Recent Advances in Cancer Fusion Transcript Detection

Extensive investigation of gene fusions in cancer has led to the discovery of novel biomarkers and therapeutic targets. To date, most studies have neglected chromosomal rearrangement-independent fusion transcripts and complex fusion structures such as double or triple-hop fusions, and fusion-circRNAs. In this review, we untangle fusion-related terminology and propose a classification system involving both gene and transcript fusions. We highlight the importance of RNA-level fusions and how long-read sequencing approaches can improve detection and characterization. Moreover, we discuss novel bioinformatic tools to identify fusions in long-read sequencing data and strategies to experimentally validate and functionally characterize fusion transcripts

Performance of a Large-Area GEM Detector Prototype for the Upgrade of the CMS Muon Endcap System

Gas Electron Multiplier (GEM) technology is being considered for the forward muon upgrade of the CMS experiment in Phase 2 of the CERN LHC. Its first implementation is planned for the GE1/1 system in the $1.5 < \mid\eta\mid < 2.2$ region of the muon endcap mainly to control muon level-1 trigger rates after the second long LHC shutdown. A GE1/1 triple-GEM detector is read out by 3,072 radial strips with 455 $\mu$rad pitch arranged in eight $\eta$-sectors. We assembled a full-size GE1/1 prototype of 1m length at Florida Tech and tested it in 20-120 GeV hadron beams at Fermilab using Ar/CO$_{2}$ 70:30 and the RD51 scalable readout system. Four small GEM detectors with 2-D readout and an average measured azimuthal resolution of 36 $\mu$rad provided precise reference tracks. Construction of this largest GEM detector built to-date is described. Strip cluster parameters, detection efficiency, and spatial resolution are studied with position and high voltage scans. The plateau detection efficiency is [97.1 $\pm$ 0.2 (stat)]\%. The azimuthal resolution is found to be [123.5 $\pm$ 1.6 (stat)] $\mu$rad when operating in the center of the efficiency plateau and using full pulse height information. The resolution can be slightly improved by $\sim$ 10 $\mu$rad when correcting for the bias due to discrete readout strips. The CMS upgrade design calls for readout electronics with binary hit output. When strip clusters are formed correspondingly without charge-weighting and with fixed hit thresholds, a position resolution of [136.8 $\pm$ 2.5 stat] $\mu$rad is measured, consistent with the expected resolution of strip-pitch/$\sqrt{12}$ = 131.3 $\mu$rad. Other $\eta$-sectors of the detector show similar response and performance.Comment: 8 pages, 32 figures, submitted to Proc. 2014 IEEE Nucl. Sci. Symposium, Seattle, WA, reference adde

Search for MSSM Higgs bosons decaying to μ+μ-in proton-proton collisions at √s=13TeV

A search is performed for neutral non-standard-model Higgs bosons decaying to two muons in the context of the minimal supersymmetric standard model (MSSM). Proton-proton collision data recorded by the CMS experiment at the CERN Large Hadron Collider at a center-of-mass energy of 13TeVwere used, corresponding to an integrated luminosity of 35.9fb-1. The search is sensitive to neutral Higgs bosons produced via the gluon fusion process or in association with a bbquark pair. No significant deviations from the standard model expectation are observed. Upper limits at 95% confidence level are set in the context of the mmod+hand phenomenological MSSM scenarios on the parameter tanβas a function of the mass of the pseudoscalar Aboson, in the range from 130 to 600GeV. The results are also used to set a model-independent limit on the product of the branching fraction for the decay into a muon pair and the cross section for the production of a scalar neutral boson, either via gluon fusion, or in association with bquarks, in the mass range from 130 to 1000GeV

Overview of large area triple-GEM detectors for the CMS forward muon upgrade

In order to cope with the harsh environment expected from the high luminosity LHC, the CMS forward muon system requires an upgrade. The two main challenges expected in this environment are an increase in the trigger rate and increased background radiation leading to a potential degradation of the particle ID performance. Additionally, upgrades to other subdetectors of CMS allow for extended coverage for particle tracking, and adding muon system coverage to this region will further enhance the performance of CMS

