Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes

Simple and Realistic Composite Higgs Models in Flat Extra Dimensions

We construct new composite Higgs/gauge-Higgs unification (GHU) models in flat space that overcome all the difficulties found in the past in attempting to construct models of this sort. The key ingredient is the introduction of large boundary kinetic terms for gauge (and fermion) fields. We focus our analysis on the electroweak symmetry breaking pattern and the electroweak precision tests and show how both are compatible with each other. Our models can be seen as effective TeV descriptions of analogue warped models. We point out that, as far as electroweak TeV scale physics is concerned, one can rely on simple and more flexible flat space models rather than considering their unavoidably more complicated warped space counterparts. The generic collider signatures of our models are essentially undistinguishable from those expected from composite Higgs/warped GHU models, namely a light Higgs, colored fermion resonances below the TeV scale and sizable deviations to the Higgs and top coupling.Comment: 30 figures, 9 figures; v2: minor improvements, one reference added, version to appear in JHE

Search for direct pair production of the top squark in all-hadronic final states in proton-proton collisions at s√=8 TeV with the ATLAS detector

The results of a search for direct pair production of the scalar partner to the top quark using an integrated luminosity of 20.1fb−1 of proton–proton collision data at √s = 8 TeV recorded with the ATLAS detector at the LHC are reported. The top squark is assumed to decay via t˜→tχ˜01 or t˜→ bχ˜±1 →bW(∗)χ˜01 , where χ˜01 (χ˜±1 ) denotes the lightest neutralino (chargino) in supersymmetric models. The search targets a fully-hadronic final state in events with four or more jets and large missing transverse momentum. No significant excess over the Standard Model background prediction is observed, and exclusion limits are reported in terms of the top squark and neutralino masses and as a function of the branching fraction of t˜ → tχ˜01 . For a branching fraction of 100%, top squark masses in the range 270–645 GeV are excluded for χ˜01 masses below 30 GeV. For a branching fraction of 50% to either t˜ → tχ˜01 or t˜ → bχ˜±1 , and assuming the χ˜±1 mass to be twice the χ˜01 mass, top squark masses in the range 250–550 GeV are excluded for χ˜01 masses below 60 GeV

Annealing study and thermal investigation on bismuth sulfide thin films prepared by chemical bath deposition in basic medium

This is a post-peer-review, pre-copyedit version of an article published in Applied Physics A 124.2 (2018): 166. The final authenticated version is available online at: http://doi.org/10.1007/s00339-018-1584-7Bismuth sulfide thin films were prepared by chemical bath deposition using thiourea as sulfide ion source in basic medium. First, the effects of both the deposition parameters on films growth as well as the annealing effect under argon and sulfur atmosphere on as-deposited thin films were studied. The parameters were found to be influential using the Doehlert matrix experimental design methodology. Ranges for a maximum surface mass of films (3 mg cm-2) were determined. A well crystallized major phase of bismuth sulfide with stoichiometric composition was achieved at 190°C for 3 hours. The prepared thin films were characterized using Grazing Incidence X-ray diffraction (GIXRD), Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray analysis (EDX). Second, the band gap energy value was found to be 1.5 eV. Finally, the thermal properties have been studied for the first time by means of the electropyroelectric (EPE) technique. Indeed, the thermal conductivity varied in the range of 1.20 - 0.60 W m-1 K-1 while the thermal diffusivity values increased in terms of the annealing effect ranging from 1.8 to 3.5 10-7 m2s-1This work was financially supported by the Tunisian Ministry of Higher Education and Scientific Research and by the WINCOST (ENE2016-80788-C5-2-R) project funded by the Spanish Ministry of Economy and Competitivenes

Inducible clindamycin resistance and nasal carriage rates of Staphylococcus aureus among healthcare workers and community members

Background: Nasal carriage of Staphylococcus aureus is becoming an increasing problem among  healthcare workers and community individualsObjectives: To determine the prevalence of methicillin-resistant S. aureus (MRSA) nasal colonization and inducible clindamycin resistance (ICR) of S. aureus among healthcare workers at Soba University Hospital and community members in Khartoum State, Sudan.Methods: Five hundred nasal swabs samples were collected during March 2009 to April 2010. Isolates were identified using conventional laboratory assays and MRSA determined by the disk diffusion method. The D-test was performed for detection of ICR isolates with Clinical Laboratory Standard Institute guidelines.Results: Of the 114 S. aureus isolated, 20.2% represented MRSA. The occurrence of MRSA was  significantly higher among healthcare worker than community individuals [32.7% (18/55) vs. 6.9% (5/59)] (p=0.001). Overall the 114 S. aureus isolates tested for ICR by D-test, 29 (25.4%) yielded inducible resistance. Significantly higher (p=0.026) ICR was detected among MRSA (43.5%) than methicillin-susceptible S. aureus (MSSA) (20.9%).Conclusion: MRSA nasal carriage among healthcare workers needs infection control practice in hospitals to prevent transmission of MRSA. The occurrence of ICR in S. aureus is of a great concern, D- test should be carried out routinely in our hospitals to avoid therapeutic failure.Keywords: S. aureus nasal carriage, healthcare workers, community members, inducible clindamycin resistanc

Tear fluid biomarkers in ocular and systemic disease: potential use for predictive, preventive and personalised medicine

In the field of predictive, preventive and personalised medicine, researchers are keen to identify novel and reliable ways to predict and diagnose disease, as well as to monitor patient response to therapeutic agents. In the last decade alone, the sensitivity of profiling technologies has undergone huge improvements in detection sensitivity, thus allowing quantification of minute samples, for example body fluids that were previously difficult to assay. As a consequence, there has been a huge increase in tear fluid investigation, predominantly in the field of ocular surface disease. As tears are a more accessible and less complex body fluid (than serum or plasma) and sampling is much less invasive, research is starting to focus on how disease processes affect the proteomic, lipidomic and metabolomic composition of the tear film. By determining compositional changes to tear profiles, crucial pathways in disease progression may be identified, allowing for more predictive and personalised therapy of the individual. This article will provide an overview of the various putative tear fluid biomarkers that have been identified to date, ranging from ocular surface disease and retinopathies to cancer and multiple sclerosis. Putative tear fluid biomarkers of ocular disorders, as well as the more recent field of systemic disease biomarkers, will be shown

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Measurement of the t(t)over-bar production cross section in the dilepton channel in pp collisions at √s=8 TeV

The top-antitop quark (t (t) over bar) production cross section is measured in proton-proton collisions at root s = 8 TeV with the CMS experiment at the LHC, using a data sample corresponding to an integrated luminosity of 5.3 fb(-1). The measurement is performed by analysing events with a pair of electrons or muons, or one electron and one muon, and at least two jets, one of which is identified as originating from hadronisation of a bottom quark. The measured cross section is 239 +/- 2 (stat.) +/- 11 (syst.) +/- 6 (lum.) pb, for an assumed top-quark mass of 172.5 GeV, in agreement with the prediction of the standard model

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Can Absence of Cardiac Activity on Point-of-Care Echocardiography Predict Death in Out-of-Hospital Cardiac Arrest?

AimThe purpose of this systematic review and meta-analysis was to evaluate the accuracy of the absence of cardiac motion on point-of-care echocardiography (PCE) in predicting termination of resuscitation (TOR), short-term death (STD), and long-term death (LTD), in adult patients with cardiac arrest of all etiologies in out-of-hospital and emergency department setting.MethodsA systematic review and meta-analysis was conducted based on PRISMA guidelines. A literature search in Medline, EMBASE, Cochrane, WHO registry, and ClinicalTrials.gov was performed from inspection to August 2022. Risk of bias was evaluated using QUADAS-2 tool. Meta-analysis was divided into medical cardiac arrest (MCA) and traumatic cardiac arrest (TCA). Sensitivity and specificity were calculated using bivariate random-effects, and heterogeneity was analyzed using I2 statistic.ResultsA total of 27 studies (3657 patients) were included in systematic review. There was a substantial variation in methodologies across the studies, with notable difference in inclusion criteria, PCE timing, and cardiac activity definition. In MCA (15 studies, 2239 patients), the absence of cardiac activity on PCE had a sensitivity of 72% [95% CI 62–80%] and specificity of 80% [95% CI 58–92%] to predict LTD. Although the low numbers of studies in TCA preluded meta-analysis, all patients who lacked cardiac activity on PCE eventually died.ConclusionsThe absence of cardiac motion on PCE for MCA predicts higher likelihood of death but does not have sufficient accuracy to be used as a stand-alone tool to terminate resuscitation. In TCA, the absence of cardiac activity is associated with 100% mortality rate, but low number of patients requires further studies to validate this finding. Future work would benefit from a standardized protocol for PCE timing and agreement on cardiac activity definition