Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

A search for t (t)over-bar resonances with the ATLAS detector in 2.05 fb(-1) of proton-proton collisions at root s=7 TeV

A search for top quark pair resonances in final states containing at least one electron or muon has been performed with the ATLAS experiment at the CERN Large Hadron Collider. The search uses a data sample corresponding to an integrated luminosity of 2.05 fb(-1), which was recorded in 2011 at a proton-proton centre-of-mass energy of 7 TeV. No evidence for a resonance is found and limits are set on the production cross-section times branching ratio to t (t) over bar for narrow and wide resonances. For narrow Z' bosons, the observed 95 % Bayesian credibility level limits range from 9.3 pb to 0.95 pb for masses in the range of m(Z') = 500 GeV to m(Z') = 1300 GeV. The corresponding excluded mass region for a leptophobic topcolour Z' boson (Kaluza-Klein gluon excitation in the Randall-Sundrum model) is m(Z') < 880 GeV (m(gKK) < 1130 GeV). RI Wemans, Andre/A-6738-2012; Cirkovic, Predrag/G-8059-2012; Fazio, Salvatore /G-5156-2010; Fabbri, Laura/H-3442-2012; Villa, Mauro/C-9883-2009; Jones, Roger/H-5578-2011; valente, paolo/A-6640-2010; Takai, Helio/C-3301-2012; Delmastro, Marco/I-5599-2012; Livan, Michele/D-7531-201

Search for anomaly-mediated supersymmetry breaking with the ATLAS detector based on a disappearing-track signature in pp collisions at root s=7 TeV

In models of anomaly-mediated supersymmetry breaking (AMSB), the lightest chargino is predicted to have a lifetime long enough to be detected in collider experiments. This letter explores AMSB scenarios in pp collisions at root s = 7 TeV by attempting to identify decaying charginos which result in tracks that appear to have few associated hits in the outer region of the tracking system. The search was based on data corresponding to an integrated luminosity of 1.02 fb(-1) collected with the ATLAS detector in 2011. The p(T) spectrum of candidate tracks is found to be consistent with the expectation from Standard Model background processes and constraints on the lifetime and the production cross section were obtained. In the minimal AMSB framework with m(3/2) 0, a chargino having mass below 92 GeV and a lifetime between 0.5 ns and 2 ns is excluded at 95 % confidence level. RI Fazio, Salvatore /G-5156-2010; valente, paolo/A-6640-2010; Doyle, Anthony/C-5889-2009; Alexa, Calin/F-6345-2010; Gutierrez, Phillip/C-1161-2011; Pacheco Pages, Andres/C-5353-2011; Moorhead, Gareth/B-6634-2009; Livan, Michele/D-7531-2012; Takai, Helio/C-3301-2012; Petrucci, Fabrizio/G-8348-2012; Smirnov, Sergei/F-1014-2011; Wemans, Andre/A-6738-2012; Jones, Roger/H-5578-2011; Fabbri, Laura/H-3442-2012; Kurashige, Hisaya/H-4916-2012; Villa, Mauro/C-9883-2009; Delmastro, Marco/I-5599-201

Search for excited leptons in proton-proton collisions at root s=7 TeV with the ATLAS detector

The ATLAS detector is used to search for excited leptons in the electromagnetic radiative decay channel l* -> l gamma. Results are presented based on the analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 2.05 fb(-1). No evidence for excited leptons is found, and limits are set on the compositeness scale Lambda as a function of the excited lepton mass m(l*). In the special case where Lambda = m(l*), excited electron and muon masses below 1.87 TeV and 1.75 TeV are excluded at 95% C.L., respectively. RI Li, Xuefei/C-3861-2012; Smirnova, Lidia/D-8089-2012; Sivoklokov, Sergey/D-8150-2012; Smirnov, Sergei/F-1014-2011; Gladilin, Leonid/B-5226-2011; Barreiro, Fernando/D-9808-2012; Prokoshin, Fedor/E-2795-2012; valente, paolo/A-6640-2010; Fazio, Salvatore /G-5156-2010; Orlov, Ilya/E-6611-2012; Doyle, Anthony/C-5889-2009; Alexa, Calin/F-6345-2010; Gutierrez, Phillip/C-1161-2011; Pacheco Pages, Andres/C-5353-2011; Moorhead, Gareth/B-6634-2009; Livan, Michele/D-7531-2012; Takai, Helio/C-3301-2012; Petrucci, Fabrizio/G-8348-2012; Wemans, Andre/A-6738-2012; Jones, Roger/H-5578-2011; Fabbri, Laura/H-3442-2012; Kurashige, Hisaya/H-4916-2012; Villa, Mauro/C-9883-2009; Delmastro, Marco/I-5599-201

