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The transverse-momentum (pT) spectra and coalescence parameters B2 of (anti)deuterons are measured in pp collisions at s√=13 TeV in and out of jets. In this measurement, the direction of the leading particle with the highest pT in the event (pleadT>5 GeV/c) is used as an approximation for the jet axis. The event is consequently divided into three azimuthal regions and the jet signal is obtained as the difference between the Toward region, that contains jet fragmentation products in addition to the underlying event (UE), and the Transverse region, which is dominated by the UE. The coalescence parameter in the jet is found to be approximately a factor of 10 larger than that in the underlying event. This experimental observation is consistent with the coalescence picture and can be attributed to the smaller average phase-space distance between nucleons inside the jet cone as compared to the underlying event. The results presented in this Letter are compared to predictions from a simple nucleon coalescence model, where the phase space distributions of nucleons are generated using PYTHIA 8 with the Monash 2013 tuning, and to predictions from a deuteron production model based on ordinary nuclear reactions with parametrized energy-dependent cross sections tuned on data. The latter model is implemented in PYTHIA 8.3. Both models reproduce the observed large difference between in-jet and out-of-jet coalescence parameters.
Femtoscopic correlations with the particle pair combinations K0SK0S and K0SK± are studied in pp collisions at s√=5.02 and 13 TeV by the ALICE experiment. At both energies, boson source parameters are extracted for both pair combinations, by fitting models based on Gaussian size distributions of the sources, to the measured two-particle correlation functions. The interaction model used for the K0SK0S analysis includes quantum statistics and strong final-state interactions through the f0(980) and a0(980) resonances. The model used for the K0SK± analysis includes only the final-state interaction through the a0 resonance. Source parameters extracted in the present work are compared with published values from pp collisions at s√= 7 TeV and the different pair combinations are found to be consistent. From the observation that the strength of the K0SK0S correlations is significantly greater than the strength of the K0SK± correlations, the new results are compatible with the a0 resonance being a tetraquark state of the form (q1,q2¯¯¯¯¯,s,s¯¯¯), where q1 and q2 are u or d quarks.
Angular correlations of heavy-flavour and charged particles in high-energy proton-proton collisions are sensitive to the production mechanisms of heavy quarks and to their fragmentation as well as hadronisation processes. The measurement of the azimuthal-correlation function of prompt D mesons with charged particles in proton-proton collisions at a centre-of-mass energy of s√=13 TeV with the ALICE detector is reported, considering D0, D+, and D∗+ mesons in the transverse-momentum interval 3<pT<36 GeV/c at midrapidity (|y|<0.5), and charged particles with pT>0.3 GeV/c and pseudorapidity |η|<0.8. This measurement has an improved precision and provides an extended transverse-momentum coverage compared to previous ALICE measurements at lower energies. The study is also performed as a function of the charged-particle multiplicity, showing no modifications of the correlation function with multiplicity within uncertainties. The properties and the transverse-momentum evolution of the near- and away-side correlation peaks are studied and compared with predictions from various Monte Carlo event generators. Among those considered, PYTHIA8 and POWHEG+PYTHIA8 provide the best description of the measured observables. The obtained results can provide guidance on tuning the generators.
This article presents groomed jet substructure measurements in pp and Pb−Pb collisions at sNN−−−√=5.02 TeV with the ALICE detector. The Soft Drop grooming algorithm provides access to the hard parton splittings inside a jet by removing soft wide-angle radiation. We report the groomed jet momentum splitting fraction, zg, and the (scaled) groomed jet radius, θg. Charged-particle jets are reconstructed at midrapidity using the anti-kT algorithm with resolution parameters R=0.2 and R=0.4. In heavy-ion collisions, the large underlying event poses a challenge for the reconstruction of groomed jet observables, since fluctuations in the background can cause groomed parton splittings to be misidentified. By using strong grooming conditions to reduce this background, we report these observables fully corrected for detector effects and background fluctuations for the first time. A narrowing of the θg distribution in Pb−Pb collisions compared to pp collisions is seen, which provides direct evidence of the modification of the angular structure of jets in the quark−gluon plasma. No significant modification of the zg distribution in Pb−Pb collisions compared to pp collisions is observed. These results are compared with a variety of theoretical models of jet quenching, and provide constraints on jet energy-loss mechanisms and coherence effects in the quark−gluon plasma.
Fluctuation measurements are important sources of information on the mechanism of particle production at LHC energies. This article reports the first experimental results on third-order cumulants of the net-proton distributions in Pb−Pb collisions at a center-of-mass energy sNN−−−√=5.02 TeV recorded by the ALICE detector. The results on the second-order cumulants of net-proton distributions at sNN−−−√=2.76 and 5.02 TeV are also discussed in view of effects due to the global and local baryon number conservation. The results demonstrate the presence of long-range rapidity correlations between protons and antiprotons. Such correlations originate from the early phase of the collision. The experimental results are compared with HIJING and EPOS model calculations, and the dependence of the fluctuation measurements on the phase-space coverage is examined in the context of lattice quantum chromodynamics (LQCD) and hadron resonance gas (HRG) model estimations. The measured third-order cumulants are consistent with zero within experimental uncertainties of about 4% and are described well by LQCD and HRG predictions.
The study of the azimuthal anisotropy of inclusive muons produced in p-Pb collisions at sNN−−−√=8.16 TeV, using the ALICE detector at the LHC is reported. The measurement of the second-order Fourier coefficient of the particle azimuthal distribution, v2, is performed as a function of transverse momentum pT in the 0-20% high-multiplicity interval at both forward (2.03<yCMS<3.53) and backward (−4.46<yCMS<−2.96) rapidities over a wide pT range, 0.5<pT<10 GeV/c, in which a dominant contribution of muons from heavy-flavour hadron decays is expected at pT>2 GeV/c. The v2 coefficient of inclusive muons is extracted using two different techniques, namely two-particle cumulants, used for the first time for heavy-flavour measurements, and forward-central two-particle correlations. Both techniques give compatible results. A positive v2 is measured at both forward and backward rapidities with a significance larger than 4.7σ and 7.6σ, respectively, in the interval 2<pT<6 GeV/c. Comparisons with previous measurements in p-Pb collisions at sNN−−−√=5.02 TeV, and with AMPT and CGC-based theoretical calculations are discussed. The findings impose new constraints on the theoretical interpretations of the origin of the collective behaviour in small collision systems.
