Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Nuclear modification of Y states in pPb collisions at √sNN = 5.02 TeV

Production cross sections of Υ(1S), Υ(2S), and Υ(3S) states decaying into μ+μ− in proton-lead (pPb) collisions are reported using data collected by the CMS experiment at √sNN = 5.02 TeV. A comparison is made with corresponding cross sections obtained with pp data measured at the same collision energy and scaled by the Pb nucleus mass number. The nuclear modification factor for Υ(1S) is found to be RpPb(Υ(1S)) = 0.806±0.024 (stat)±0.059 (syst). Similar results for the excited states indicate a sequential suppression pattern, such that RpPb(Υ(1S)) > RpPb(Υ(2S)) > RpPb(Υ(3S)). The suppression of all states is much less pronounced in pPb than in PbPb collisions, and independent of transverse momentum p Υ T and center-of-mass rapidity y Υ CM of the individual Υ state in the studied range p Υ T < 30 GeV/c and |y Υ CM| < 1.93. Models that incorporate final-state effects of bottomonia in pPb collisions are in better agreement with the data than those which only assume initial-state modifications

Effects of warming on the structure of aquatic communities in tropical bromeliad microecosystems

Abstract Freshwaters are among the most vulnerable ecosystems to climate warming, with projected temperature increases over the coming decades leading to significant losses of aquatic biodiversity. Experimental studies that directly warm entire natural ecosystems in the tropics are needed, for understanding the disturbances on aquatic communities. Therefore, we conducted an experiment to test the impacts of predicted future warming on density, alpha diversity, and beta diversity of freshwater aquatic communities, inhabiting natural microecosystems—Neotropical tank bromeliads. Aquatic communities within the tanks bromeliads were experimentally exposed to warming, with temperatures ranging from 23.58 to 31.72°C. Linear regression analysis was used to test the impacts of warming. Next, distance‐based redundancy analysis was performed to assess how warming might alter total beta diversity and its components. This experiment was conducted across a gradient of habitat size (bromeliad water volume) and availability of detrital basal resources. A combination of the highest detritus biomass and higher experimental temperatures resulted in the greatest density of flagellates. However, the density of flagellates declined in bromeliads with higher water volume and lower detritus biomass. Moreover, the combination of the highest water volume and high temperature reduced density of copepods. Finally, warming changed microfauna species composition, mostly through species substitution (βrepl component of total beta‐diversity). These findings indicate that warming strongly structures freshwater communities by reducing or increasing densities of different aquatic communities groups. It also enhances beta‐diversity, and many of these effects are modulated by habitat size or detrital resources

The ecological role of permanent ponds in Europe ::a review of dietary linkages to terrestrial ecosystems via emerging insects

Permanent ponds are valuable freshwater systems and biodiversity hotspots. They provide diverse ecosystem services (ES), including water quality improvement and supply, food provisioning and biodiversity support. This is despite being under significant pressure from multiple anthropogenic stressors and the impacts of ongoing global change. However, ponds are largely overlooked in management plans and legislation, and ecological research has focused on large freshwater ecosystems, such as rivers or lakes. Protection of ponds is often insufficient or indirectly provided via associated habitats such as wetlands. This phenomenon is likely exacerbated due to lacking a full-scale understanding of the importance of ponds. In this review, we provided a detailed overview of permanent ponds across Europe, including their usages and the biodiversity they support. By discussing the concepts of pondscape and metacommunity theory, we highlighted the importance of connectivity among and between ponds and identified fluxes of emerging insects as another ES of ponds. Those insects are rich in essential nutrients such as polyunsaturated fatty acids (PUFA), which are delivered through them to the terrestrial environment, however the extent and impact of this ES remains largely unexplored. Several potential stressors, especially related to ongoing global change, which influence pond diversity and integrity were discussed. To conclude this review, we provided our insights on future pond management. Adaptive measures, taking into account the pond system per se within the pondscape, were found to be the most promising to mitigate the loss of natural ponds and restore and conserve natural small water bodies as refuges and diversity hotspots in increasingly urbanized landscapes

The ecological role of permanent ponds in Europe: a review of dietary linkages to terrestrial ecosystems via emerging insects

Permanent ponds are valuable freshwater systems and biodiversity hotspots. They provide diverse ecosystem services (ES), including water quality improvement and supply, food provisioning and biodiversity support. This is despite being under significant pressure from multiple anthropogenic stressors and the impacts of ongoing global change. However, ponds are largely overlooked in management plans and legislation, and ecological research has focused on large freshwater ecosystems, such as rivers or lakes. Protection of ponds is often insufficient or indirectly provided via associated habitats such as wetlands. This phenomenon is likely exacerbated due to lacking a full-scale understanding of the importance of ponds. In this review, we provided a detailed overview of permanent ponds across Europe, including their usages and the biodiversity they support. By discussing the concepts of pondscape and metacommunity theory, we highlighted the importance of connectivity among and between ponds and identified fluxes of emerging insects as another ES of ponds. Those insects are rich in essential nutrients such as polyunsaturated fatty acids (PUFA), which are delivered through them to the terrestrial environment, however the extent and impact of this ES remains largely unexplored. Several potential stressors, especially related to ongoing global change, which influence pond diversity and integrity were discussed. To conclude this review, we provided our insights on future pond management. Adaptive measures, taking into account the pond system per se within the pondscape, were found to be the most promising to mitigate the loss of natural ponds and restore and conserve natural small water bodies as refuges and diversity hotspots in increasingly urbanized landscapes

