Analysis of the dynamic co-expression network of heart regeneration in the zebrafish.

The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration

Beam Test Performance Studies of CMS Phase-2 Outer Tracker Module Prototypes

International audienceA new tracking detector will be installed as part of the Phase-2 upgrade of the CMS detector for the high-luminosity LHC era. This tracking detector includes the Inner Tracker, equipped with silicon pixel sensor modules, and the Outer Tracker, consisting of modules with two parallel stacked silicon sensors. The Outer Tracker front-end ASICs will be able to correlate hits from charged particles in these two sensors to perform on-module discrimination of transverse momenta $p_\mathrm{T}$. The $p_\mathrm{T}$ information is generated at a frequency of 40 MHz and will be used in the Level-1 trigger decision of CMS. Prototypes of the so-called 2S modules were tested at the Test Beam Facility at DESY Hamburg between 2019 and 2020. These modules use the final front-end ASIC, the CMS Binary Chip (CBC), and for the first time the Concentrator Integrated Circuit (CIC), optical readout and on-module power conversion. In total, seven modules were tested, one of which was assembled with sensors irradiated with protons. An important aspect was to show that it is possible to read out modules synchronously. A cluster hit efficiency of about 99.75% was achieved for all modules. The CBC $p_\mathrm{T}$ discrimination mechanism has been verified to work together with the CIC and optical readout. The measured module performance meets the requirements for operation in the upgraded CMS tracking detector

Evaluation of planar silicon pixel sensors with the RD53A readout chip for the Phase-2 Upgrade of the CMS Inner Tracker

The Large Hadron Collider (LHC) at CERN will undergo an upgrade in order to increase its luminosity to $7.5 \times 10^{34}$ cm$^{-2}$s$^{-1}$. The increased luminosity during this High-Luminosity running phase\\ (HL-LHC), starting around 2029, means a higher rate of proton-proton interactions, hence a larger ionizing dose and particle fluence for the detectors. The current tracking system of the CMS experiment will be fully replaced in order to cope with the new operating conditions. Prototype planar pixel sensors for the CMS Inner Tracker with square $50 \mu$m $\times \; 50 \mu$m and rectangular $100 \mu$m $\times \; 25 \mu$m pixels read out by the RD53A chip were characterized in the lab and at the DESY-II testbeam facility in order to identify designs that meet the requirements of CMS at the HL-LHC. A spatial resolution of approximately 3.4$\mu$m (2$\mu$m) is obtained using the modules with $50 \mu$m $\times \; 50 \mu$m ($100 \mu$m $\times \; 25 \mu$m) pixels at the optimal angle of incidence before irradiation. After irradiation to a 1 MeV neutron equivalent fluence of $\Phi_{\rm eq} = 5.3 \times 10^{15}$ cm$^{-2}$, a resolution of 9.4$\mu$m is achieved at a bias voltage of 800 V using a module with $50 \mu$m $\times \; 50 \mu$m pixel size. All modules retain a hit efficiency in excess of 99\% after irradiation to fluences up to $2.1 \times 10^{16}$ cm$^{-2}$. Further studies of the electrical properties of the modules, especially crosstalk, are also presented in this paper.The Large Hadron Collider at CERN will undergo an upgrade inorder to increase its luminosity to7.5 × 10$^{34}$ cm$^{-2}$s$^{-1}$. The increased luminosityduring this High-Luminosity running phase, starting around 2029,means a higher rate of proton-proton interactions, hence a largerionizing dose and particle fluence for the detectors. The currenttracking system of the CMS experiment will be fully replaced inorder to cope with the new operating conditions. Prototype planarpixel sensors for the CMS Inner Tracker with square50 μm × 50 μm and rectangular100 μm × 25 μm pixels read out by theRD53A chip were characterized in the lab and at the DESY-II testbeamfacility in order to identify designs that meet the requirements ofCMS during the High-Luminosity running phase. A spatial resolutionof approximately 3.4 μm (2 μm) is obtained using themodules with 50 μm × 50 μm(100 μm × 25 μm) pixels at the optimalangle of incidence before irradiation. After irradiation to a 1 MeVneutron equivalent fluence ofΦ$_{eq}$ = 5.3 × 10$^{15}$ cm$^{-2}$, a resolution of9.4 μm is achieved at a bias voltage of 800 V using a modulewith 50 μm × 50 μm pixel size. All modulesretain a hit efficiency in excess of 99% after irradiation tofluences up to 2.1 × 10$^{16}$ cm$^{-2}$. Further studies ofthe electrical properties of the modules, especially crosstalk, arealso presented in this paper.The Large Hadron Collider (LHC) at CERN will undergo an upgrade in order to increase its luminosity to $7.5 \times 10^{34}$ cm$^{-2}$s$^{-1}$. The increased luminosity during this High-Luminosity running phase (HL-LHC), starting around 2029, means a higher rate of proton-proton interactions, hence a larger ionizing dose and particle fluence for the detectors. The current tracking system of the CMS experiment will be fully replaced in order to cope with the new operating conditions. Prototype planar pixel sensors for the CMS Inner Tracker with square $50 \mu$m $\times \; 50 \mu$m and rectangular $100 \mu$m $\times \; 25 \mu$m pixels read out by the RD53A chip were characterized in the lab and at the DESY-II testbeam facility in order to identify designs that meet the requirements of CMS at the HL-LHC. A spatial resolution of approximately 3.4$\mu$m (2$\mu$m) is obtained using the modules with $50 \mu$m $\times \; 50 \mu$m ($100 \mu$m $\times \; 25 \mu$m) pixels at the optimal angle of incidence before irradiation. After irradiation to a 1 MeV neutron equivalent fluence of $\Phi_{\rm eq} = 5.3 \times 10^{15}$ cm$^{-2}$, a resolution of 9.4$\mu$m is achieved at a bias voltage of 800 V using a module with $50 \mu$m $\times \; 50 \mu$m pixel size. All modules retain a hit efficiency in excess of 99% after irradiation to fluences up to $2.1 \times 10^{16}$ cm$^{-2}$. Further studies of the electrical properties of the modules, especially crosstalk, are also presented in this paper

Beam test performance of a prototype module with Short Strip ASICs for the CMS HL-LHC tracker upgrade

International audienceThe Short Strip ASIC (SSA) is one of the four front-endchips designed for the upgrade of the CMS Outer Tracker for the HighLuminosity LHC. Together with the Macro-Pixel ASIC (MPA) it willinstrument modules containing a strip and a macro-pixel sensorstacked on top of each other. The SSA provides both full readout ofthe strip hit information when triggered, and, together with theMPA, correlated clusters called stubs from the two sensors for useby the CMS Level-1 (L1) trigger system. Results from the firstprototype module consisting of a sensor and two SSA chips arepresented. The prototype module has been characterized at theFermilab Test Beam Facility using a 120 GeV proton beam

Evaluation of HPK n+n^+-pp planar pixel sensors for the CMS Phase-2 upgrade

International audienceTo cope with the challenging environment of the planned high luminosity upgrade of the Large Hadron Collider (HL-LHC), sched-uled to start operation in 2029, CMS will replace its entire tracking system. The requirements for the tracker are largely determinedby the long operation time of 10 years with an instantaneous peak luminosity of up to 7.5 × 1034 cm−2 s−1 in the ultimate perfor-mance scenario. Depending on the radial distance from the interaction point, the silicon sensors will receive a particle fluencecorresponding to a non-ionizing energy loss of up to Φeq = 3.5 × 1016 cm−2. This paper focuses on planar pixel sensor design andqualification up to a fluence of Φeq = 1.4 × 1016 cm−2.For the development of appropriate planar pixel sensors an R&D program was initiated, which includes n+-p sensors on 150 mm(6”) wafers with an active thickness of 150 μm with pixel sizes of 100 × 25 μm2 and 50 × 50 μm2 manufactured by Hamamatsu.Single chip modules with ROC4Sens and RD53A readout chips were made. Irradiation with protons and neutrons, as well was anextensive test beam campaign at DESY were carried out. This paper presents the investigation of various assemblies mainly withROC4Sens readout chips. It demonstrates that multiple designs fulfill the requirements in terms of breakdown voltage, leakagecurrent and efficiency. The single point resolution for 50 × 50 μm2 pixels is measured as 4.0 μm for non-irradiated samples, and6.3 μm after irradiation to Φeq = 7.2 × 1015 cm−2