The study of the azimuthal anisotropy of inclusive muons produced in p-Pb collisions at sNN−−−√=8.16 TeV, using the ALICE detector at the LHC is reported. The measurement of the second-order Fourier coefficient of the particle azimuthal distribution, v2, is performed as a function of transverse momentum pT in the 0-20% high-multiplicity interval at both forward (2.03<yCMS<3.53) and backward (−4.46<yCMS<−2.96) rapidities over a wide pT range, 0.5<pT<10 GeV/c, in which a dominant contribution of muons from heavy-flavour hadron decays is expected at pT>2 GeV/c. The v2 coefficient of inclusive muons is extracted using two different techniques, namely two-particle cumulants, used for the first time for heavy-flavour measurements, and forward-central two-particle correlations. Both techniques give compatible results. A positive v2 is measured at both forward and backward rapidities with a significance larger than 4.7σ and 7.6σ, respectively, in the interval 2<pT<6 GeV/c. Comparisons with previous measurements in p-Pb collisions at sNN−−−√=5.02 TeV, and with AMPT and CGC-based theoretical calculations are discussed. The findings impose new constraints on the theoretical interpretations of the origin of the collective behaviour in small collision systems.
The multiplicity dependence of jet production in pp collisions at the centre-of-mass energy of s√=13 TeV is studied for the first time. Jets are reconstructed from charged particles using the anti-kT algorithm with resolution parameters R varying from 0.2 to 0.7. The jets are measured in the pseudorapidity range |ηjet|<0.9−R and in the transverse momentum range 5<pchT,jet<140 GeV/c. The multiplicity intervals are categorised by the ALICE forward detector V0. The pT differential cross section of charged-particle jets are compared to leading order (LO) and next-to-leading order (NLO) perturbative quantum chromodynamics (pQCD) calculations. It is found that the data are better described by the NLO calculation, although the NLO prediction overestimates the jet cross section below 20 GeV/c. The cross section ratios for different R are also measured and compared to model calculations. These measurements provide insights into the angular dependence of jet fragmentation. The jet yield increases with increasing self-normalised charged-particle multiplicity. This increase shows only a weak dependence on jet transverse momentum and resolution parameter at the highest multiplicity. While such behaviour is qualitatively described by the present version of PYTHIA, quantitative description may require implementing new mechanisms for multi-particle production in hadronic collisions.
The multiplicity dependence of jet production in pp collisions at the centre-of-mass energy of s√=13 TeV is studied for the first time. Jets are reconstructed from charged particles using the anti-kT algorithm with resolution parameters R varying from 0.2 to 0.7. The jets are measured in the pseudorapidity range |ηjet|<0.9−R and in the transverse momentum range 5<pchT,jet<140 GeV/c. The multiplicity intervals are categorised by the ALICE forward detector V0. The pT differential cross section of charged-particle jets are compared to leading order (LO) and next-to-leading order (NLO) perturbative quantum chromodynamics (pQCD) calculations. It is found that the data are better described by the NLO calculation, although the NLO prediction overestimates the jet cross section below 20 GeV/c. The cross section ratios for different R are also measured and compared to model calculations. These measurements provide insights into the angular dependence of jet fragmentation. The jet yield increases with increasing self-normalised charged-particle multiplicity. This increase shows only a weak dependence on jet transverse momentum and resolution parameter at the highest multiplicity. While such behaviour is qualitatively described by the present version of PYTHIA, quantitative description may require implementing new mechanisms for multi-particle production in hadronic collisions.
This article presents the first measurement of the interaction between charm hadrons and nucleons. The two-particle momentum correlations of pD− and p¯¯¯D+ pairs are measured by the ALICE Collaboration in high-multiplicity pp collisions at s√=13 TeV. The data are compatible with the Coulomb-only interaction hypothesis within (1.1-1.5)σ. The level of agreement slightly improves if an attractive nucleon(N)D¯¯¯¯ strong interaction is considered, in contrast to most model predictions which suggest an overall repulsive interaction. This measurement allows for the first time an estimation of the 68% confidence level interval for the isospin I=0 inverse scattering length of the ND¯¯¯¯ state f−10, I=0∈[−0.4,0.9] fm−1, assuming negligible interaction for the isospin I=1 channel.
This Letter presents the first measurement of the interaction between charm hadrons and nucleons. The two-particle momentum correlations of pD− and p¯¯¯D+ pairs are measured by the ALICE Collaboration in high-multiplicity pp collisions at s√=13 TeV. The data are compatible with the Coulomb-only interaction hypothesis within (1.1-1.5)σ. Considering an attractive nucleon(N)D¯¯¯¯ strong interaction, in contrast to most model predictions which suggest an overall repulsive interaction, slightly improves the level of agreement. This measurement allows for the first time an estimation of the 68% confidence level interval for the isospin I=0 inverse scattering length of the ND¯¯¯¯ state f−10, I=0∈[−0.4,0.9] fm−1, assuming negligible interaction for the isospin I=1 channel.
We present the first measurement of event-by-event fluctuations in the kaon sector in Pb-Pb collisions at sNN−−−√= 2.76 TeV with the ALICE detector at the LHC. The robust fluctuation correlator νdyn is used to evaluate the magnitude of fluctuations of the relative yields of neutral and charged kaons, as well as the relative yields of charged kaons, as a function of collision centrality and selected kinematic ranges. While the correlator νdyn[K+,K−] exhibits a scaling approximately in inverse proportion of the charged particle multiplicity, νdyn[K0S,K±] features a significant deviation from such scaling. Within uncertainties, the value of νdyn[K0S,K±] is independent of the selected transverse momentum interval, while it exhibits a pseudorapidity dependence. The results are compared with HIJING, AMPT and EPOS-LHC predictions, and are further discussed in the context of the possible production of disoriented chiral condensates in central Pb-Pb collisions.
The pseudorapidity density of charged particles with minimum transverse momentum (pT) thresholds of 0.15, 0.5, 1, and 2 GeV/c was measured in pp collisions at centre-of-mass energies of √s = 5.02 and 13 TeV with the ALICE detector. The study is carried out for inelastic collisions with at least one primary charged particle having a pseudorapidity (η) within ±0.8 and pT larger than the corresponding threshold. The measurements were also performed for inelastic and non-single-diffractive events as well as for inelastic events with at least one charged particle having |η| < 1 in pp collisions at √s = 5.02 TeV for the first time at the LHC. The measurements are compared to the PYTHIA 6, PYTHIA 8, and EPOS-LHC models. In general, the models describe the pseudorapidity dependence of particle production well, however, discrepancies are observed for event classes including diffractive events and for the highest transverse momentum threshold (pT > 2 GeV/c), highlighting the importance of such measurements for tuning event generators. The new measurements agree within uncertainties with results from the ATLAS and CMS experiments.
Antimatter particles such as positrons and antiprotons abound in the cosmos. Much less common are light antinuclei, composed of antiprotons and antineutrons, which can be produced in our galaxy via high-energy cosmic-ray collisions with the interstellar medium or could also originate from the annihilation of the still undiscovered dark-matter particles. On Earth, the only way to produce and study antinuclei with high precision is to create them at high-energy particle accelerators like the Large Hadron Collider (LHC). Though the properties of elementary antiparticles have been studied in detail, knowledge of the interaction of light antinuclei with matter is rather limited. This work focuses on the determination of the disappearance probability of \ahe\ when it encounters matter particles and annihilates or disintegrates. The material of the ALICE detector at the LHC serves as a target to extract the inelastic cross section for \ahe\ in the momentum range of 1.17≤p<10 GeV/c. This inelastic cross section is measured for the first time and is used as an essential input to calculations of the transparency of our galaxy to the propagation of 3He¯¯¯¯¯¯ stemming from dark-matter decays and cosmic-ray interactions within the interstellar medium. A transparency of about 50% is estimated using the GALPROP program for a specific dark-matter profile and a standard set of propagation parameters. For cosmic-ray sources, the obtained transparency with the same propagation scheme varies with increasing 3He¯¯¯¯¯¯ momentum from 25% to 90%. The absolute uncertainties associated to the 3He¯¯¯¯¯¯ inelastic cross section measurements are of the order of 10%−15%. The reported results indicate that 3He¯¯¯¯¯¯ nuclei can travel long distances in the galaxy, and can be used to study cosmic-ray interactions and dark-matter decays.
In our Galaxy, light antinuclei composed of antiprotons and antineutrons can be produced through high-energy cosmic-ray collisions with the interstellar medium or could also originate from the annihilation of dark-matter particles that have not yet been discovered. On Earth, the only way to produce and study antinuclei with high precision is to create them at high-energy particle accelerators. Although the properties of elementary antiparticles have been studied in detail, the knowledge of the interaction of light antinuclei with matter is limited. We determine the disappearance probability of 3He¯¯¯¯¯¯ when it encounters matter particles and annihilates or disintegrates within the ALICE detector at the Large Hadron Collider. We extract the inelastic interaction cross section, which is then used as input to calculations of the transparency of our Galaxy to the propagation of 3He¯¯¯¯¯¯ stemming from dark-matter annihilation and cosmic-ray interactions within the interstellar medium. For a specific dark-matter profile, we estimate a transparency of about 50%, whereas it varies with increasing 3He¯¯¯¯¯¯ momentum from 25% to 90% for cosmic-ray sources. The results indicate that 3He¯¯¯¯¯¯ nuclei can travel long distances in the Galaxy, and can be used to study cosmic-ray interactions and dark-matter annihilation.
An excess of J/ψ yield at very low transverse momentum (pT<0.3 GeV/c), originating from coherent photoproduction, is observed in peripheral and semicentral hadronic Pb−Pb collisions at a center-of-mass energy per nucleon pair of √sNN=5.02 TeV. The measurement is performed with the ALICE detector via the dimuon decay channel at forward rapidity (2.5<y<4). The nuclear modification factor at very low pT and the coherent photoproduction cross section are measured as a function of centrality down to the 10% most central collisions. These results extend the previous study at √sNN=2.76 TeV, confirming the clear excess over hadronic production in the pT range 0−0.3 GeV/c and the centrality range 70−90%, and establishing an excess with a significance greater than 5σ also in the 50−70% and 30−50% centrality ranges. The results are compared with earlier measurements at √sNN=2.76 TeV and with different theoretical predictions aiming at describing how coherent photoproduction occurs in hadronic interactions with nuclear overlap.
The ALICE Collaboration reports the first fully-corrected measurements of the N-subjettiness observable for track-based jets in heavy-ion collisions. This study is performed using data recorded in pp and Pb−Pb collisions at centre-of-mass energies of √s=7 TeV and √sNN=2.76\,TeV, respectively. In particular the ratio of 2-subjettiness to 1-subjettiness, τ2/τ1, which is sensitive to the rate of two-pronged jet substructure, is presented. Energy loss of jets traversing the strongly interacting medium in heavy-ion collisions is expected to change the rate of two-pronged substructure relative to vacuum. The results are presented for jets with a resolution parameter of R=0.4 and charged jet transverse momentum of 40≤pT,jet≤60 GeV/c, which constitute a larger jet resolution and lower jet transverse momentum interval than previous measurements in heavy-ion collisions. This has been achieved by utilising a semi-inclusive hadron-jet coincidence technique to suppress the larger jet combinatorial background in this kinematic region. No significant modification of the τ2/τ1 observable for track-based jets in Pb--Pb collisions is observed relative to vacuum PYTHIA6 and PYTHIA8 references at the same collision energy. The measurements of τ2/τ1, together with the splitting aperture angle ΔR, are also performed in pp collisions at √s=7 TeV for inclusive jets. These results are compared with PYTHIA calculations at √s=7 TeV, in order to validate the model as a vacuum reference for the Pb−Pb centre-of-mass energy. The PYTHIA references for τ2/τ1 are shifted to larger values compared to the measurement in pp collisions. This hints at a reduction in the rate of two-pronged jets in Pb--Pb collisions compared to pp collisions.
Understanding the production mechanism of light (anti)nuclei is one of the key challenges of nuclear physics and has important consequences for astrophysics, since it provides an input for indirect dark-matter searches in space. In this paper, the latest results about the production of light (anti)nuclei in pp collisions at s√=13 TeV are presented, focusing on the comparison with the predictions of coalescence and thermal models. For the first time, the coalescence parameters B2 for deuterons and B3 for helions are compared with parameter-free theoretical predictions that are directly constrained by the femtoscopic measurement of the source radius in the same event class. A fair description of the data with a Gaussian wave function is observed for both deuteron and helion, supporting the coalescence mechanism for the production of light (anti)nuclei in pp collisions. This method paves the way for future investigations of the internal structure of more complex nuclear clusters, including the hypertriton.
