Intratumoral heterogeneity analysis reveals hidden associations between protein expression losses and patient survival in clear cell renal cell carcinoma.

Intratumoral heterogeneity (ITH) is a prominent feature of kidney cancer. It is not known whether it has utility in finding associations between protein expression and clinical parameters. We used ITH that is detected by immunohistochemistry (IHC) to aid the association analysis between the loss of SWI/SNF components and clinical parameters.160 ccRCC tumors (40 per tumor stage) were used to generate tissue microarray (TMA). Four foci from different regions of each tumor were selected. IHC was performed against PBRM1, ARID1A, SETD2, SMARCA4, and SMARCA2. Statistical analyses were performed to correlate biomarker losses with patho-clinical parameters. Categorical variables were compared between groups using Fisher\u27s exact tests. Univariate and multivariable analyses were used to correlate biomarker changes and patient survivals. Multivariable analyses were performed by constructing decision trees using the classification and regression trees (CART) methodology. IHC detected widespread ITH in ccRCC tumors. The statistical analysis of the Truncal loss (root loss) found additional correlations between biomarker losses and tumor stages than the traditional Loss in tumor (total) . Losses of SMARCA4 or SMARCA2 significantly improved prognosis for overall survival (OS). Losses of PBRM1, ARID1A or SETD2 had the opposite effect. Thus Truncal Loss analysis revealed hidden links between protein losses and patient survival in ccRCC

The role of radiative losses in the late evolution of pulse-heated coronal loops/strands

Radiative losses from optically thin plasma are an important ingredient for modeling plasma confined in the solar corona. Spectral models are continuously updated to include the emission from more spectral lines, with significant effects on radiative losses, especially around 1 MK. We investigate the effect of changing the radiative losses temperature dependence due to upgrading of spectral codes on predictions obtained from modeling plasma confined in the solar corona. The hydrodynamic simulation of a pulse-heated loop strand is revisited comparing results using an old and a recent radiative losses function. We find significant changes in the plasma evolution during the late phases of plasma cooling: when the recent radiative loss curve is used, the plasma cooling rate increases significantly when temperatures reach 1-2 MK. Such more rapid cooling occurs when the plasma density is larger than a threshold value, and therefore in impulsive heating models that cause the loop plasma to become overdense. The fast cooling has the effect of steepening the slope of the emission measure distribution of coronal plasmas with temperature at temperatures lower than ~2 MK. The effects of changes in the radiative losses curves can be important for modeling the late phases of the evolution of pulse-heated coronal loops, and, more in general, of thermally unstable optically thin plasmas.Comment: 16 pages, 7 figures, accepted for publicatio

Observations and Interpretation of a Low Coronal Shock Wave Observed in the EUV by the SDO/AIA

Taking advantage of both the high temporal and spatial resolution of the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO), we studied a limb coronal shock wave and its associated extreme ultraviolet (EUV) wave that occurred on 2010 June 13. Our main findings are (1) the shock wave appeared clearly only in the channels centered at 193 \AA and 211 \AA as a dome-like enhancement propagating ahead of its associated semi-spherical CME bubble; (2) the density compression of the shock is 1.56 according to radio data and the temperature of the shockis around 2.8 MK; (3) the shock wave first appeared at 05:38 UT, 2 minutes after the associated flare has started and 1 minute after its associated CME bubble appeared;(4) the top of the dome-like shock wave set out from about 1.23 R\odot and the thickness of the shocked layer is ~ 2\times10^4 km; (5) the speed of the shock wave is consistent with a slight decrease from about 600 km/s to 550 km/s; (6) the lateral expansion of the shock wave suggests a constant speed around 400 km/s, which varies at different heights and directions. Our findings support the view that the coronal shock wave is driven by the CME bubble, and the on-limb EUV wave is consistent with a fast wave or at least includes the fast wave component.Comment: 24 pages,8 Figures and 6 movies. It is scheduled for publication on the Astrophysical Journal on the August 1, 2011, Issue 736 -

