A scalable monitoring for the CMS Filter Farm based on elasticsearch

A flexible monitoring system has been designed for the CMS File-based Filter Farm making use of modern data mining and analytics components. All the metadata and monitoring information concerning data flow and execution of the HLT are generated locally in the form of small documents using the JSON encoding. These documents are indexed into a hierarchy of elasticsearch (es) clusters along with process and system log information. Elasticsearch is a search server based on Apache Lucene. It provides a distributed, multitenant-capable search and aggregation engine. Since es is schema-free, any new information can be added seamlessly and the unstructured information can be queried in non-predetermined ways. The leaf es clusters consist of the very same nodes that form the Filter Farm thus providing natural horizontal scaling. A separate central" es cluster is used to collect and index aggregated information. The fine-grained information, all the way to individual processes, remains available in the leaf clusters. The central es cluster provides quasi-real-time high-level monitoring information to any kind of client. Historical data can be retrieved to analyse past problems or correlate them with external information. We discuss the design and performance of this system in the context of the CMS DAQ commissioning for LHC Run 2

Search for new resonances decaying via WZ to leptons in proton–proton collisions at √s = 8 TeV

A search is performed in proton–proton collisions at √s = 8 TeV for exotic particles decaying via WZ to fully leptonic final states with electrons, muons, and neutrinos. The data set corresponds to an integrated luminosity of 19.5 fb[superscript −1]. No significant excess is observed above the expected standard model background. Upper bounds at 95% confidence level are set on the production cross section of a W′ boson as predicted by an extended gauge model, and on the W′WZ coupling. The expected and observed mass limits for a W′ boson, as predicted by this model, are 1.55 and 1.47 TeV, respectively. Stringent limits are also set in the context of low-scale technicolor models under a range of assumptions for the model parameters.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Search for heavy neutrinos and W bosons with right-handed couplings in proton–proton collisions at √s = 8 TeV

A search for heavy, right-handed neutrinos, Nℓ ( ℓ=e,μ ), and right-handed W[subscript R] bosons, which arise in the left-right symmetric extensions of the standard model, has been performed by the CMS experiment. The search was based on a sample of two lepton plus two jet events collected in proton–proton collisions at a center-of-mass energy of 8 TeV corresponding to an integrated luminosity of 19.7 fb[superscript −1]. For models with strict left-right symmetry, and assuming only one N[subscript ℓ] flavor contributes significantly to the W[subscript R] decay width, the region in the two-dimensional (M[subscript WR],M[subscript Nℓ]) mass plane excluded at a 95 % confidence level extends to approximately M[subscript WR]=3.0TeV and covers a large range of neutrino masses below the W[subscript R] boson mass, depending on the value of M[subscript WR]. This search significantly extends the (M[subscript WR],M[subscript Nℓ]) exclusion region beyond previous results.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Search for the standard model Higgs boson decaying to bottom quarks in pp collisions at √s = 7 TeV

A search for the standard model Higgs boson (H) decaying to b[bar over b] when produced in association with weak vector bosons (V) is reported for the following modes: W(μν)H, W(eν)H, Z(μμ)H, Z(ee)H and Z(νν)H. The search is performed in a data sample corresponding to an integrated luminosity of 4.7 fb[superscript −1], recorded by the CMS detector in proton–proton collisions at the LHC with a center-of-mass energy of 7 TeV. No significant excess of events above the expectation from background is observed. Upper limits on the VH production cross section times the H→b[bar over b] branching ratio, with respect to the expectations for a standard model Higgs boson, are derived for a Higgs boson in the mass range 110–135 GeV. In this range, the observed 95% confidence level upper limits vary from 3.4 to 7.5 times the standard model prediction; the corresponding expected limits vary from 2.7 to 6.7 times the standard model prediction.European Organization for Nuclear ResearchUnited States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation.