Background: Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion.
Results: By applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Ae. aegypti, sampled along an altitudinal temperature gradient in Nepal (200- 1300m), we identify adaptive traits and describe the species’ genomic footprint of climate adaptation to colder ecoregions. We found two clusters of differentiation with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300m) and all other lowland populations (≤ 800 m). We revealed non-synonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern.
Conclusion: Other than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. This finding either indicates a differential invasion history to Nepal or local high-altitude adaptation explaining the population’s phenotypic cold tolerance. In any case, this highland population can be assumed to carry pre-adapted alleles relevant for the species’ invasion into colder ecoregions worldwide that way expanding their climate niche.
The production of inclusive, prompt and non-prompt J/ψ was studied for the first time at midrapidity (−1.37<ycms<0.43) in p−Pb collisions at sNN−−−√=8.16 TeV with the ALICE detector at the LHC. The inclusive J/ψ mesons were reconstructed in the dielectron decay channel in the transverse momentum (pT) interval 0<pT<14 GeV/c and the prompt and non-prompt contributions were separated on a statistical basis for pT>2 GeV/c. The study of the J/ψ mesons in the dielectron channel used for the first time in ALICE online single-electron triggers from the Transition Radiation Detector, providing a data sample corresponding to an integrated luminosity of 689±13μb−1. The proton−proton reference cross section for inclusive J/ψ was obtained based on interpolations of measured data at different centre-of-mass energies and a universal function describing the pT-differential J/ψ production cross sections. The pT-differential nuclear modification factors RpPb of inclusive, prompt, and non-prompt J/ψ are consistent with unity and described by theoretical models implementing only nuclear shadowing.
The most precise measurements to date of the 3ΛH lifetime τ and Λ separation energy BΛ are obtained using the data sample of Pb-Pb collisions at √sNN = 5.02 TeV collected by ALICE at the LHC. The 3ΛH is reconstructed via its charged two-body mesonic decay channel (3ΛH→ 3He + π− and the charge-conjugate process). The measured values τ=[253±11 (stat.)±6 (syst.)] ps and BΛ=[72±63 (stat.)±36 (syst.)] keV are compatible with predictions from effective field theories and conclusively confirm that the 3ΛH is a weakly-bound system.
The most precise measurements to date of the 3ΛH lifetime τ and Λ separation energy BΛ are obtained using the data sample of Pb-Pb collisions at √sNN = 5.02 TeV collected by ALICE at the LHC. The 3ΛH is reconstructed via its charged two-body mesonic decay channel (3ΛH→ 3He + π− and the charge-conjugate process). The measured values τ=[253±11 (stat.)±6 (syst.)] ps and BΛ=[72±63 (stat.)±35 (syst.)] keV are compatible with predictions from effective field theories and conclusively confirm that the 3ΛH is a weakly-bound system.
The establishment and maintenance of protected areas(PAs) is viewed as a key action in delivering post-2020 biodiversity targets. PAs often need to meet a multitude of objectives, ranging from biodiversity protection to ecosystem service provision and climate change mitigation. As available land and conservation funding are limited, optimizing resources by selecting the most beneficial PAs is vital. Here we present a decision support tool that enables a flexible approach to PA selection on a global scale, allowing different conservation objectives to be weighted and prioritized according to user-specified preferences. We apply the tool across 1347 terrestrial PAs and highlight frequent trade-offs among different objectives, e.g., between biodiversity protection and ecosystem integrity. These results indicate that decision makers must usually decide among conflicting objectives. To assist this our decision support tool provides an explicitly value-based approach that can help resolve such conflicts by considering divergent societal and political demands and values.
Spontaneous brain activity builds the foundation for human cognitive processing during external demands. Neuroimaging studies based on functional magnetic resonance imaging (fMRI) identified specific characteristics of spontaneous (intrinsic) brain dynamics to be associated with individual differences in general cognitive ability, i.e., intelligence. However, fMRI research is inherently limited by low temporal resolution, thus, preventing conclusions about neural fluctuations within the range of milliseconds. Here, we used resting-state electroencephalographical (EEG) recordings from 144 healthy adults to test whether individual differences in intelligence (Raven’s Advanced Progressive Matrices scores) can be predicted from the complexity of temporally highly resolved intrinsic brain signals. We compared different operationalizations of brain signal complexity (multiscale entropy, Shannon entropy, Fuzzy entropy, and specific characteristics of microstates) regarding their relation to intelligence. The results indicate that associations between brain signal complexity measures and intelligence are of small effect sizes (r ~ .20) and vary across different spatial and temporal scales. Specifically, higher intelligence scores were associated with lower complexity in local aspects of neural processing, and less activity in task-negative brain regions belonging to the defaultmode network. Finally, we combined multiple measures of brain signal complexity to show that individual intelligence scores can be significantly predicted with a multimodal model within the sample (10-fold cross-validation) as well as in an independent sample (external replication, N = 57). In sum, our results highlight the temporal and spatial dependency of associations between intelligence and intrinsic brain dynamics, proposing multimodal approaches as promising means for future neuroscientific research on complex human traits.
Significance Statement Spontaneous brain activity builds the foundation for intelligent processing - the ability of humans to adapt to various cognitive demands. Using resting-state EEG, we extracted multiple aspects of temporally highly resolved intrinsic brain dynamics to investigate their relationship with individual differences in intelligence. Single associations were of small effect sizes and varied critically across spatial and temporal scales. However, combining multiple measures in a multimodal cross-validated prediction model, allows to significantly predict individual intelligence scores in unseen participants. Our study adds to a growing body of research suggesting that observable associations between complex human traits and neural parameters might be rather small and proposes multimodal prediction approaches as promising tool to derive robust brain-behavior relations despite limited sample sizes.
Although vaccines are currently used to control the coronavirus disease 2019 (COVID-19) pandemic, treatment options are urgently needed for those who cannot be vaccinated and for future outbreaks involving new severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) strains or coronaviruses not covered by current vaccines. Thus far, few existing antivirals are known to be effective against SARS-CoV-2 and clinically successful against COVID-19.