A Deep Chandra X-ray Spectrum of the Accreting Young Star TW Hydrae

We present X-ray spectral analysis of the accreting young star TW Hydrae from a 489 ks observation using the Chandra High Energy Transmission Grating. The spectrum provides a rich set of diagnostics for electron temperature T_e, electron density N_e, hydrogen column density N_H, relative elemental abundances and velocities and reveals its source in 3 distinct regions of the stellar atmosphere: the stellar corona, the accretion shock, and a very large extended volume of warm postshock plasma. The presence of Mg XII, Si XIII, and Si XIV emission lines in the spectrum requires coronal structures at ~10 MK. Lower temperature lines (e.g., from O VIII, Ne IX, and Mg XI) formed at 2.5 MK appear more consistent with emission from an accretion shock. He-like Ne IX line ratio diagnostics indicate that T_e = 2.50 +/- 0.25 MK and N_e = 3.0 +/- 0.2 x 10^(12) cm^(-3) in the shock. These values agree well with standard magnetic accretion models. However, the Chandra observations significantly diverge from current model predictions for the postshock plasma. This gas is expected to cool radiatively, producing O VII as it flows into an increasingly dense stellar atmosphere. Surprisingly, O VII indicates N_e = 5.7 ^(+4.4}_(-1.2) x 10^(11) cm^(-3), five times lower than N_e in the accretion shock itself, and ~7 times lower than the model prediction. We estimate that the postshock region producing O VII has roughly 300 times larger volume, and 30 times more emitting mass than the shock itself. Apparently, the shocked plasma heats the surrounding stellar atmosphere to soft X-ray emitting temperatures and supplies this material to nearby large magnetic structures -- which may be closed magnetic loops or open magnetic field leading to mass outflow. (Abridged)Comment: 13 pages (emulateapj style), 10 figures, ApJ, in pres

In vitro activity of ceftazidime, ceftaroline and aztreonam alone and in combination with avibactam against European Gram-negative and Gram-positive clinical isolates

Recent clinical isolates of key Gram-negative and Gram-positive bacteria were collected in 2012 from hospitalised patients in medical centres in four European countries (France, Germany, Italy and Spain) and were tested using standard broth microdilution methodology to assess the impact of 4 mg/L avibactam on the in vitro activities of ceftazidime, ceftaroline and aztreonam. Against Enterobacteriaceae, addition of avibactam significantly enhanced the level of activity of these antimicrobials. MIC90 values (minimum inhibitory concentration that inhibits 90% of the isolates) of ceftazidime, ceftaroline and aztreonam for Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Enterobacter aerogenes, Citrobacter freundii and Morganella morganii were reduced up to 128-fold or greater when combined with avibactam. A two-fold reduction in the MIC90 of ceftazidime to 8 mg/L was noted in Pseudomonas aeruginosa isolates when combined with avibactam, whereas little effect of avibactam was noted on the MIC values of the test compounds when tested against Acinetobacter baumannii isolates. Avibactam had little effect on the excellent activity of ceftazidime, ceftaroline and aztreonam against Haemophilus influenzae. It had no impact on the in vitro activity of ceftazidime and ceftaroline against staphylococci and streptococci. This study demonstrates that addition of avibactam enhances the activities of ceftazidime, ceftaroline and aztreonam against Enterobacteriaceae and P. aeruginosa but not against A. baumannii

The changing carbon cycle of the coastal ocean

The carbon cycle of the coastal ocean is a dynamic component of the global carbon budget. But the diverse sources and sinks of carbon and their complex interactions in these waters remain poorly understood. Here we discuss the sources, exchanges and fates of carbon in the coastal ocean and how anthropogenic activities have altered the carbon cycle. Recent evidence suggests that the coastal ocean may have become a net sink for atmospheric carbon dioxide during post-industrial times. Continued human pressures in coastal zones will probably have an important impact on the future evolution of the coastal ocean's carbon budget

On Solving the Coronal Heating Problem

This article assesses the current state of understanding of coronal heating, outlines the key elements of a comprehensive strategy for solving the problem, and warns of obstacles that must be overcome along the way.Comment: Accepted by Solar Physics; Published by Solar Physic

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 the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal