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Die durch die Covid-19-Pandemie bedingte Umstellung der Präsenzlehre auf digitale Lehr- und Lernformate stellte Lehrende und Studierende gleichermaßen vor eine Herausforderung. Innerhalb kürzester Zeit musste die Nutzung von Plattformen und digitalen Tools erlernt und getestet werden. Der Beitrag stellt exemplarisch Dienste und Werkzeuge von CLARIAH-DE vor und erläutert, wie die digitale Forschungsinfrastruktur Lehrende und Studierende auch im Rahmen der digitalen Lehre unterstützen kann.
The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.
HLA-DRB1 and HLA-DQB1 genetic diversity modulates response to lithium in bipolar affective disorders
(2021)
Bipolar affective disorder (BD) is a severe psychiatric illness, for which lithium (Li) is the gold standard for acute and maintenance therapies. The therapeutic response to Li in BD is heterogeneous and reliable biomarkers allowing patients stratification are still needed. A GWAS performed by the International Consortium on Lithium Genetics (ConLiGen) has recently identified genetic markers associated with treatment responses to Li in the human leukocyte antigens (HLA) region. To better understand the molecular mechanisms underlying this association, we have genetically imputed the classical alleles of the HLA region in the European patients of the ConLiGen cohort. We found our best signal for amino-acid variants belonging to the HLA-DRB1*11:01 classical allele, associated with a better response to Li (p < 1 × 10−3; FDR < 0.09 in the recessive model). Alanine or Leucine at position 74 of the HLA-DRB1 heavy chain was associated with a good response while Arginine or Glutamic acid with a poor response. As these variants have been implicated in common inflammatory/autoimmune processes, our findings strongly suggest that HLA-mediated low inflammatory background may contribute to the efficient response to Li in BD patients, while an inflammatory status overriding Li anti-inflammatory properties would favor a weak response.
Determining how the elevation of the Northern Andes has evolved over time is of paramount importance for understanding the response of the Northern Andes to deformational and geodynamic processes and its role as an orographic barrier for atmospheric vapor transport over geologic time. However, a fundamental requirement when using stable isotope data for paleoaltimetry reconstructions is knowledge about the present-day changes of δ18O and δD with elevation (isotopic lapse rate). This study defines the present-day river isotopic lapse rate near the Equator (∼3°S) based on analysis of δ18O and δD of surface waters collected from streams across the Western Cordillera and the Inter-Andean depression in Southern Ecuador. The results for the two domains show a decrease of δ18O with elevation which fits a linear regression with a slope of −0.18‰/100 m (R2 = 0.73, n = 83). However, we establish a present-day lapse rate of −0.15‰/100 m for δ18O (R2 = 0.88, n = 19) and -1.4‰/100 m for δD (R2 = 0.93, n = 19) from water samples collected along the west facing slopes of the Western Ecuadorian Cordillera which is mainly subject to moisture transport from the Pacific. We argue that this empirical relationship, consistent with those obtained in different tropical areas of the world, can inform stable isotope paleoaltimetry reconstructions in tropical latitudes.
Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.
We report first results on elliptic flow of identified particles at midrapidity in Au+Au collisions at sqrt[sNN] = 130 GeV using the STAR TPC at RHIC. The elliptic flow as a function of transverse momentum and centrality differs significantly for particles of different masses. This dependence can be accounted for in hydrodynamic models, indicating that the system created shows a behavior consistent with collective hydrodynamical flow. The fit to the data with a simple model gives information on the temperature and flow velocities at freeze-out.