As part of an immediate response to the COVID-19 pandemic, a high-throughput, high content imaging–based SARS-CoV-2 infection assay was developed in VeroE6-eGFP cells and was used to screen a library of 5676 compounds that passed phase 1 clinical trials. Eight candidates (nelfinavir, RG-12915, itraconazole, chloroquine, hydroxychloroquine, sematilide, remdesivir, and doxorubicin) with in vitro anti–SARS-CoV-2 activity in VeroE6-eGFP and/or Caco-2 cell lines were identified. However, apart from remdesivir, toxicity and pharmacokinetic data did not support further clinical development of these compounds for COVID-19 treatment.
Vaccines are central to controlling the coronavirus disease 2019 (COVID-19) pandemic but the durability of protection is limited for currently approved COVID-19 vaccines. Further, the emergence of variants of concern (VoCs) that evade immune recognition has reduced vaccine effectiveness, compounding the problem. Here, we show that a single dose of a murine cytomegalovirus (MCMV)-based vaccine, which expresses the spike (S) protein of the virus circulating early in the pandemic (MCMVS), protects highly susceptible K18-hACE2 mice from clinical symptoms and death upon challenge with a lethal dose of D614G SARS-CoV-2. Moreover, MCMVS vaccination controlled two immune-evading VoCs, the Beta (B.1.135) and the Omicron (BA.1) variants in BALB/c mice, and S-specific immunity was maintained for at least 5 months after immunization, where neutralizing titers against all tested VoCs were higher at 5-months than at 1-month post-vaccination. Thus, cytomegalovirus (CMV)-based vector vaccines might allow for long-term protection against COVID-19.
NAD is a coenzyme central to metabolism that was also found to serve as a 5’-terminal cap of bacterial and eukaryotic RNA species. The presence and functionality of NAD-capped RNAs (NAD-RNAs) in the archaeal domain remain to be characterized in detail. Here, by combining LC-MS and NAD captureSeq methodology, we quantified the total levels of NAD-RNAs and determined the identity of NAD-RNAs in the two model archaea, Sulfolobus acidocaldarius and Haloferax volcanii. A complementary differential RNA-Seq (dRNA-Seq) analysis revealed that NAD transcription start sites (NAD-TSS) correlate with well-defined promoter regions and often overlap with primary transcription start sites (pTSS). The population of NAD-RNAs in the two archaeal organisms shows clear differences, with S. acidocaldarius possessing more capped small non-coding RNAs (sncRNAs) and leader sequences. The NAD-cap did not prevent 5’→3’ exonucleolytic activity by the RNase Saci-aCPSF2. To investigate enzymes that facilitate the removal of the NAD-cap, four Nudix proteins of S. acidocaldarius were screened. None of the recombinant proteins showed NAD decapping activity. Instead, the Nudix protein Saci_NudT5 showed activity after incubating NAD-RNAs at elevated temperatures. Hyperthermophilic environments promote the thermal degradation of NAD into the toxic product ADPR. Incorporating NAD into RNAs and the regulation of ADPR-RNA decapping by Saci_NudT5 is proposed to provide additional layers of maintaining stable NAD levels in archaeal cells.
Importance: This study reports the first characterization of 5’-terminally modified RNA molecules in Archaea and establishes that NAD-RNA modifications, previously only identified in the other two domains of life, are also prevalent in the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii. We screened for NUDIX hydrolases that could remove the NAD-RNA cap and showed that none of these enzymes removed NAD modifications, but we discovered an enzyme that hydrolyzes ADPR-RNA. We propose that these activities influence the stabilization of NAD and its thermal degradation to potentially toxic ADPR products at elevated growth temperatures.
In a dynamic environment, the already limited information that human working memory can maintain needs to be constantly updated to optimally guide behaviour. Indeed, previous studies showed that working memory representations are continuously being transformed during delay periods leading up to a response. This goes hand-in-hand with the removal of task-irrelevant items. However, does such removal also include veridical, original stimuli, as they were prior to transformation? Here we aimed to assess the neural representation of task-relevant transformed representations, compared to the no-longer-relevant veridical representations they originated from. We applied multivariate pattern analysis to electroencephalographic data during maintenance of orientation gratings with and without mental rotation. During maintenance, we perturbed the representational network by means of a visual impulse stimulus, and were thus able to successfully decode veridical as well as imaginary, transformed orientation gratings from impulse-driven activity. On the one hand, the impulse response reflected only task-relevant (cued), but not task-irrelevant (uncued) items, suggesting that the latter were quickly discarded from working memory. By contrast, even though the original cued orientation gratings were also no longer task-relevant after mental rotation, these items continued to be represented next to the rotated ones, in different representational formats. This seemingly inefficient use of scarce working memory capacity was associated with reduced probe response times and may thus serve to increase precision and flexibility in guiding behaviour in dynamic environments.
Several clinically used drugs are derived from microorganisms that often produce them via non-ribosomal peptide synthetases (NRPS), giant megasynthases that activate and connect individual amino acids in an assembly line fashion. Since NRPS are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would allow the biotechnological generation of several different peptides including linear, cyclic and further modified derivatives. Here we describe a detailed phylogenetic analysis of several bacterial NRPS that led to the identification of a new recombination breakpoint within the thiolation (T) domain important in natural NRPS evolution. From this an evolutionary-inspired eXchange Unit between T domains (XUT) approach was developed, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as was shown for the specific production of a proteasome inhibitor, designed and assembled from five different NRPS fragments.
Many clinically used drugs are derived from or inspired by bacterial natural products that often are biosynthesised via non-ribosomal peptide synthetases (NRPS), giant megasynthases that activate and join individual amino acids in an assembly line fashion. Since NRPS are not limited to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would allow the biotechnological generation of complex peptides including linear, cyclic and further modified natural product analogues, e.g. to optimise natural product leads. Here we describe a detailed phylogenetic analysis of several bacterial NRPS that led to the identification of a new recombination breakpoint within the thiolation (T) domain that is important for natural NRPS evolution. From this, an evolution-inspired eXchange Unit between T domains (XUT) approach was developed which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
Quantitative MRI maps of human neocortex explored using cell type-specific gene expression analysis
(2022)
Quantitative MRI (qMRI) allows extraction of reproducible and robust parameter maps. However, the connection to underlying biological substrates remains murky, especially in the complex, densely packed cortex. We investigated associations in human neocortex between qMRI parameters and neocortical cell types by comparing the spatial distribution of the qMRI parameters longitudinal relaxation rate (R1), effective transverse relaxation rate (R2∗), and magnetization transfer saturation (MTsat) to gene expression from the Allen Human Brain Atlas, then combining this with lists of genes enriched in specific cell types found in the human brain. As qMRI parameters are magnetic field strength-dependent, the analysis was performed on MRI data at 3T and 7T. All qMRI parameters significantly covaried with genes enriched in GABA- and glutamatergic neurons, i.e. they were associated with cytoarchitecture. The qMRI parameters also significantly covaried with the distribution of genes enriched in astrocytes (R2∗ at 3T, R1 at 7T), endothelial cells (R1 and MTsat at 3T), microglia (R1 and MTsat at 3T, R1 at 7T), and oligodendrocytes (R1 at 7T). These results advance the potential use of qMRI parameters as biomarkers for specific cell types.
