Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

The Pixel Luminosity Telescope: a detector for luminosity measurement at CMS using silicon pixel sensors

The Pixel Luminosity Telescope is a silicon pixel detector dedicated to luminosity measurement at the CMS experiment at the LHC. It is located approximately 1.75 m from the interaction point and arranged into 16 “telescopes”, with eight telescopes installed around the beam pipe at either end of the detector and each telescope composed of three individual silicon sensor planes. The per-bunch instantaneous luminosity is measured by counting events where all three planes in the telescope register a hit, using a special readout at the full LHC bunch-crossing rate of 40 MHz. The full pixel information is read out at a lower rate and can be used to determine calibrations, corrections, and systematic uncertainties for the online and offline measurements. This paper details the commissioning, operational history, and performance of the detector during Run 2 (2015–18) of the LHC, as well as preparations for Run 3, which will begin in 2022

Sandy coastlines under threat of erosion

Sandy beaches occupy more than one-third of the global coastline(1) and have high socioeconomic value related to recreation, tourism and ecosystem services(2). Beaches are the interface between land and ocean, providing coastal protection from marine storms and cyclones(3). However the presence of sandy beaches cannot be taken for granted, as they are under constant change, driven by meteorological(4,5), geological(6) and anthropogenic factors(1,7). A substantial proportion of the world's sandy coastline is already eroding(1,7), a situation that could be exacerbated by climate change(8,9). Here, we show that ambient trends in shoreline dynamics, combined with coastal recession driven by sea level rise, could result in the near extinction of almost half of the world's sandy beaches by the end of the century. Moderate GHG emission mitigation could prevent 40% of shoreline retreat. Projected shoreline dynamics are dominated by sea level rise for the majority of sandy beaches, but in certain regions the erosive trend is counteracted by accretive ambient shoreline changes; for example, in the Amazon, East and Southeast Asia and the north tropical Pacific. A substantial proportion of the threatened sandy shorelines are in densely populated areas, underlining the need for the design and implementation of effective adaptive measures. Erosion is a major problem facing sandy beaches that will probably worsen with climate change and sea-level rise. Half the world's beaches, many of which are in densely populated areas, could disappear by the end of the century under current trends; mitigation could lessen retreat by 40%.info:eu-repo/semantics/publishedVersio

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of MedicinePeer Reviewe

Search for new physics in multijet events with at least one photon and large missing transverse momentum in proton-proton collisions at 13 TeV

A search for new physics in final states consisting of at least one photon, multiple jets, and large missing transverse momentum is presented, using proton-proton collision events at a center-of-mass energy of 13 TeV. The data correspond to an integrated luminosity of 137 fb−1, recorded by the CMS experiment at the CERN LHC from 2016 to 2018. The events are divided into mutually exclusive bins characterized by the missing transverse momentum, the number of jets, the number of b-tagged jets, and jets consistent with the presence of hadronically decaying W, Z, or Higgs bosons. The observed data are found to be consistent with the prediction from standard model processes. The results are interpreted in the context of simplified models of pair production of supersymmetric particles via strong and electroweak interactions. Depending on the details of the signal models, gluinos and squarks of masses up to 2.35 and 1.43 TeV, respectively, and electroweakinos of masses up to 1.23 TeV are excluded at 95% confidence level

First measurement of the top quark pair production cross section in proton-proton collisions at s \sqrt{s} = 13.6 TeV

The first measurement of the top quark pair (tt¯) production cross section in proton-proton collisions at s√ = 13.6 TeV is presented. Data recorded with the CMS detector at the CERN LHC in Summer 2022, corresponding to an integrated luminosity of 1.21 fb−1, are analyzed. Events are selected with one or two charged leptons (electrons or muons) and additional jets. A maximum likelihood fit is performed in event categories defined by the number and flavors of the leptons, the number of jets, and the number of jets identified as originating from b quarks. An inclusive tt¯ production cross section of 881 ± 23 (stat + syst) ± 20 (lumi) pb is measured, in agreement with the standard model prediction of 924+32−40 pb

Measurements of inclusive and differential cross sections for the Higgs boson production and decay to four-leptons in proton-proton collisions at s \sqrt{s} = 13 TeV

Measurements of the inclusive and differential fiducial cross sections for the Higgs boson production in the H → ZZ → 4ℓ (ℓ = e, μ) decay channel are presented. The results are obtained from the analysis of proton-proton collision data recorded by the CMS experiment at the CERN LHC at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 138 fb−1. The measured inclusive fiducial cross section is 2.73 ± 0.26 fb, in agreement with the standard model expectation of 2.86 ± 0.1 fb. Differential cross sections are measured as a function of several kinematic observables sensitive to the Higgs boson production and decay to four leptons. A set of double-differential measurements is also performed, yielding a comprehensive characterization of the four leptons final state. Constraints on the Higgs boson trilinear coupling and on the bottom and charm quark coupling modifiers are derived from its transverse momentum distribution. All results are consistent with theoretical predictions from the standard model