The production of J/ψ is measured at midrapidity (|y|<0.9) in proton-proton collisions at s√ = 5.02 and 13 TeV, through the dielectron decay channel, using the ALICE detector at the Large Hadron Collider. The data sets used for the analyses correspond to integrated luminosities of Lint = 19.4 ± 0.4 nb−1 and Lint = 32.2 ± 0.5 nb−1 at s√ = 5.02 and 13 TeV, respectively. The fraction of non-prompt J/ψ mesons, i.e. those originating from the decay of beauty hadrons, is measured down to a transverse momentum pT = 2 GeV/c (1 GeV/c) at s√ = 5.02 TeV (13 TeV). The pT and rapidity (y) differential cross sections, as well as the corresponding values integrated over pT and y, are carried out separately for prompt and non-prompt J/ψ mesons. The results are compared with measurements from other experiments and theoretical calculations based on quantum chromodynamics (QCD). The shape of the pT and y distributions of beauty quarks predicted by state-of-the-art perturbative QCD models are used to extrapolate the bb¯¯¯ pair cross section at midrapidity and in the total phase space. The total bb¯¯¯ cross sections are found to be σbb¯¯¯=502±16(stat.)±51(syst.)+2−3(extr.) μb and σbb¯¯¯=218±37(stat.)±32(syst.)+8.2−9.1(extr.)μb at s√ = 13 and 5.02 TeV, respectively. The value at s√ = 13 TeV is obtained from the combination of ALICE and LHCb measurements.
Measurements of elliptic (v2) and triangular (v3) flow coefficients of π±, K±, p+p¯¯¯, K0S, and Λ+Λ¯¯¯¯ obtained with the scalar product method in Xe-Xe collisions at sNN−−−√ = 5.44 TeV are presented. The results are obtained in the rapidity range |y| < 0.5 and reported as a function of transverse momentum, pT, for several collision centrality classes. The flow coefficients exhibit a particle mass dependence for pT < 3 GeV/c, while a grouping according to particle type (i.e., meson and baryon) is found at intermediate transverse momenta (3 < pT < 8 GeV/c). The magnitude of the baryon v2 is larger than that of mesons up to pT = 6 GeV/c. The centrality dependence of the shape evolution of the pT-differential v2 is studied for the various hadron species. The v2 coefficients of π±, K±, and p+p¯¯¯ are reproduced by MUSIC hydrodynamic calculations coupled to a hadronic cascade model (UrQMD) for pT < 1 GeV/c. A comparison with vn measurements in the corresponding centrality intervals in Pb-Pb collisions at sNN−−−√ = 5.02 TeV yields an enhanced v2 in central collisions and diminished value in semicentral collisions.
Two-particle Azimuthal correlations are measured with the ALICE apparatus in pp collisions at s√=13 TeV to explore strangeness- and multiplicity-related effects in the fragmentation of jets and the transition regime between bulk and hard production, probed with the condition that a strange meson (KS0) or baryon (Λ) with transverse momentum pT>3 GeV/c is produced. Azimuthal correlations between kaons or Λ hyperons with other hadrons are presented at midrapidity for a broad range of the trigger (3<ptriggT<20 GeV/c) and associated particle pT (1 GeV/c <passocT<ptriggT), for minimum-bias events and as a function of the event multiplicity. The near- and away-side peak yields are compared for the case of either KS0 or Λ(Λ¯¯¯¯) being the trigger particle with that of inclusive hadrons (a sample dominated by pions). In addition, the measurements are compared with predictions from PYTHIA 8 and EPOS LHC event generators.
We report on the inclusive J/ψ production cross section measured at the CERN Large Hadron Collider in proton–proton collisions at a center-of-mass energy s√ = 13 TeV. The J/ψ mesons are reconstructed in the e+e− decay channel and the measurements are performed at midrapidity (|y|<0.9) in the transverse-momentum interval 0<pT<40 GeV/c, using a minimum-bias data sample corresponding to an integrated luminosity Lint=32.2 nb−1 and an Electromagnetic Calorimeter triggered data sample with Lint=8.3 pb−1. The pT-integrated J/ψ production cross section at midrapidity, computed using the minimum-bias data sample, is dσ/dy|y=0=8.97±0.24 (stat)±0.48 (syst)±0.15 (lumi) μb. An approximate logarithmic dependence with the collision energy is suggested by these results and available world data, in agreement with model predictions. The integrated and pT-differential measurements are compared with measurements in pp collisions at lower energies and with several recent phenomenological calculations based on the non-relativistic QCD and Color Evaporation models.