Candida boidinii NAD+-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential applications in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of the wild-type CbFDH at cryogenic and ambient temperatures as well as Val120Thr mutant at cryogenic temperature determined at the Turkish Light Source "Turkish DeLight". The structures reveal new hydrogen bonds between Thr120 and water molecules in the mutant CbFDH's active site, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, our findings provide invaluable insights into future protein engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.
Background Eukaryotic gene expression is controlled by cis-regulatory elements (CREs) including promoters and enhancers which are bound by transcription factors (TFs). Differential expression of TFs and their putative binding sites on CREs cause tissue and developmental-specific transcriptional activity. Consolidating genomic data sets can offer further insights into the accessibility of CREs, TF activity, and thus gene regulation. However, the integration and analysis of multi-modal data sets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined ChIP-seq and RNA-seq data exist, they do not offer good usability, have limited support for large-scale data processing, and provide only minimal functionality for visual result interpretation.
Results We developed TF-Prioritizer, an automated java pipeline to prioritize condition-specific TFs derived from multi-modal data. TF-Prioritizer creates an interactive, feature-rich, and user-friendly web report of its results. To showcase the potential of TF-Prioritizer, we identified known active TFs (e.g., Stat5, Elf5, Nfib, Esr1), their target genes (e.g., milk proteins and cell-cycle genes), and newly classified lactating mammary gland TFs (e.g., Creb1, Arnt).
Conclusion TF-Prioritizer accepts ChIP-seq and RNA-seq data, as input and suggests TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.
Background: Blood donation saves lives. Provided they are in good health, male volunteers can donate as often as six times per year from the age of 18 into their late sixties. The burden of blood donation is very unevenly distributed, with a small minority of altruistic individuals providing this critical resource. While the consequences of persistent iron depletion in blood donors have been studied in the context of cancer and coronary heart disease, potential effects of the erythropoietic stress from repetitive large-volume phlebotomy remain unexplored. We sought to investigate if and how repeated blood donations affect the clonal composition of the hematopoietic stem and progenitor cell (HSPC) compartment.
Methods: 105 healthy, male individuals with an extensive blood donation history (median of 120 donations per donor; median age of 66 yrs.) were screened for the presence of clonal hematopoiesis (CH) using a sequencing panel covering 141 genes commonly mutated in human myeloid neoplasms. The control cohort consisted of 103 healthy, male donors with a median of 5 donations per donor and a median age of 63. Donors positive for CH were subsequently studied longitudinally. The pathogenicity of detected variants was compared using established scoring systems. Finally, to assess the functional consequences of blood-donation induced CH, selected CH mutations were introduced by CRISPR-mediated editing into HSPCs from human cord blood (CB) or bone marrow (BM). The effect of these mutations was tested under different stress stimuli using functional ex vivo long-term culture initiating cells (LTC-IC) assays.
Results: Compared to the control cohort, frequent donors were significantly more likely to have mutations in genes encoding for epigenetic modifiers (44.7 vs. 22.3 %), most specifically in the two genes most commonly mutated in CH, DNMT3A and TET2 (35.2 vs. 20.3 %). However, no difference in the variant allele frequency (VAF) of detected mutations was found between the groups. Longitudinal analysis revealed that the majority of the mutations remained at a stable VAF over an observation period of approximately one year. Three DNMT3A variants from the frequent donor cohort were introduced into healthy HSPCs and functionally analyzed: All expanded in response to EPO, but none responded to LPS or IFNγ stimulation. This contrasted with the leukemogenic DNMT3A R882H mutation, which did not expand in the presence of EPO but instead responded strongly to inflammatory stimuli.
Conclusions: Frequent whole blood donation is associated with a higher prevalence of CH driven by mutations in genes encoding for epigenetic modifiers, with DNMT3A and TET2 being the most common. This increased CH prevalence is not associated with a higher pathogenicity of the associated variants and is likely a result of the selection of clones with improved responsiveness to EPO under the condition of bleeding stress. Our data show that even highly frequent blood donations over many years is not increasing the risk for malignant clones further underscoring the safety of repetitive blood donations. To our knowledge, this is the first CH study analyzing a cohort of individuals known for their superior health and survival, able to donate blood until advanced age. Thus, our analysis possibly identified mutations associated with beneficial outcomes, rather than a disease condition, such as mutations in DNMT3A that mediated the improved expansion of HSPCs in EPO enriched environments. Our data support the notion of ongoing Darwinian evolution in humans at the somatic stem cell level and present EPO as one of the environmental factors to which HSPCs with specific mutations may respond with superior fitness.
Difficulty producing intelligible speech is a common and debilitating symptom of Parkinson’s disease (PD). Yet, both the robust evaluation of speech impairments and the identification of the affected brain systems are challenging. We examine the spectral and spatial definitions of the functional neuropathology underlying reduced speech quality in patients with PD using a new approach to characterize speech impairments and a novel brain-imaging marker. We found that the interactive scoring of speech impairments in PD (N=59) is reliable across non-expert raters, and better related to the hallmark motor and cognitive impairments of PD than automatically-extracted acoustical features. By relating these speech impairment ratings to neurophysiological deviations from healthy adults (N=65), we show that articulation impairments in patients with PD are robustly predicted from aberrant activity in the left inferior frontal cortex, and that functional connectivity of this region with somatomotor cortices mediates the influence of cognitive decline on speech deficits.
