹ of ATLAS data

The differential cross section for isolated-photon production in pp collisions is measured at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC using an integrated luminosity of 36.1 fb−1. The differential cross section is presented as a function of the photon transverse energy in different regions of photon pseudorapidity. The differential cross section as a function of the absolute value of the photon pseudorapidity is also presented in different regions of photon transverse energy. Next-to-leading-order QCD calculations from Jetphox and Sherpa as well as next-to-next-to-leading-order QCD calculations from Nnlojet are compared with the measurement, using several parameterisations of the proton parton distribution functions. The predictions provide a good description of the data within the experimental and theoretical uncertainties

Constraints on mediator-based dark matter and scalar dark energy models using root s= 13 TeV pp collision data collected by the ATLAS detector

Constraints on selected mediator-based dark matter models and a scalar dark energy model using up to 37 fb−1s√ = 13 TeV pp collision data collected by the ATLAS detector at the LHC during 2015-2016 are summarised in this paper. The results of experimental searches in a variety of final states are interpreted in terms of a set of spin-1 and spin-0 single-mediator dark matter simplified models and a second set of models involving an extended Higgs sector plus an additional vector or pseudo-scalar mediator. The searches considered in this paper constrain spin-1 leptophobic and leptophilic mediators, spin-0 colour-neutral and colour-charged mediators and vector or pseudo-scalar mediators embedded in extended Higgs sector models. In this case, also s√ = 8 TeV pp collision data are used for the interpretation of the results. The results are also interpreted for the first time in terms of light scalar particles that could contribute to the accelerating expansion of the universe (dark energy).ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWFW, Austria; FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq, Brazil; FAPESP, Brazil; NSERC, Canada; NRC, Canada; CFI, Canada; CERN; CONICYT, Chile; CAS, China; MOST, China; NSFC, China; COLCIENCIAS, Colombia; MSMT CR, Czech Republic; MPO CR, Czech Republic; VSC CR, Czech Republic; DNRF, Denmark; DNSRC, Denmark; IN2P3-CNRS, CEA-DRF/IRFU, France; SRNSFG, Georgia; BMBF, Germany; HGF, Germany; MPG, Germany; GSRT, Greece; RGC, Hong Kong SAR, China; ISF, Israel; Benoziyo Center, Israel; INFN, Italy; MEXT, Japan; JSPS, Japan; CNRST, Morocco; NWO, Netherlands; RCN, Norway; MNiSW, Poland; NCN, Poland; FCT, Portugal; MNE/IFA, Romania; MES of Russia, Russian Federation; NRC KI, Russian Federation; JINR; MESTD, Serbia; MSSR, Slovakia; ARRS, Slovenia; MIZS, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC, Sweden; Wallenberg Foundation, Sweden; SERI, Switzerland; SNSF, Switzerland; Canton of Bern, Switzerland; Canton of Geneva, Switzerland; MOST, Taiwan; TAEK, Turkey; STFC, United Kingdom; DOE, United States of America; NSF, United States of America; BCKDF, Canada; CANARIE, Canada; CRC, Canada; Compute Canada, Canada; COST, European Union; ERC, European Union; ERDF, European Union; Horizon 2020, European Union; Marie Sk lodowska-Curie Actions, European Union; Investissements d' Avenir Labex and Idex, ANR, France; DFG, Germany; AvH Foundation, Germany; Herakleitos programme; Thales programme; Aristeia programme; EU-ESF, Greece; Greek NSRF, Greece; BSF-NSF, Israel; GIF, Israel; CERCA Programme Generalitat de Catalunya, Spain; Royal Society, United Kingdom; Leverhulme Trust, United KingdomOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Fluctuations of anisotropic flow in Pb+Pb collisions at s NN = 5. 02 TeV with the ATLAS detector

Abstract: Multi-particle azimuthal cumulants are measured as a function of centrality and transverse momentum using 470 μb−1 of Pb+Pb collisions at sNN = 5.02 TeV with the ATLAS detector at the LHC. These cumulants provide information on the event-by-event fluctuations of harmonic flow coefficients vn and correlated fluctuations between two harmonics vn and vm. For the first time, a non-zero four-particle cumulant is observed for dipolar flow, v1. The four-particle cumulants for elliptic flow, v2, and triangular flow, v3, exhibit a strong centrality dependence and change sign in ultra-central collisions. This sign change is consistent with significant non-Gaussian fluctuations in v2 and v3. The four-particle cumulant for quadrangular flow, v4, is found to change sign in mid-central collisions. Correlations between two harmonics are studied with three- and four-particle mixed-harmonic cumulants, which indicate an anti-correlation between v2 and v3, and a positive correlation between v2 and v4. These correlations decrease in strength towards central collisions and either approach zero or change sign in ultra-central collisions. To investigate the possible flow fluctuations arising from intrinsic centrality or volume fluctuations, the results are compared between two different event classes used for centrality definitions. In peripheral and mid-central collisions where the cumulant signals are large, only small differences are observed. In ultra-central collisions, the differences are much larger and transverse momentum dependent. These results provide new information to disentangle flow fluctuations from the initial and final states, as well as new insights on the influence of centrality fluctuations

Measurement of differential cross sections for single diffractive dissociation in s = 8 TeV pp collisions using the ATLAS ALFA spectrometer

Abstract: A dedicated sample of Large Hadron Collider proton-proton collision data at centre-of-mass energy s = 8 TeV is used to study inclusive single diffractive dissociation, pp → X p. The intact final-state proton is reconstructed in the ATLAS ALFA forward spectrometer, while charged particles from the dissociated system X are measured in the central detector components. The fiducial range of the measurement is −4.0 < log10ξ < −1.6 and 0.016 < |t| < 0.43 GeV2, where ξ is the proton fractional energy loss and t is the squared four-momentum transfer. The total cross section integrated across the fiducial range is 1.59 ± 0.13 mb. Cross sections are also measured differentially as functions of ξ, t, and ∆η, a variable that characterises the rapidity gap separating the proton and the system X . The data are consistent with an exponential t dependence, dσ/dt ∝ eBt with slope parameter B = 7.65 ± 0.34 GeV−2. Interpreted in the framework of triple Regge phenomenology, the ξ dependence leads to a pomeron intercept of α(0) = 1.07 ± 0.09

Erratum to: Search for diboson resonances in hadronic final states in 139 fb⁻¹ of pp collisions at s = 13 TeV with the ATLAS detector (Journal of High Energy Physics, (2019), 2019, 9, (91), 10.1007/JHEP09(2019)091)

A mistake was identified for the paper [1] in the treatment of the radion [2] cross-sections, which resulted in multiple changes

Measurement of the transverse momentum distribution of Drell–Yan lepton pairs in proton–proton collisions at s = 13 TeV with the ATLAS detector

Abstract: This paper describes precision measurements of the transverse momentum pTℓℓ (ℓ=e, μ) and of the angular variable ϕη∗ distributions of Drell–Yan lepton pairs in a mass range of 66–116 GeV. The analysis uses data from 36.1 fb-1 of proton–proton collisions at a centre-of-mass energy of s=13TeV collected by the ATLAS experiment at the LHC in 2015 and 2016. Measurements in electron-pair and muon-pair final states are performed in the same fiducial volumes, corrected for detector effects, and combined. Compared to previous measurements in proton–proton collisions at s=7 and 8TeV, these new measurements probe perturbative QCD at a higher centre-of-mass energy with a different composition of initial states. They reach a precision of 0.2% for the normalized spectra at low values of pTℓℓ. The data are compared with different QCD predictions, where it is found that predictions based on resummation approaches can describe the full spectrum within uncertainties