Study of the B +→ J / ψ Λ ¯ p decay in proton-proton collisions at √s = 8 TeV

A study of the B +→ J / ψ Λ ¯ p decay using proton-proton collision data collected at s = 8 TeV by the CMS experiment at the LHC, corresponding to an integrated luminosity of 19.6 fb−1, is presented. The ratio of branching fractions B(B+→J/ψΛ¯p)/B(B+→J/ψK∗(892)+) is measured to be (1.054 ± 0.057(stat) ± 0.035(syst) ± 0.011(B))%, where the last uncertainty reflects the uncertainties in the world-average branching fractions of Λ ¯ and K*(892) + decays to reconstructed final states. The invariant mass distributions of the J / ψ Λ ¯ , J/ψp, and Λ ¯ p systems produced in the B +→ J / ψ Λ¯ p decay are investigated and found to be inconsistent with the pure phase space hypothesis. The analysis is extended by using a model-independent angular amplitude analysis, which shows that the observed invariant mass distributions are consistent with the contributions from excited kaons decaying to the Λ ¯ p system. [Figure not available: see fulltext.

A novel application of Fiber Bragg Grating (FBG) sensors in MPGD

We present a novel application of Fiber Bragg Grating (FBG) sensors in the construction and characterisation of Micro Pattern Gaseous Detector (MPGD), with particular attention to the realisation of the largest triple (Gas electron Multiplier) GEM chambers so far operated, the GE1/1 chambers of the CMS experiment at LHC. The GE1/1 CMS project consists of 144 GEM chambers of about 0.5 m2 active area each, employing three GEM foils per chamber, to be installed in the forward region of the CMS endcap during the long shutdown of LHC in 2108-2019. The large active area of each GE1/1 chamber consists of GEM foils that are mechanically stretched in order to secure their flatness and the consequent uniform performance of the GE1/1 chamber across its whole active surface. So far FBGs have been used in high energy physics mainly as high precision positioning and re-positioning sensors and as low cost, easy to mount, low space consuming temperature sensors. FBGs are also commonly used for very precise strain measurements in material studies. In this work we present a novel use of FBGs as flatness and mechanical tensioning sensors applied to the wide GEM foils of the GE1/1 chambers. A network of FBG sensors have been used to determine the optimal mechanical tension applied and to characterise the mechanical tension that should be applied to the foils. We discuss the results of the test done on a full-sized GE1/1 final prototype, the studies done to fully characterise the GEM material, how this information was used to define a standard assembly procedure and possible future developments.Comment: 4 pages, 4 figures, presented by Luigi Benussi at MPGD 2015 (Trieste, Italy). arXiv admin note: text overlap with arXiv:1512.0848

Search for new neutral Higgs bosons through the H → ZA→ ℓ+ℓ−b b ¯ process in pp collisions at √s = 13 TeV

This paper reports on a search for an extension to the scalar sector of the standard model, where a new CP-even (odd) boson decays to a Z boson and a lighter CP-odd (even) boson, and the latter further decays to a b quark pair. The Z boson is reconstructed via its decays to electron or muon pairs. The analysed data were recorded in proton-proton collisions at a center-of-mass energy s = 13 TeV, collected by the CMS experiment at the LHC during 2016, corresponding to an integrated luminosity of 35.9 fb−1. Data and predictions from the standard model are in agreement within the uncertainties. Upper limits at 95% confidence level are set on the production cross section times branching fraction, with masses of the new bosons up to 1000 GeV. The results are interpreted in the context of the two-Higgs-doublet model. [Figure not available: see fulltext.]

Operational experience with the GEM detector assembly lines for the CMS forward muon upgrade

The CMS Collaboration has been developing large-area triple-gas electron multiplier (GEM) detectors to be installed in the muon Endcap regions of the CMS experiment in 2019 to maintain forward muon trigger and tracking performance at the High-Luminosity upgrade of the Large Hadron Collider (LHC); 10 preproduction detectors were built at CERN to commission the first assembly line and the quality controls (QCs). These were installed in the CMS detector in early 2017 and participated in the 2017 LHC run. The collaboration has prepared several additional assembly and QC lines for distributed mass production of 160 GEM detectors at various sites worldwide. In 2017, these additional production sites have optimized construction techniques and QC procedures and validated them against common specifications by constructing additional preproduction detectors. Using the specific experience from one production site as an example, we discuss how the QCs make use of independent hardware and trained personnel to ensure fast and reliable production. Preliminary results on the construction status of CMS GEM detectors are presented with details of the assembly sites involvement

Development and performance of Triple-GEM detectors for the upgrade of the muon system of the CMS experiment

The CMS Collaboration is evaluating GEM detectors for the upgrade of the muon system. This contribution will focus on the R&D performed on chambers design features and will discuss the performance of the upgraded detector