ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing.

The zinc finger e-box binding homeobox 1 (ZEB1) transcription factor is a master regulator of the epithelial to mesenchymal transition (EMT), and of the reverse mesenchymal to epithelial transition (MET) processes. ZEB1 plays an integral role in mediating cell state transitions during cell lineage specification, wound healing and disease. EMT/MET are characterized by distinct changes in molecular and cellular phenotype that are generally context-independent. Posterior polymorphous corneal dystrophy (PPCD), associated with ZEB1 insufficiency, provides a new biological context in which to understand and evaluate the classic EMT/MET paradigm. PPCD is characterized by a cadherin-switch and transition to an epithelial-like transcriptomic and cellular phenotype, which we study in a cell-based model of PPCD generated using CRISPR-Cas9-mediated ZEB1 knockout in corneal endothelial cells (CEnCs). Transcriptomic and functional studies support the hypothesis that CEnC undergo a MET-like transition in PPCD, termed endothelial to epithelial transition (EnET), and lead to the conclusion that EnET may be considered a corollary to the classic EMT/MET paradigm

Reproducibility of fluorescent expression from engineered biological constructs in E. coli

We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.Peer reviewe

Review of top quark mass measurements in CMS

International audienceThe top quark mass is one of the most intriguing parameters of the standard model (SM). Its value indicates a Yukawa coupling close to unity, and the resulting strong ties to the Higgs physics make the top quark mass a crucial ingredient for understanding essential aspects of the electroweak sector of the SM. While it is such an important parameter of the SM, its measurement and interpretation in terms of the Lagrangian parameter are challenging. The CMS Collaboration has performed multiple measurements of the top quark mass, addressing these challenges from different angles: highly precise `direct' measurements, using the top quark decay products, as well as `indirect' measurements aiming at accurate interpretations in terms of the Lagrangian parameter. Recent mass measurements using Lorentz-boosted top quarks are particularly promising, opening a new avenue of measurements based on top quark decay products contained in a single particle jet, with superior prospects for accurate theoretical interpretations. Moreover, dedicated studies of the dominant uncertainties in the modelling of the signal processes have been performed. This review offers the first comprehensive overview of these measurements performed by the CMS Collaboration using the data collected at centre-of-mass energies of 7, 8, and 13 TeV

Portable acceleration of CMS computing workflows with coprocessors as a service

International audienceComputing demands for large scientific experiments, such as the CMS experiment at the CERN LHC, will increase dramatically in the next decades. To complement the future performance increases of software running on central processing units (CPUs), explorations of coprocessor usage in data processing hold great potential and interest. Coprocessors are a class of computer processors that supplement CPUs, often improving the execution of certain functions due to architectural design choices. We explore the approach of Services for Optimized Network Inference on Coprocessors (SONIC) and study the deployment of this as-a-service approach in large-scale data processing. In the studies, we take a data processing workflow of the CMS experiment and run the main workflow on CPUs, while offloading several machine learning (ML) inference tasks onto either remote or local coprocessors, specifically graphics processing units (GPUs). With experiments performed at Google Cloud, the Purdue Tier-2 computing center, and combinations of the two, we demonstrate the acceleration of these ML algorithms individually on coprocessors and the corresponding throughput improvement for the entire workflow. This approach can be easily generalized to different types of coprocessors and deployed on local CPUs without decreasing the throughput performance. We emphasize that the SONIC approach enables high coprocessor usage and enables the portability to run workflows on different types of coprocessors

