Perspectives on the use of transcriptomics to advance biofuels

As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.clos

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

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

Search for excited electrons singly produced in proton–proton collisions at \sqrt{s} = 13 TeV with the ALAS experiment at the LHC

A search for excited electrons produced in pp collisions at s√ = 13 TeV via a contact interaction qq¯→ee∗ is presented. The search uses 36.1 fb −1 of data collected in 2015 and 2016 by the ATLAS experiment at the Large Hadron Collider. Decays of the excited electron into an electron and a pair of quarks ( eqq¯ ) are targeted in final states with two electrons and two hadronic jets, and decays via a gauge interaction into a neutrino and a W boson ( νW ) are probed in final states with an electron, missing transverse momentum, and a large-radius jet consistent with a hadronically decaying W boson. No significant excess is observed over the expected backgrounds. Upper limits are calculated for the pp→ee∗→eeqq¯ and pp→ee∗→eνW production cross sections as a function of the excited electron mass me∗ at 95% confidence level. The limits are translated into lower bounds on the compositeness scale parameter Λ of the model as a function of me∗ . For me∗<0.5 TeV , the lower bound for Λ is 11 TeV . In the special case of me∗=Λ , the values of me∗<4.8 TeV are excluded. The presented limits on Λ are more stringent than those obtained in previous searches

Dijet azimuthal correlations and conditional yields in pp and p plus Pb collisions at √{S}^NN=5.02 TeV with the ATLAS detector

This paper presents a measurement of forward-forward and forward-central dijet azimuthal angular correlations and conditional yields in proton-proton (pp) and proton-lead (p + Pb) collisions as a probe of the nuclear gluon density in regions where the fraction of the average momentum per nucleon carried by the parton entering the hard scattering is low. In these regions, gluon saturation can modify the rapidly increasing parton distribution function of the gluon. The analysis utilizes 25 pb^{-1} of pp data and 360 mp^{-1} of p + Pb data, both at {S}^NN=5.02 TeV, collected in 2015 and 2016, respectively, with the ATLAS detector at the Large Hadron Collider. The measurement is performed in the center-of-mass frame of the nucleon-nucleon system in the rapidity range between -4.0 and 4.0 using the two highest transverse-momentum jets in each event, with the highest transverse-momentum jet restricted to the forward rapidity range. No significant broadening of azimuthal angular correlations is observed for forward-forward or forward-central dijets in p + Pb compared to pp collisions. For forward-forward jet pairs in the proton-going direction, the ratio of conditional yields in p + Pb collisions to those in pp collisions is suppressed by approximately 20%, with no significant dependence on the transverse momentum of the dijet system. No modification of conditional yields is observed for forward-central dijets

Measurement of jet-substructure observables in top quark, W boson and light jet production in proton-proton collisions at √s=13 TeV with the ATLAS detector

A measurement of jet substructure observables is presented using data collected in 2016 by the ATLAS experiment at the LHC with proton-proton collisions at s√ = 13 TeV. Large-radius jets groomed with the trimming and soft-drop algorithms are studied. Dedicated event selections are used to study jets produced by light quarks or gluons, and hadronically decaying top quarks and W bosons. The observables measured are sensitive to substructure, and therefore are typically used for tagging large-radius jets from boosted massive particles. These include the energy correlation functions and the N-subjettiness variables. The number of subjets and the Les Houches angularity are also considered. The distributions of the substructure variables, corrected for detector effects, are compared to the predictions of various Monte Carlo event generators. They are also compared between the large-radius jets originating from light quarks or gluons, and hadronically decaying top quarks and W bosons

Search for the Production of a Long-Lived Neutral Particle Decaying within the ATLAS Hadronic Calorimeter in Association with a Z Boson from pp Collisions at √s = 13 TeV