Search for diphoton events with large missing transverse momentum in 1 fb(-1) of 7 TeV proton-proton collision data with the ATLAS detector ATLAS Collaboration

A search for diphoton events with large missing transverse momentum has been performed using 1.07 fb(-1) of proton-proton collision data at root s = 7 TeV recorded with the ATLAS detector. No excess of events was observed above the Standard Model prediction and 95% Confidence Level (CL) upper limits are set on the production cross section for new physics. The limits depend on each model parameter space and vary as follows: sigma < (22-129) fb in the context of a generalised model of gauge-mediated supersymmetry breaking (GGM) with a bino-like lightest neutralino, sigma < (27-91) fb in the context of a minimal model of gauge-mediated supersymmetry breaking (SPS8), and sigma < (15-27) fb in the context of a specific model with one universal extra dimension (UED). A 95% CL lower limit of 805 GeV, for bino masses above 50 GeV, is set on the GGM gluino mass. Lower limits of 145 TeV and 1.23 TeV are set on the SPS8 breaking scale Lambda and on the UED compactification scale 1/R, respectively. These limits provide the most stringent tests of these models to date. (C) 2012 CERN. Published by Elsevier B.V. All rights reserved

Measurement of D*(+/-) meson production in jets from pp collisions at root s=7 TeV with the ATLAS detector

This paper reports a measurement of D*(+/-) meson production in jets from proton- proton collisions at a center- of- mass energy of root s = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb(-1) for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range vertical bar eta vertical bar D-0 pi(+), D-0 -> K-pi(+), and its charge conjugate. The production rate is found to be N(D*(+/-))/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*(+/-) mesons that carry a fraction z of the jet momentum in the range 0.3< z< 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum

Searches for supersymmetry with the ATLAS detector using final states with two leptons and missing transverse momentum in root s=7 TeV proton-proton collisions

Results of three searches are presented for the production of supersymmetric particles decaying into final states with missing transverse momentum and exactly two isolated leptons, e or mu. The analysis uses a data sample collected during the first half of 2011 that corresponds to a total integrated luminosity of 1 fb(-1) of root s = 7 TeV proton-proton collisions recorded with the ATLAS detector at the Large Hadron Collider. Opposite-sign and same-sign dilepton events are separately studied, with no deviations from the Standard Model expectation observed. Additionally, in opposite-sign events, a search is made for an excess of same-flavour over different-flavour lepton pairs. Effective production cross sections in excess of 9.9 fb for opposite-sign events containing supersymmetric particles with missing transverse momentum greater than 250 GeV are excluded at 95% CL For same-sign events containing supersymmetric particles with missing transverse momentum greater than 100 GeV, effective production cross sections in excess of 14.8 fb are excluded at 95% CL The latter limit is interpreted in a simplified electroweak gaugino production model excluding chargino masses up to 200 GeV, under the assumption that slepton decay is dominant. (C) 2012 CERN. Published by Elsevier B.V. All rights reserved

Search for heavy neutrinos and right-handed W bosons in events with two leptons and jets in pp collisions at root s=7 TeV with the ATLAS detector

This letter reports on a search for hypothetical heavy neutrinos, N, and right-handed gauge bosons, W-R, in events with high transverse momentum objects which include two reconstructed leptons and at least one hadronic jet. The results were obtained from data corresponding to an integrated luminosity of 2.1 fb(-1) collected in proton-proton collisions at root s = 7 TeV with the ATLAS detector at the CERN Large Hadron Collider. No excess above the Standard Model background expectation is observed. Excluded mass regions for Majorana and Dirac neutrinos are presented using two approaches for interactions that violate lepton and lepton-flavor numbers. One approach uses an effective operator framework, the other approach is guided by the Left-Right Symmetric Model. The results described in this letter represent the most stringent limits to date on the masses of heavy neutrinos and W-R bosons obtained in direct searches