aCGHViewer: A Generic Visualization Tool For aCGH data

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/

aCGHViewer: A Generic Visualization Tool For aCGH data APPLICATION NOTE

Abstract: Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available a

Search for long-lived particles decaying to a pair of muons in proton-proton collisions at s \sqrt{s} = 13 TeV

An inclusive search for long-lived exotic particles decaying to a pair of muons is presented. The search uses data collected by the CMS experiment at the CERN LHC in proton-proton collisions at $\sqrt{s}$ = 13 TeV in 2016 and 2018 and corresponding to an integrated luminosity of 97.6 fb$^{−1}$. The experimental signature is a pair of oppositely charged muons originating from a common secondary vertex spatially separated from the pp interaction point by distances ranging from several hundred μm to several meters. The results are interpreted in the frameworks of the hidden Abelian Higgs model, in which the Higgs boson decays to a pair of long-lived dark photons Z$_{D}$, and of a simplified model, in which long-lived particles are produced in decays of an exotic heavy neutral scalar boson. For the hidden Abelian Higgs model with m(Z$_{D}$) greater than 20 GeV and less than half the mass of the Higgs boson, they provide the best limits to date on the branching fraction of the Higgs boson to dark photons for cτ(Z$_{D}$) (varying with m(Z$_{D}$)) between 0.03 and ≈0.5 mm, and above ≈0.5 m. Our results also yield the best constraints on long-lived particles with masses larger than 10 GeV produced in decays of an exotic scalar boson heavier than the Higgs boson and decaying to a pair of muons.[graphic not available: see fulltext

Measurement of the double-differential inclusive jet cross section in proton-proton collisions at s\sqrt{s} = 5.02 TeV

The inclusive jet cross section is measured as a function of jet transverse momentum $p_\mathrm{T}$ and rapidity $y$. The measurement is performed using proton-proton collision data at $\sqrt{s}$ = 5.02 TeV, recorded by the CMS experiment at the LHC, corresponding to an integrated luminosity of 27.4 pb$^{-1}$. The jets are reconstructed with the anti-$k_\mathrm{T}$ algorithm using a distance parameter of $R$ = 0.4, within the rapidity interval $\lvert y\rvert$$\lt$ 2, and across the kinematic range 0.06 $\lt$$p_\mathrm{T}$$\lt$ 1 TeV. The jet cross section is unfolded from detector to particle level using the determined jet response and resolution. The results are compared to predictions of perturbative quantum chromodynamics, calculated at both next-to-leading order and next-to-next-to-leading order. The predictions are corrected for nonperturbative effects, and presented for a variety of parton distribution functions and choices of the renormalization/factorization scales and the strong coupling $\alpha_\mathrm{S}$

Search for CPCP violation in ttH and tH production in multilepton channels in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceThe charge-parity (CP) structure of the Yukawa interaction between the Higgs (H) boson and the top quark is measured in a data sample enriched in the t$\overline{\textrm{t}}$H and tH associated production, using 138 fb$^{−1}$ of data collected in proton-proton collisions at $\sqrt{s}$ = 13 TeV by the CMS experiment at the CERN LHC. The study targets events where the H boson decays via H → WW or H → ττ and the top quarks decay via t → Wb: the W bosons decay either leptonically or hadronically, and final states characterized by the presence of at least two leptons are studied. Machine learning techniques are applied to these final states to enhance the separation of CP -even from CP -odd scenarios. Two-dimensional confidence regions are set on κ$_{t}$ and $\overset{\sim }{\kappa } _{t}$, which are respectively defined as the CP -even and CP -odd top-Higgs Yukawa coupling modifiers. No significant fractional CP -odd contributions, parameterized by the quantity |${f}_{CP}^{\textrm{Htt}}$| are observed; the parameter is determined to be |${f}_{CP}^{\textrm{Htt}}$| = 0.59 with an interval of (0.24, 0.81) at 68% confidence level. The results are combined with previous results covering the H → ZZ and H → γγ decay modes, yielding two- and one-dimensional confidence regions on κ$_{t}$ and $\overset{\sim }{\kappa } _{t}$, while |${f}_{CP}^{\textrm{Htt}}$| is determined to be |${f}_{CP}^{\textrm{Htt}}$| = 0.28 with an interval of |${f}_{CP}^{\textrm{Htt}}$| < 0.55 at 68% confidence level, in agreement with the standard model CP -even prediction of |${f}_{CP}^{\textrm{Htt}}$| = 0.[graphic not available: see fulltext