Review of top quark mass measurements in CMS

International audienceThe top quark mass is one of the most intriguing parameters of the standard model (SM). Its value indicates a Yukawa coupling close to unity, and the resulting strong ties to the Higgs physics make the top quark mass a crucial ingredient for understanding essential aspects of the electroweak sector of the SM. While it is such an important parameter of the SM, its measurement and interpretation in terms of the Lagrangian parameter are challenging. The CMS Collaboration has performed multiple measurements of the top quark mass, addressing these challenges from different angles: highly precise `direct' measurements, using the top quark decay products, as well as `indirect' measurements aiming at accurate interpretations in terms of the Lagrangian parameter. Recent mass measurements using Lorentz-boosted top quarks are particularly promising, opening a new avenue of measurements based on top quark decay products contained in a single particle jet, with superior prospects for accurate theoretical interpretations. Moreover, dedicated studies of the dominant uncertainties in the modelling of the signal processes have been performed. This review offers the first comprehensive overview of these measurements performed by the CMS Collaboration using the data collected at centre-of-mass energies of 7, 8, and 13 TeV

Search for a resonance decaying to a W boson and a photon in proton-proton collisions at s= \sqrt{s} = 13 TeV using leptonic W boson decays

A search for a new charged particle X with mass between 0.3 and 2.0 TeV decaying to a W boson and a photon is presented, using proton-proton collision data at a center-of-mass energy of 13 TeV, collected by the CMS experiment and corresponding to an integrated luminosity of 138 fb$^{-1}$. Particle X has electric charge $\pm$1 and is assumed to have spin 0. The search is performed using the electron and muon decays of the W boson. No significant excess above the predicted background is observed. The upper limit at 95% confidence level on the product of the production cross section of the X and its branching fraction to a W boson and a photon is found to be 94 (137) fb for a 0.3 TeV resonance and 0.75 (0.81) fb for a 2.0 TeV resonance, for an X width-to-mass ratio of 0.01% (5%). This search presents the most stringent constraints to date on the existence of such resonances across the probed mass range. A statistical combination with an earlier study based on the hadronic decay mode of the W boson is also performed, and the upper limit at 95% confidence level for a 2.0 TeV resonance is reduced to 0.50 (0.63) fb for an X width-to-mass ratio of 0.01% (5%).A search for a new charged particle X with mass between 0.3 and 2.0 TeV decaying to a W boson and a photon is presented, using proton-proton collision data at a center-of-mass energy of 13 TeV, collected by the CMS experiment and corresponding to an integrated luminosity of 138 fb$^{-1}$. Particle X has electric charge $\pm$1 and is assumed to have spin 0. The search is performed using the electron and muon decays of the W boson. No significant excess above the predicted background is observed. The upper limit at 95% confidence level on the product of the production cross section of the X and its branching fraction to a W boson and a photon is found to be 94 (137) fb for a 0.3 TeV resonance and 0.75 (0.81) fb for a 2.0 TeV resonance, for an X width-to-mass ratio of 0.01% (5%). This search presents the most stringent constraints to date on the existence of such resonances across the probed mass range. A statistical combination with an earlier study based on the hadronic decay mode of the W boson is also performed, and the upper limit at 95% confidence level for a 2.0 TeV resonance is reduced to 0.50 (0.63) fb for an X width-to-mass ratio of 0.01% (5%)

Search for CP violation in D0→KS0KS0 \mathrm{D^0}\to\mathrm{K^0_S}\mathrm{K^0_S} decays in proton-proton collisions at s= \sqrt{s} = 13 TeV