OBJECTIVES: The interaction between the immune system and tumor cells is an important feature for the prognosis and treatment of cancer. Multiplex immunohistochemistry (mIHC) and multiplex immunofluorescence (mIF) analyses are emerging technologies that can be used to help quantify immune cell subsets, their functional state, and their spatial arrangement within the tumor microenvironment. METHODS: The Society for Immunotherapy of Cancer (SITC) convened a task force of pathologists and laboratory leaders from academic centers as well as experts from pharmaceutical and diagnostic companies to develop best practice guidelines for the optimization and validation of mIHC/mIF assays across platforms. RESULTS: Representative outputs and the advantages and disadvantages of mIHC/mIF approaches, such as multiplexed chromogenic IHC, multiplexed immunohistochemical consecutive staining on single slide, mIF (including multispectral approaches), tissue-based mass spectrometry, and digital spatial profiling are discussed. CONCLUSIONS: mIHC/mIF technologies are becoming standard tools for biomarker studies and are likely to enter routine clinical practice in the near future. Careful assay optimization and validation will help ensure outputs are robust and comparable across laboratories as well as potentially across mIHC/mIF platforms. Quantitative image analysis of mIHC/mIF output and data management considerations will be addressed in a complementary manuscript from this task force

The molecular basis of breast cancer pathological phenotypes

The histopathological evaluation of morphological features in breast tumours provides prognostic information to guide therapy. Adjunct molecular analyses provide further diagnostic, prognostic and predictive information. However, there is limited knowledge of the molecular basis of morphological phenotypes in invasive breast cancer. This study integrated genomic, transcriptomic and protein data to provide a comprehensive molecular profiling of morphological features in breast cancer. Fifteen pathologists assessed 850 invasive breast cancer cases from The Cancer Genome Atlas (TCGA). Morphological features were significantly associated with genomic alteration, DNA methylation subtype, PAM50 and microRNA subtypes, proliferation scores, gene expression and/or RPPA subtype. Marked nuclear pleomorphism, necrosis, inflammation and high mitotic count were associated with Basal-like subtype and have similar molecular basis. Omics-based signatures were constructed to predict morphological features. The association of morphology transcriptome signatures with overall survival in oestrogen receptor (ER)-positive and ER-negative breast cancer was first assessed using the METABRIC dataset; signatures that remained prognostic in the METABRIC multivariate analysis were further evaluated in five additional datasets. The transcriptomic signature of epithelial tubule formation was prognostic in ER-positive breast cancer. No signature was prognostic in ER-negative. This study provided new insights into the molecular basis of breast cancer morphological phenotypes. The integration of morphological with molecular data has potential to refine breast cancer classification, predict response to therapy, enhance our understanding of breast cancer biology and improve clinical management. This work is publicly accessible at www.dx.ai/tcga_breast

Measurement of the production cross section for pairs of isolated photons in pp collisions at √s = 7 TeV

The integrated and differential cross sections for the production of pairs of isolated photons is measured in proton-proton collisions at a centre-of-mass energy of 7 TeV with the CMS detector at the LHC. A data sample corresponding to an integrated luminosity of 36 pb[superscript −1] is analysed. A next-to-leading-order perturbative QCD calculation is compared to the measurements. A discrepancy is observed for regions of the phase space where the two photons have an azimuthal angle difference Δφ ≲ 2.8 rad.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Search for the standard model Higgs boson decaying into two photons in pp collisions at √s = 7 TeV

A search for a Higgs boson decaying into two photons is described. The analysis is performed using a dataset recorded by the CMS experiment at the LHC from pp collisions at a center-of-mass energy of 7 TeV, which corresponds to an integrated luminosity of 4.8 fb[superscript −1]. Limits are set on the cross section of the standard model Higgs boson decaying to two photons. The expected exclusion limit at 95% confidence level is between 1.4 and 2.4 times the standard model cross section in the mass range between 110 and 150 GeV. The analysis of the data excludes, at 95% confidence level, the standard model Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The largest excess of events above the expected standard model background is observed for a Higgs boson mass hypothesis of 124 GeV with a local significance of 3.1σ . The global significance of observing an excess with a local significance ⩾3.1σ anywhere in the search range 110–150 GeV is estimated to be 1.8σ. More data are required to ascertain the origin of this excess.United States. Dept. of EnergyNational Science Foundation (U.S.