Genomic reconstruction of the SARS-CoV-2 epidemic in England

AbstractThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.</jats:p

Electron and photon reconstruction and identification with the CMS experiment at the CERN LHC

CERN for the benefit of the CMS collaboration: et al. The performance is presented of the reconstruction and identification algorithms for electrons and photons with the CMS experiment at the LHC. The reported results are based on proton-proton collision data collected at a center-of-mass energy of 13 TeV and recorded in 2016–2018, corresponding to an integrated luminosity of 136 fb^-1. Results obtained from lead-lead collision data collected at √(sNN)=5.02 TeV are also presented. Innovative techniques are used to reconstruct the electron and photon signals in the detector and to optimize the energy resolution. Events with electrons and photons in the final state are used to measure the energy resolution and energy scale uncertainty in the recorded events. The measured energy resolution for electrons produced in Z boson decays in proton-proton collision data ranges from 2 to 5%, depending on electron pseudorapidity and energy loss through bremsstrahlung in the detector material. The energy scale in the same range of energies is measured with an uncertainty smaller than 0.1 (0.3)% in the barrel (endcap) region in proton-proton collisions and better than 1 (3)% in the barrel (endcap) region in heavy ion collisions. The timing resolution for electrons from Z boson decays with the full 2016–2018 proton-proton collision data set is measured to be 200 ps. Individuals have received support from the Marie-Curie program and the European Research Council and Horizon 2020 Grant, contract Nos. 675440, 724704, 752730, and 765710 (European Union); the Programa de Excelencia María de Maeztu, and the Programa Severo Ochoa del Principado de Asturias Peer reviewe

Muon identification using multivariate techniques in the CMS experiment in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceThe identification of prompt and isolated muons, as well as muons from heavy-flavour hadron decays, is an important task. We developed two multivariate techniques to provide highly efficient identification for muons with transverse momentum greater than 10\GeV. One provides a continuous variable as an alternative to a cut-based identification selection and offers a better discrimination power against misidentified muons. The other one selects prompt and isolated muons by using isolation requirements to reduce the contamination from nonprompt muons arising in heavy-flavour hadron decays. Both algorithms are developed using 59.7 fb$^{-1}$ of proton-proton collisions data at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV collected in 2018 with the CMS experiment at the CERN LHC

Search for exotic decays of the Higgs boson to a pair of pseudoscalars in the μμ\mu\mubb and ττ\tau\taubb final states

International audienceA search for exotic decays of the Higgs boson (H) with a mass of 125 GeV to a pair of light pseudoscalars $\mathrm{a}_1$ is performed in final states where one pseudoscalar decays to two b quarks and the other to a pair of muons or $\tau$ leptons. A data sample of proton-proton collisions at $\sqrt{s}$ = 13 TeV corresponding to an integrated luminosity of 138 fb$^{-1}$ recorded with the CMS detector is analyzed. No statistically significant excess is observed over the standard model backgrounds. Upper limits are set at 95% confidence level (CL) on the Higgs boson branching fraction to $\mu\mu$bb and to $\tau\tau$bb, via a pair of $\mathrm{a}_1$s. The limits depend on the pseudoscalar mass $m_{\mathrm{a}_1}$ and are observed to be in the range (0.17-3.3) $\times$ 10$^{-4}$ and (1.7-7.7) $\times$ 10$^{2}$ in the $\mu\mu$bb and $\tau\tau$bb final states, respectively. In the framework of models with two Higgs doublets and a complex scalar singlet (2HDM+S), the results of the two final states are combined to determine model-independent upper limits on the branching fraction $\mathcal{B}$(H $\to$ $\mathrm{a}_1\mathrm{a}_1$ $\to$ $\ell\ell$bb) at 95% CL, with $\ell$ being a muon or a $\tau$ lepton. For different types of 2HDM+S, upper bounds on the branching fraction $\mathcal{B}$(H $\to$ $\mathrm{a}_1\mathrm{a}_1$) are extracted from the combination of the two channels. In most of the Type II 2HDM+S parameter space, $\mathcal{B}($H $\to$ $\mathrm{a}_1\mathrm{a}_1$) values above 0.23 are excluded at 95% CL for $m_{\mathrm{a}_1}$ values between 15 and 60 GeV

Search for direct production of GeV-scale resonances decaying to a pair of muons in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceA search for direct production of low-mass dimuon resonances is performed using $\sqrt{s}$ = 13 TeV proton-proton collision data collected by the CMS experiment during the 2017-2018 operation of the CERN LHC with an integrated luminosity of 96.6 fb$^{-1}$. The search exploits a dedicated high-rate trigger stream that records events with two muons with transverse momenta as low as 3 GeV but does not include the full event information. The search is performed by looking for narrow peaks in the dimuon mass spectrum in the ranges of 1.1-2.6 GeV and 4.2-7.9 GeV. No significant excess of events above the expectation from the standard model background is observed. Model-independent limits on production rates of dimuon resonances within the experimental fiducial acceptance are set. Competitive or world's best limits are set at 90% confidence level for a minimal dark photon model and for a scenario with two Higgs doublets and an extra complex scalar singlet (2HDM+S). Values of the squared kinetic mixing coefficient $\varepsilon^2$ in the dark photon model above 10$^{-6}$ are excluded over most of the mass range of the search. In the 2HDM+S, values of the mixing angle $\sin(\theta_\text{H})$ above 0.08 are excluded over most of the mass range of the search with a fixed ratio of the Higgs doublets vacuum expectation $\tan\beta$ = 0.5