This Letter presents a search for the production of a long-lived neutral particle (Z_{d}) decaying within the ATLAS hadronic calorimeter, in association with a standard model (SM) Z boson produced via an intermediate scalar boson, where Z → L⁺ L⁻ (L = e, μ). The data used were collected by the ATLAS detector during 2015 and 2016 pp collisions with a center-of-mass energy of √s = 13 TeV at the Large Hadron Collider and correspond to an integrated luminosity of 36.1 ± 08.fb⁻¹. No significant excess of events is observed above the expected background. Limits on the production cross section of the scalar boson times its decay branching fraction into the long-lived neutral particle are derived as a function of the mass of the intermediate scalar boson, the mass of the long-lived neutral particle, and its c_{τ} from a few centimeters to one hundred meters. In the case that the intermediate scalar boson is the SM Higgs boson, its decay branching fraction to a long-lived neutral particle with a c_{τ} approximately between 0.1 and 7 m is excluded with a 95% confidence level up to 10% for m_{Z}_{d} between 5 and 15 GeV

Search for heavy charged long-lived particles in the ATLAS detector in 36.1 fb−1 of proton-proton collision data at √s=13 TeV

A search for heavy charged long-lived particles is performed using a data sample of 36.1     fb − 1 of proton-proton collisions at √ s = 13     TeV collected by the ATLAS experiment at the Large Hadron Collider. The search is based on observables related to ionization energy loss and time of flight, which are sensitive to the velocity of heavy charged particles traveling significantly slower than the speed of light. Multiple search strategies for a wide range of lifetimes, corresponding to path lengths of a few meters, are defined as model independently as possible, by referencing several representative physics cases that yield long-lived particles within supersymmetric models, such as gluinos/squarks ( R -hadrons), charginos and staus. No significant deviations from the expected Standard Model background are observed. Upper limits at 95% confidence level are provided on the production cross sections of long-lived R -hadrons as well as directly pair-produced staus and charginos. These results translate into lower limits on the masses of long-lived gluino, sbottom and stop R -hadrons, as well as staus and charginos of 2000, 1250, 1340, 430, and 1090 GeV, respectively

Search for heavy long-lived multicharged particles in proton-proton collisions at √s=13 TeV using the ATLAS detector

A search for heavy long-lived multicharged particles is performed using the ATLAS detector at the LHC. Data with an integrated luminosity of 36.1     fb − 1 collected in 2015 and 2016 from proton-proton collisions at √ s = 13     TeV are examined. Particles producing anomalously high ionization, consistent with long-lived massive particles with electric charges from | q | = 2 e to | q | = 7 e , are searched for. No events are observed, and 95% confidence level cross-section upper limits are interpreted as lower mass limits for a Drell-Yan production model. Multicharged particles with masses between 50 and 980–1220 GeV (depending on their electric charge) are excluded

Measurement of W^±Z production cross sections and gauge boson polarisation in pp collisions at √s=13 TeV with the ATLAS detector

This work is licensed under a Creative Commons Attribution 4.0 International License.This paper presents measurements of ± production cross sections in pp collisions at a centre-of-mass energy of 13 TeV. The data were collected in 2015 and 2016 by the ATLAS experiment at the Large Hadron Collider, and correspond to an integrated luminosity of 36.1 fb−1. The ± candidate events are reconstructed using leptonic decay modes of the gauge bosons into electrons and muons. The measured inclusive cross section in the detector fiducial region for a single leptonic decay mode is fid.±→ℓ′ℓℓ=63.7± 1.0 (stat.)± 2.3 (syst.)± 1.4 (lumi.) fb, reproduced by the next-to-next-to-leading-order Standard Model prediction of 61.5+1.4−1.3 fb. Cross sections for + and − production and their ratio are presented as well as differential cross sections for several kinematic observables. An analysis of angular distributions of leptons from decays of W and Z bosons is performed for the first time in pair-produced events in hadronic collisions, and integrated helicity fractions in the detector fiducial region are measured for the W and Z bosons separately. Of particular interest, the longitudinal helicity fraction of pair-produced vector bosons is also measured