Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

Post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are debilitating, clinically heterogeneous and of unknown molecular etiology. A transcriptome-wide investigation was performed in 165 acutely infected hospitalized individuals who were followed clinically into the post-acute period. Distinct gene expression signatures of post-acute sequelae were already present in whole blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell-associated gene expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in individuals with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development

High-density disc reflection spectroscopy of low-mass active galactic nuclei

The standard alpha-disc model predicts an anti-correlation between the density of the inner accretion disc and the black hole mass times square of the accretion rate, as seen in higher mass ($M_{\rm BH}>10^{6} M_{\odot}$) active galactic nuclei (AGNs). In this work, we test the predictions of the alpha-disc model and study the properties of the inner accretion flow for the low-mass end ($M_{\rm BH}\approx 10^{5-6}M_{\odot}$) of AGNs. We utilize a new high-density disc reflection model where the density parameter varies from $n_{\rm e}=10^{15}$ to $10^{20}$ cm$^{-3}$ and apply it to the broadband X-ray (0.3-10 keV) spectra of the low-mass AGN sample. The sources span a wide range of Eddington fractions and are consistent with being sub-Eddington or near-Eddington. The X-ray spectra reveal a soft X-ray excess below $\sim 1.5$ keV which is well modeled by high-density reflection from an ionized accretion disc of density $n_{\rm e}\sim 10^{18}$ cm$^{-3}$ on average. The results suggest a radiation pressure-dominated disc with an average of 70% fraction of the disc power transferred to the corona, consistent with that observed in higher mass AGNs. We show that the disc density higher than $10^{15}$ cm$^{-3}$ can result from the radiation pressure compression when the disc surface does not hold a strong magnetic pressure gradient. We find tentative evidence for a drop in black hole spin at low-mass regimes.Comment: 20 pages, 10 figures, 6 tables. Accepted for publication in MNRA

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

Recent studies strongly indicate that aberrations in the control of gene expression might contribute to the initiation and progression of Alzheimer's disease (AD). In particular, alternative splicing has been suggested to play a role in spontaneous cases of AD. Previous transcriptome profiling of AD models and patient samples using microarrays delivered conflicting results. This study provides, for the first time, transcriptomic analysis for distinct regions of the AD brain using RNA-Seq next-generation sequencing technology. Illumina RNA-Seq analysis was used to survey transcriptome profiles from total brain, frontal and temporal lobe of healthy and AD post-mortem tissue. We quantified gene expression levels, splicing isoforms and alternative transcript start sites. Gene Ontology term enrichment analysis revealed an overrepresentation of genes associated with a neuron's cytological structure and synapse function in AD brain samples. Analysis of the temporal lobe with the Cufflinks tool revealed that transcriptional isoforms of the apolipoprotein E gene, APOE-001, -002 and -005, are under the control of different promoters in normal and AD brain tissue. We also observed differing expression levels of APOE-001 and -002 splice variants in the AD temporal lobe. Our results indicate that alternative splicing and promoter usage of the APOE gene in AD brain tissue might reflect the progression of neurodegeneration

The Colour Distribution of Galaxies at Redshift Five

We present the results of a study investigating the rest-frame ultra-violet (UV) spectral slopes of redshift z~5 Lyman-break galaxies (LBGs). By combining deep Hubble Space Telescope imaging of the CANDELS and HUDF fields with ground-based imaging from the UKIDSS Ultra Deep Survey (UDS), we have produced a large sample of z~5 LBGs spanning an unprecedented factor of >100 in UV luminosity. Based on this sample we find a clear colour-magnitude relation (CMR) at z~5, such that the rest-frame UV slopes (beta) of brighter galaxies are notably redder than their fainter counterparts. We determine that the z~5 CMR is well described by a linear relationship of the form: d beta = (-0.12 +/- 0.02) d Muv, with no clear evidence for a change in CMR slope at faint magnitudes (i.e. Muv > -18.9). Using the results of detailed simulations we are able, for the first time, to infer the intrinsic (i.e. free from noise) variation of galaxy colours around the CMR at z~5. We find significant (12 sigma) evidence for intrinsic colour variation in the sample as a whole. Our results also demonstrate that the width of the intrinsic UV slope distribution of z~5 galaxies increases from Delta(beta)=0.1 at Muv=-18 to Delta(beta)=0.4 at Muv=-21. We suggest that the increasing width of the intrinsic galaxy colour distribution and the CMR itself are both plausibly explained by a luminosity independent lower limit of beta=-2.1, combined with an increase in the fraction of red galaxies in brighter UV-luminosity bins.Comment: 13 pages, 8 colour figures. Updated in response to referee report; accepted in MNRA

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

<p>Abstract</p> <p>Background</p> <p>Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other <it>Populus </it>species.</p> <p>Results</p> <p>Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought.</p> <p>Conclusions</p> <p>In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.</p

Measurement of VH, H → b b ¯ production as a function of the vector-boson transverse momentum in 13 TeV pp collisions with the ATLAS detector

Cross-sections of associated production of a Higgs boson decaying into bottom-quark pairs and an electroweak gauge boson, W or Z, decaying into leptons are measured as a function of the gauge boson transverse momentum. The measurements are performed in kinematic fiducial volumes defined in the `simplified template cross-section' framework. The results are obtained using 79.8 fb-1 of proton-proton collisions recorded by the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 13 TeV. All measurements are found to be in agreement with the Standard Model predictions, and limits are set on the parameters of an effective Lagrangian sensitive to modifications of the Higgs boson couplings to the electroweak gauge bosons

Search for heavy neutral Higgs bosons produced in association with b-quarks and decaying into b-quarks at root s=13 TeV with the ATLAS detector

A search for heavy neutral Higgs bosons produced in association with one or two b -quarks and decaying to b -quark pairs is presented using 27.8  fb − 1 of √ s = 13  TeV proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider during 2015 and 2016. No evidence of a signal is found. Upper limits on the heavy neutral Higgs boson production cross section times its branching ratio to b ¯ b are set, ranging from 4.0 to 0.6 pb at 95% confidence level over a Higgs boson mass range of 450 to 1400 GeV. Results are interpreted within the two-Higgs-doublet model and the minimal supersymmetric Standard Model

Measurement of single top-quark production in association with a W boson in the single-lepton channel at \sqrt{s} = 8\,\text {TeV} with the ATLAS detector

The production cross-section of a top quark in association with a W boson is measured using proton–proton collisions at \sqrt{s} = 8\,\text {TeV}. The dataset corresponds to an integrated luminosity of 20.2\,\text {fb}^{-1}, and was collected in 2012 by the ATLAS detector at the Large Hadron Collider at CERN. The analysis is performed in the single-lepton channel. Events are selected by requiring one isolated lepton (electron or muon) and at least three jets. A neural network is trained to separate the tW signal from the dominant t{\bar{t}} background. The cross-section is extracted from a binned profile maximum-likelihood fit to a two-dimensional discriminant built from the neural-network output and the invariant mass of the hadronically decaying W boson. The measured cross-section is \sigma _{tW} = 26 \pm 7\,\text {pb}, in good agreement with the Standard Model expectation