Search for a charged Higgs boson decaying into a heavy neutral Higgs boson and a W boson in proton-proton collisions at s=\sqrt{s} = 13 TeV

A search for a charged Higgs boson ${\mathrm{\tilde{H}^{\pm}}}$ decaying into a heavy neutral Higgs boson H and a W boson is presented. The analysis targets the H decay into a pair of tau leptons with at least one of them decaying hadronically and with an additional electron or muon present in the event. The search is based on proton-proton collision data recorded by the CMS experiment during 2016-2018 at $\sqrt{s} =$ 13 TeV, corresponding to an integrated luminosity of 138 fb$^{-1}$. The data are consistent with standard model background expectations. Upper limits at 95% confidence level are set on the product of the cross section and branching fraction for an ${\mathrm{\tilde{H}^{\pm}}}$ in the mass range of 300-700 GeV, assuming an H with a mass of 200 GeV. The observed limits range from 0.085 pb for an ${\mathrm{\tilde{H}^{\pm}}}$ mass of 300 GeV to 0.019 pb for a mass of 700 GeV. These are the first limits on ${\mathrm{\tilde{H}^{\pm}}}$ production in the ${\mathrm{\tilde{H}^{\pm}}} \to \mathrm{H} \mathrm{W^{\pm}}$ decay channel at the LHC.A search for a charged Higgs boson H$^{±}$ decaying into a heavy neutral Higgs boson H and a W boson is presented. The analysis targets the H decay into a pair of tau leptons with at least one of them decaying hadronically and with an additional electron or muon present in the event. The search is based on proton-proton collision data recorded by the CMS experiment during 2016–2018 at $\sqrt{s}$ = 13 TeV, corresponding to an integrated luminosity of 138 fb$^{−1}$. The data are consistent with standard model background expectations. Upper limits at 95% confidence level are set on the product of the cross section and branching fraction for an H$^{±}$ in the mass range of 300–700 GeV, assuming an H with a mass of 200 GeV. The observed limits range from 0.085 pb for an H$^{±}$ mass of 300 Ge V to 0.019 pb for a mass of 700 GeV. These are the first limits on H$^{±}$ production in the H$^{±}$→ HW$^{±}$ decay channel at the LHC.[graphic not available: see fulltext]A search for a charged Higgs boson H$^\pm$ decaying into a heavy neutral Higgs boson H and a W boson is presented. The analysis targets the H decay into a pair of tau leptons with at least one of them decaying hadronically and with an additional electron or muon present in the event. The search is based on proton-proton collision data recorded by the CMS experiment during 2016-2018 at $\sqrt{s}$ = 13 TeV, corresponding to an integrated luminosity of 138 fb$^{-1}$. The data are consistent with standard model background expectations. Upper limits at 95% confidence level are set on the product of the cross section and branching fraction for an H$^\pm$ in the mass range of 300-700 GeV, assuming an H with a mass of 200 GeV. The observed limits range from 0.085 pb for an H$^\pm$ mass of 300 GeV to 0.019 pb for a mass of 700 GeV. These are the first limits on H$^\pm$ production in the H$^\pm$ $\to$ HW$^\pm$ decay channel at the LHC

Search for central exclusive production of top quark pairs in proton-proton collisions at s\sqrt{s} = 13 TeV with tagged protons

International audienceA search for the central exclusive production of top quark-antiquark pairs ($\mathrm{t\bar{t}}$) is performed for the first time using proton-tagged events in proton-proton collisions at the LHC at a centre-of-mass energy of 13 TeV. The data correspond to an integrated luminosity of 29.4 fb$^{-1}$. The $\mathrm{t\bar{t}}$ decay products are reconstructed using the central CMS detector, while forward protons are measured in the CMS-TOTEM precision proton spectrometer. An observed (expected) upper bound on the production cross section of 0.59 (1.14) pb is set at 95% confidence level, for collisions of protons with fractional momentum losses between 2 and 20%