A search is reported for charge-parity CP violation in $\mathrm{D^0}\to\mathrm{K^0_S}\mathrm{K^0_S}$ decays, using data collected in proton-proton collisions at $\sqrt{s} =$ 13 TeV recorded by the CMS experiment in 2018. The analysis uses a dedicated data set that corresponds to an integrated luminosity of 41.6 fb$^{-1}$, which consists of about 10 billion events containing a pair of b hadrons, nearly all of which decay to charm hadrons. The flavor of the neutral $\mathrm{D}$ meson is determined by the pion charge in the reconstructed decays $\mathrm{D}^{*+}\to\mathrm{D^0}\pi^{+}$ and $\mathrm{D}^{*-}\to\overline{\mathrm{D}}^{0}\pi^{-}$. The CP asymmetry in $\mathrm{D^0}\to\mathrm{K^0_S}\mathrm{K^0_S}$ is measured to be $A_{CP}(\mathrm{K^0_S}\mathrm{K^0_S}) =$ (6.2 $\pm$ 3.0 $\pm$ 0.2 $\pm$ 0.8)%, where the three uncertainties represent the statistical uncertainty, the systematic uncertainty, and the uncertainty in the measurement of the CP asymmetry in the $\mathrm{D^0}\to\mathrm{K^0_S}\pi^{+}\pi^{-}$ decay. This is the first CP asymmetry measurement by CMS in the charm sector as well as the first to utilize a fully hadronic final state.A search is reported for charge-parity D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$$CP$ violation in D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ decays, using data collected in proton-proton collisions at $\sqrt{s}$ = 13 TeV recorded by the CMS experiment in 2018. The analysis uses a dedicated data set that corresponds to an integrated luminosity of 41.6 fb$^{-1}$, which consists of about 10 billion events containing a pair of ẖadrons, nearly all of which decay to charm hadrons. The flavor of the neutral D meson is determined by the pion charge in the reconstructed decays D$^{*+}$$\to$ D$^0\pi^+$ and D$^{*-}$$\to$ D$^0\pi^-$. The D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$$CP$ asymmetry in D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ is measured to be $A_{CP}$( K$^0_\mathrm{S}$K$^0_\mathrm{S}$) = (6.2 $\pm$ 3.0 $\pm$ 0.2 $\pm$ 0.8)%, where the three uncertainties represent the statistical uncertainty, the systematic uncertainty, and the uncertainty in the measurement of the D$^0$ $\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ $CP$ asymmetry in the D$^0$ $\to$ K$^0_\mathrm{S}\pi^+\pi^-$ decay. This is the first D$^0$ $\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ $CP$ asymmetry measurement by CMS in the charm sector as well as the first to utilize a fully hadronic final state

Elliptic anisotropy measurement of the f0_0(980) hadron in proton-lead collisions and evidence for its quark-antiquark composition

International audienceDespite the f$_0$(980) hadron having been discovered half a century ago, the question about its quark content has not been settled: it might be an ordinary quark-antiquark ($\mathrm{q\bar{q}}$) meson, a tetraquark ($\mathrm{q\bar{q}q\bar{q}}$) exotic state, a kaon-antikaon ($\mathrm{K\bar{K}}$) molecule, or a quark-antiquark-gluon ($\mathrm{q\bar{q}g}$) hybrid. This paper reports strong evidence that the f$_0$(980) state is an ordinary $\mathrm{q\bar{q}}$ meson, inferred from the scaling of elliptic anisotropies ($v_2$) with the number of constituent quarks ($n_\mathrm{q}$), as empirically established using conventional hadrons in relativistic heavy ion collisions. The f$_0$(980) state is reconstructed via its dominant decay channel f$_0$(980) $\to$$\pi^+\pi^-$, in proton-lead collisions recorded by the CMS experiment at the LHC, and its $v_2$ is measured as a function of transverse momentum ($p_\mathrm{T}$). It is found that the $n_q$ = 2 ($\mathrm{q\bar{q}}$ state) hypothesis is favored over $n_q$ = 4 ($\mathrm{q\bar{q}q\bar{q}}$ or $\mathrm{K\bar{K}}$ states) by 7.7, 6.3, or 3.1 standard deviations in the $p_\mathrm{T}$$\lt$ 10, 8, or 6 GeV/$c$ ranges, respectively, and over $n_\mathrm{q}$ = 3 ($\mathrm{q\bar{q}g}$ hybrid state) by 3.5 standard deviations in the $p_\mathrm{T}$$\lt$ 8 GeV/$c$ range. This result represents the first determination of the quark content of the f$_0$(980) state, made possible by using a novel approach, and paves the way for similar studies of other exotic hadron candidates