Evaluation of HPK n+n^+-pp planar pixel sensors for the CMS Phase-2 upgrade

To cope with the challenging environment of the planned high luminosity upgrade of the Large Hadron Collider (HL-LHC), scheduled to start operation in 2029, CMS will replace its entire tracking system. The requirements for the tracker are largely determined by the long operation time of 10~years with an instantaneous peak luminosity of up to $7.5\times 10^{34}$~cm$^{-2}$s$^{-1}$ in the ultimate performance scenario. Depending on the radial distance from the interaction point, the silicon sensors will receive a particle fluence corresponding to a non-ionizing energy loss of up to $\Phi_{\text{eq}} = 3.5\times 10^{16}$~cm$^{-2}$. This paper focuses on planar pixel sensor design and qualification up to a fluence of $\Phi_{\text{eq}} = 1.4\times 10^{16}$~cm$^{-2}$. For the development of appropriate planar pixel sensors an R\&D program was initiated, which includes $n^+$-$p$ sensors on 150 mm (6'') wafers with an active thickness of 150~$\mu$m with pixel sizes of $100\times 25$~$\mu$m$^2$ and $50\times 50$~$\mu$m$^2$ manufactured by Hamamatsu Photonics K.K.\ (HPK). Single chip modules with ROC4Sens and RD53A readout chips were made. Irradiation with protons and neutrons, as well was an extensive test beam campaign at DESY were carried out. This paper presents the investigation of various assemblies mainly with ROC4Sens readout chips. It demonstrates that multiple designs fulfill the requirements in terms of breakdown voltage, leakage current and efficiency. The single point resolution for $50\times 50$~$\mu$m$^2$ pixels is measured as 4.0~$\mu$m for non-irradiated samples, and 6.3~$\mu$m after irradiation to $\Phi_{\text{eq}} = 7.2\times 10^{15}$~cm$^{-2}$.To cope with the challenging environment of the planned high luminosity upgrade of the Large Hadron Collider (HL-LHC), sched- uled to start operation in 2029, CMS will replace its entire tracking system. The requirements for the tracker are largely determined by the long operation time of 10 years with an instantaneous peak luminosity of up to 7.5 × 1034 cm−2 s−1 in the ultimate perfor- mance scenario. Depending on the radial distance from the interaction point, the silicon sensors will receive a particle fluence corresponding to a non-ionizing energy loss of up to Φeq = 3.5 × 1016 cm−2. This paper focuses on planar pixel sensor design and qualification up to a fluence of Φeq = 1.4 × 1016 cm−2. For the development of appropriate planar pixel sensors an R&D program was initiated, which includes n+-p sensors on 150 mm (6”) wafers with an active thickness of 150 μm with pixel sizes of 100 × 25 μm2 and 50 × 50 μm2 manufactured by Hamamatsu. Single chip modules with ROC4Sens and RD53A readout chips were made. Irradiation with protons and neutrons, as well was an extensive test beam campaign at DESY were carried out. This paper presents the investigation of various assemblies mainly with ROC4Sens readout chips. It demonstrates that multiple designs fulfill the requirements in terms of breakdown voltage, leakage current and efficiency. The single point resolution for 50 × 50 μm2 pixels is measured as 4.0 μm for non-irradiated samples, and 6.3 μm after irradiation to Φeq = 7.2 × 1015 cm−2.To cope with the challenging environment of the planned high luminosity upgrade of the Large Hadron Collider (HL-LHC), scheduled to start operation in 2029, CMS will replace its entire tracking system. The requirements for the tracker are largely determined by the long operation time of 10 years with an instantaneous peak luminosity of up to 7.5 × 1034cm−2s−1 in the ultimate performance scenario. Depending on the radial distance from the interaction point, the silicon sensors will receive a particle fluence corresponding to a non-ionising energy loss of up to Φeq= 3.5 × 1016cm−2. This paper focuses on planar pixel sensor design and qualification up to a fluence of Φeq = 1.4 × 1016cm−2. For the development of appropriate planar pixel sensors an R&D program was initiated, which includes n+-p sensors on 150mm (6”) wafers with an active thickness of 150µm with pixel sizes of 100×25 µm2 and 50×50 µm2 manufactured by Hamamatsu Photonics K.K. (HPK). Single chip modules with ROC4Sens and RD53A readout chips were made. Irradiation with protons and neutrons, as well was an extensive test beam campaign at DESY were carried out. This paper presents the investigation of various assemblies mainly with ROC4Sens readout chips. It demonstrates that multiple designs fulfil the requirements in terms of breakdown voltage, leakage current and efficiency. The single point resolution for 50×50 µm2 pixels is measured as 4.0µm for non-irradiated samples, and 6.3µm after irradiation to Φeq = 7.2 × 1015cm−2

Observation of triple J/ψ meson production in proton-proton collisions

Protons consist of three valence quarks, two up-quarks and one down-quark, held together by gluons and a sea of quark-antiquark pairs. Collectively, quarks and gluons are referred to as partons. In a proton-proton collision, typically only one parton of each proton undergoes a hard scattering – referred to as single-parton scattering – leaving the remainder of each proton only slightly disturbed. Here, we report the study of double- and triple-parton scatterings through the simultaneous production of three J/ψ mesons, which consist of a charm quark-antiquark pair, in proton-proton collisions recorded with the CMS experiment at the Large Hadron Collider. We observed this process – reconstructed through the decays of J/ψ mesons into pairs of oppositely charged muons – with a statistical significance above five standard deviations. We measured the inclusive fiducial cross-section to be 272−104+141(stat)±17(syst)fb, and compared it to theoretical expectations for triple-J/ψ meson production in single-, double- and triple-parton scattering scenarios. Assuming factorization of multiple hard-scattering probabilities in terms of single-parton scattering cross-sections, double- and triple-parton scattering are the dominant contributions for the measured process

Strategies and performance of the CMS silicon tracker alignment during LHC Run 2

The strategies for and the performance of the CMS silicon tracking system alignment during the 2015–2018 data-taking period of the LHC are described. The alignment procedures during and after data taking are explained. Alignment scenarios are also derived for use in the simulation of the detector response. Systematic effects, related to intrinsic symmetries of the alignment task or to external constraints, are discussed and illustrated for different scenarios