Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Background: The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues. Results: Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development. Conclusion: Expression profiles obtained from public RNA-seq datasets - despite being generated by different laboratories using different methodologies - can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species

Development and validation of HERWIG 7 tunes from CMS underlying-event measurements

This paper presents new sets of parameters (“tunes”) for the underlying-event model of the HERWIG7 event generator. These parameters control the description of multiple-parton interactions (MPI) and colour reconnection in HERWIG7, and are obtained from a fit to minimum-bias data collected by the CMS experiment at s=0.9, 7, and 13Te. The tunes are based on the NNPDF 3.1 next-to-next-to-leading-order parton distribution function (PDF) set for the parton shower, and either a leading-order or next-to-next-to-leading-order PDF set for the simulation of MPI and the beam remnants. Predictions utilizing the tunes are produced for event shape observables in electron-positron collisions, and for minimum-bias, inclusive jet, top quark pair, and Z and W boson events in proton-proton collisions, and are compared with data. Each of the new tunes describes the data at a reasonable level, and the tunes using a leading-order PDF for the simulation of MPI provide the best description of the dat

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

Data availability: Tabulated results are provided in the HEPData record for this analysis71. Release and preservation of data used by the CMS Collaboration as the basis for publications is guided by the CMS policy as stated in CMS data preservation, re-use and open access policy.Code availability: The CMS core software is publically available at https://github.com/cms-sw/cmssw.Copyright . 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+141−104(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.SCOAP3.Change history: 27 February 2023A Correction to this paper has been published: https://doi.org/10.1038/s41567-023-01992-

Search for low-mass dilepton resonances in Higgs boson decays to four-lepton final states in proton–proton collisions at √s=13TeV

Data Availability: This manuscript has no associated data or the data will not be deposited. [Authors’ comment: For CMS Release and preservation of data used by the CMS Collaboration as the basis for publications is guided by the CMS policy as stated in “CMS data preservation, re-use and open access policy” (https://cms-docdb.cern.ch/cgi-bin/PublicDocDB/RetrieveFile?docid=6032&filename=CMSDataPolicyV1.2.pdf&version=2).]Copyright © CERN for the benefit of the CMS collaboration 2022. A search for low-mass dilepton resonances in Higgs boson decays is conducted in the four-lepton final state. The decay is assumed to proceed via a pair of beyond the standard model particles, or one such particle and a Z boson. The search uses proton–proton collision data collected with the CMS detector at the CERN LHC, corresponding to an integrated luminosity of 137fb−1, at a center-of-mass energy s√=13TeV. No significant deviation from the standard model expectation is observed. Upper limits at 95% confidence level are set on model-independent Higgs boson decay branching fractions. Additionally, limits on dark photon and axion-like particle production, based on two specific models, are reported.SCOAP3

Measurement of the mass dependence of the transverse momentum of lepton pairs in Drell–Yan production in proton–proton collisions at √s = 13TeV

Data Availability Statement This manuscript has no associated data or the data will not be deposited. [Authors’ comment: Release and preservation of data used by the CMS Collaboration as the basis for publications is guided by the CMS policy as stated in https://cms-docdb.cern.ch/cgi-bin/PublicDocDB/RetrieveFile?docid=6032 &filename=CMSDataPolicyV1.2.pdf &version=2 CMS data preservation, re-use and open access policy.]A preprint version of the article is available at arXiv:2205.04897v2 [hep-ex], https://arxiv.org/abs/2205.04897v2. Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/SMP-20-003 (CMS Public Pages). Report number: CMS-SMP-20-003, CERN-EP-2022-053.The double differential cross sections of the Drell–Yan lepton pair (ℓ+ℓ- , dielectron or dimuon) production are measured as functions of the invariant mass mℓℓ , transverse momentum pT(ℓℓ) , and φη∗ . The φη∗ observable, derived from angular measurements of the leptons and highly correlated with pT(ℓℓ) , is used to probe the low- pT(ℓℓ) region in a complementary way. Dilepton masses up to 1 TeV are investigated. Additionally, a measurement is performed requiring at least one jet in the final state. To benefit from partial cancellation of the systematic uncertainty, the ratios of the differential cross sections for various mℓℓ ranges to those in the Z mass peak interval are presented. The collected data correspond to an integrated luminosity of 36.3 fb-1 of proton–proton collisions recorded with the CMS detector at the LHC at a centre-of-mass energy of 13 TeV . Measurements are compared with predictions based on perturbative quantum chromodynamics, including soft-gluon resummation.SCOAP3

Search for long-lived particles decaying to leptons with large impact parameter in proton-proton collisions at root s=13 TeV

Copyright © CERN for the benefit of the CMS collaboration 2022. A search for new long-lived particles decaying to leptons using proton–proton collision data produced by the CERN LHC at s√=13TeV is presented. Events are selected with two leptons (an electron and a muon, two electrons, or two muons) that both have transverse impact parameter values between 0.01 and 10cm and are not required to form a common vertex. Data used for the analysis were collected with the CMS detector in 2016, 2017, and 2018, and correspond to an integrated luminosity of 118 (113)fb−1 in the ee channel (eμ and μμ channels). The search is designed to be sensitive to a wide range of models with displaced eμ, ee, and μμ final states. The results constrain several well-motivated models involving new long-lived particles that decay to displaced leptons. For some areas of the available phase space, these are the most stringent constraints to date.SCOAP3

Measurements of pp → ZZ production cross sections and constraints on anomalous triple gauge couplings at √ = 13 TeV

© 2021 The CMS Collaboration. The production of Z boson pairs in proton–proton (pp) collisions, pp → (Z/∗)(Z/∗) → 2ℓ2ℓ′, where ℓ,ℓ′ = e or μ, is studied at a center-of-mass energy of 13 TeV with the CMS detector at the CERN LHC. The data sample corresponds to an integrated luminosity of 137fb−1, collected during 2016–2018. The ZZ production cross section, tot(pp → ZZ) = 17.4 ± 0.3 (stat) ± 0.5 (syst) ± 0.4 (Theo) ± 0.3 (lumi) pb, measured for events with two pairs of opposite-sign, same-flavor leptons produced in the mass region 60 < ℓ+ℓ− < 120 GeV is consistent with standard model predictions. Differential cross sections are also measured and agree with theoretical predictions. The invariant mass distribution of the four-lepton system is used to set limits on anomalous ZZZ and ZZ couplings.SCOAP

Chemico-mineralogical changes of ultramafic topsoil during stockpiling: implications for post-mining restoration

International audienceLateritic topsoils, which are usually removed and stored apart before mining operations take place, play an essential role in the success of post-mining restoration. They contain elements to recover chemical (organic matter, nutrients) and biological (seed and bud banks, microorganisms) fertility of the soil. Conserving topsoil fertility during storage time is essential for a successful use of topsoil during restoration. In this study, different chemico-mineralogical properties of a lateritic topsoil from the Goro nickel mine (New Caledonia) were monitored from its original in situ emplacement on the soil profile, immediately after its stockpiling and after 24 months of storage. Our analyses show that topsoil experienced noticeable changes immediately after storage, mostly produced by mixing of different soil profiles. Cation Exchange Capacities and concentrations of most elements did not vary even after 24 months of storage. However, a slight reduction of Ni, Cr, K, Na and of the C:N ratio, and an increase of Ca have been observed. Stockpiling has not affected negatively the chemical fertility of the topsoil, although biological parameters should be considered to have a complete view of stockpiling sustainability