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ∼70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
Some pitfalls of measuring representational similarity using Representational Similarity Analysis
(2022)
A core challenge in cognitive and brain sciences is to assess whether different biological systems represent the world in a similar manner. Representational Similarity Analysis (RSA) is an innovative approach that addresses this problem by looking for a second-order isomorphisim in neural activation patterns. This innovation makes it easy to compare latent representations across individuals, species and computational models, and accounts for its popularity across disciplines ranging from artificial intelligence to computational neuroscience. Despite these successes, using RSA has led to difficult-to-reconcile and contradictory findings, particularly when comparing primate visual representations with deep neural networks (DNNs): even though DNNs have been shown to learn and behave in vastly different ways to humans, comparisons based on RSA have shown striking similarities in some studies. Here, we demonstrate some pitfalls of using RSA and explain how contradictory findings can arise due to false inferences about representational similarity based on RSA-scores. In a series of studies that capture increasingly plausible training and testing scenarios, we compare neural representations in computational models, primate cortex and human cortex. These studies reveal two problematic phenomena that are ubiquitous in current research: a “mimic effect”, where confounds in stimuli can lead to high RSA-scores between provably dissimilar systems, and a “modulation effect”, where RSA-scores become dependent on stimuli used for testing. Since our results bear on a number of influential findings, such as comparisons made between human visual representations and those of primates and DNNs, we provide recommendations to avoid these pitfalls and sketch a way forward to a more solid science of representation in cognitive systems.
The pitfalls of measuring representational similarity using representational similarity analysis
(2022)
A core challenge in cognitive and brain sciences is to assess whether different biological systems represent the world in a similar manner. Representational Similarity Analysis (RSA) is an innovative approach to address this problem and has become increasingly popular across disciplines ranging from artificial intelligence to computational neuroscience. Despite these successes, RSA regularly uncovers difficult-to-reconcile and contradictory findings. Here, we demonstrate the pitfalls of using RSA and explain how contradictory findings arise due to false inferences about representational similarity based on RSA-scores. In a series of studies that capture increasingly plausible training and testing scenarios, we compare neural representations in computational models, primate cortex and human cortex. These studies reveal two problematic phenomena that are ubiquitous in current research: a “mimic” effect, where confounds in stimuli can lead to high RSA-scores between provably dissimilar systems, and a “modulation effect”, where RSA-scores become dependent on stimuli used for testing. Since our results bear on a number of influential findings and the inferences drawn by current practitioners in a wide range of disciplines, we provide recommendations to avoid these pitfalls and sketch a way forward to a more solid science of representation in cognitive systems.
The pitfalls of measuring representational similarity using representational similarity analysis
(2022)
A core challenge in neuroscience is to assess whether diverse systems represent the world similarly. Representational Similarity Analysis (RSA) is an innovative approach to address this problem and has become increasingly popular across disciplines from machine learning to computational neuroscience. Despite these successes, RSA regularly uncovers difficult-to-reconcile and contradictory findings. Here we demonstrate the pitfalls of using RSA to infer representational similarity and explain how contradictory findings arise and support false inferences when left unchecked. By comparing neural representations in primate, human and computational models, we reveal two problematic phenomena that are ubiquitous in current research: a “mimic” effect, where confounds in stimuli can lead to high RSA scores between provably dissimilar systems, and a “modulation effect”, where RSA-scores become dependent on stimuli used for testing. Since our results bear on existing findings and inferences, we provide recommendations to avoid these pitfalls and sketch a way forward.
Objects that are congruent with a scene are recognised more efficiently than objects that are incongruent. Further, semantic integration of incongruent objects elicits a stronger N300/N400 EEG component. Yet, the time course and mechanisms of how contextual information supports access to semantic object information is unclear. We used computational modelling and EEG to test how context influences semantic object processing. Using representational similarity analysis, we established that EEG patterns dissociated between objects in congruent or incongruent scenes from around 300 ms. By modelling semantic processing of objects using independently normed properties, we confirm that the onset of semantic processing of both congruent and incongruent objects is similar (∼150 ms). Critically, after ∼275 ms, we discover a difference in the duration of semantic integration, lasting longer for incongruent compared to congruent objects. These results constrain our understanding of how contextual information supports access to semantic object information.
Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unknown fungal taxa. We used a Global Soil Mycobiome consortium dataset to test relative performance of various sequencing depth standardization methods (calculation of residuals, exclusion of singletons, traditional and SRS rarefaction, use of Shannon index of diversity) to find optimal protocols for statistical analyses. Altogether, we used six global surveys to infer these patterns for soil-inhabiting fungi and their functional groups. We found that residuals of log-transformed richness (including singletons) against log-transformed sequencing depth yields significantly better model estimates compared with most other standardization methods. With respect to global patterns, fungal functional groups differed in the patterns of diversity, endemicity and vulnerability to main global change predictors. Unlike α-diversity, endemicity and global-change vulnerability of fungi and most functional groups were greatest in the tropics. Fungi are vulnerable mostly to drought, heat, and land cover change. Fungal conservation areas of highest priority include wetlands and moist tropical ecosystems.
The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing, and as part of protein complexes with chromatin-modifying enzymes. SAFB proteins are approximately-100-kDa-sized dual nucleic acid-binding proteins with dedicated domains in an otherwise largely unstructured context, but whether and how they discriminate DNA- and RNA-binding has remained enigmatic. We here provide the SAFB2 DNA- and RNA-binding SAP and RRM domains in their functional boundaries and use solution NMR spectroscopy to ascribe DNA- and RNA-binding functions. We give insight into their target nucleic acid preferences and map the interfaces with respective nucleic acids on sparse data-derived SAP and RRM domain structures. Further, we provide evidence that the SAP domain exhibits intra-domain dynamics and a potential tendency to dimerise, which may expand its specifically targeted DNA sequence range. Our data provide a first molecular basis of and a starting point towards deciphering DNA- and RNA-binding functions of SAFB2 on the molecular level and serve a basis for understanding its localization to specific regions of chromatin and its involvement in the processing of specific RNA species.
The heterotetrameric human transfer RNA (tRNA) splicing endonuclease (TSEN) catalyzes the excision of intronic sequences from precursor tRNAs (pre-tRNAs)1. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH)2–8. The three-dimensional (3D) assembly of TSEN/CLP1, the mechanism of substrate recognition, and the molecular details of PCH-associated mutations are not fully understood. Here, we present cryo-electron microscopy structures of human TSEN with intron-containing pre-tRNATyrgta and pre-tRNAArgtct. TSEN exhibits broad structural homology to archaeal endonucleases9 but has evolved additional regulatory elements that are involved in handling and positioning substrate RNA. Essential catalytic residues of subunit TSEN34 are organized for the 3’ splice site which emerges from a bulge-helix configuration. The triple-nucleotide bulge at the intron/3’-exon boundary is stabilized by an arginine tweezer motif of TSEN2 and an interaction with the proximal minor groove of the helix. TSEN34 and TSEN54 define the 3’ splice site by holding the tRNA body in place. TSEN54 adapts a bipartite fold with a flexible central region required for CLP1 binding. PCH-associated mutations are located far from pre-tRNA binding interfaces explaining their negative impact on structural integrity of TSEN without abrogating its catalytic activity in vitro10. Our work defines the molecular framework of pre-tRNA recognition and cleavage by TSEN and provides a structural basis to better understand PCH in the future.
Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. Omicron sub-variants BA.4/5 have spread globally displacing the predeceasing variants. Due to the severe transmissibility and immune escape potential of BA.4/5, early monitoring was required to asses and implement countermeasures in time.
In this study, we monitored the prevalence of SARS-CoV-2 BA.4/5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North-Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability to detect BA.4/5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022 and the presence of BA.4/5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V. Finally, the mutant fractions were quantitatively monitored by digital PCR confirming BA.4/5 as the majority variant by 5th June 2022.
In conclusions, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variant spreading independent of individual test capacities.
Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. Omicron sub-variants BA.4/5 have spread globally displacing the predeceasing variants. Due to the severe transmissibility and immune escape potential of BA.4/5, early monitoring was required to asses and implement countermeasures in time.
In this study, we monitored the prevalence of SARS-CoV-2 BA.4/5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North-Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability to detect BA.4/5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022 and the presence of BA.4/5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V. Finally, the mutant fractions were quantitatively monitored by digital PCR confirming BA.4/5 as the majority variant by 5th June 2022.
In conclusions, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variant spreading independent of individual test capacities.
Background Overweight and decreased physical fitness are highly prevalent in schizophrenia, represent a major risk factor for cardio-vascular diseases and decrease the patients’ life expectancies. It is thus important to understand the underlying mechanisms that link psychopathology and weight gain. We hypothesize that the dopaminergic reward system plays an important role in this.
Methods: We analyzed the seed-based functional connectivity (FC) of the ventral tegmental area (VTA) in a group of schizophrenic patients (n = 32) and age- as well as gender matched healthy controls (n = 27). We then correlated the resting-state results with physical fitness parameters, obtained in a fitness test, and psychopathology.
Results: The seed-based connectivity analysis revealed decreased functional connections between the VTA and the anterior cingulate cortex (ACC), as well as the dorsolateral prefrontal cortex and increased functional connectivity between the VTA and the middle temporal gyrus in patients compared to healthy controls. The decreased FC between the VTA and the ACC of the patient group could further be associated with increased body fat and negatively correlated with the overall physical fitness. We found no significant correlations with psychopathology.
Conclusion: Although we did not find significant correlations with psychopathology, we could link decreased physical fitness and high body fat with dysconnectivity between the VTA and the ACC in schizophrenia. These findings demonstrate that a dysregulated reward system is not just responsible for symptomatology in schizophrenia but is also involved in comorbidities and could pave the way for future lifestyle therapy interventions.
The antiviral drugs tecovirimat, brincidofovir, and cidofovir are considered for mpox (monkeypox) treatment despite a lack of clinical evidence. Moreover, their use is affected by toxic side-effects (brincidofovir, cidofovir), limited availability (tecovirimat), and potentially by resistance formation. Hence, additional, readily available drugs are needed. Here, therapeutic concentrations of nitroxoline, a hydroxyquinoline antibiotic with a favourable safety profile in humans, inhibited the replication of 12 mpox virus isolates from the current outbreak in primary cultures of human keratinocytes and fibroblasts and a skin explant model by interference with host cell signalling. Tecovirimat, but not nitroxoline, treatment resulted in rapid resistance development. Nitroxoline remained effective against the tecovirimat-resistant strain and increased the anti-mpox virus activity of tecovirimat and brincidofovir. Moreover, nitroxoline inhibited bacterial and viral pathogens that are often co-transmitted with mpox. In conclusion, nitroxoline is a repurposing candidate for the treatment of mpox due to both antiviral and antimicrobial activity.
Our lives (and deaths) have by now been dominated for two years by COVID-19, a pandemic that has caused hundreds of millions of disease cases, millions of deaths, trillions in economic costs, and major restrictions on our freedom. Here we suggest a novel tool for controlling the COVID-19 pandemic. The key element is a method for a population-scale PCR-based testing, applied on a systematic and repeated basis. For this we have developed a low cost, highly sensitive virus-genome-based test. Using Germany as an example, we demonstrate by using a mathematical model, how useful this strategy could have been in controlling the pandemic. We show using real-world examples how this might be implemented on a mass scale and discuss the feasibility of this approach.
HER2 belongs to the ErbB sub-family of receptor tyrosine kinases and regulates cellular proliferation and growth. Different from other ErbB receptors, HER2 has no known ligand. Activation occurs through heterodimerization with other ErbB receptors and their cognate ligands. This suggests several possible activation paths of HER2 with ligand-specific, differential response, which so far remained unexplored. Using single-molecule tracking and the diffusion profile of HER2 as a proxy for activity, we measured the activation strength and temporal profile in live cells. We found that HER2 is strongly activated by EGFR-targeting ligands EGF and TGFα, yet with a distinguishable temporal fingerprint. The HER4-targeting ligands EREG and NRGβ1 showed weaker activation of HER2, a preference for EREG and a delayed response to NRGβ1. Our results indicate a selective ligand response of HER2 that may serve as a regulatory element. Our experimental approach is easily transferable to other membrane receptors targeted by multiple ligands.
Highlights
HER2 exhibits heterogeneous motion in the plasma membrane
The fraction of immobile HER2 correlates with phosphorylation levels
Diffusion properties serve as proxies for HER2 activation
HER2 exhibits ligand-specific activation strength and temporal profiles
The most basic behavioural states of animals can be described as active or passive. However, while high-resolution observations of activity patterns can provide insights into the ecology of animal species, few methods are able to measure the activity of individuals of small taxa in their natural environment. We present a novel approach in which the automated VHF radio-tracking of small vertebrates fitted with lightweight transmitters (< 0.2 g) is used to distinguish between active and passive behavioural states.
A dataset containing > 3 million VHF signals was used to train and test a random forest model in the assignment of either active or passive behaviour to individuals from two forest-dwelling bat species (Myotis bechsteinii (n = 50) and Nyctalus leisleri (n = 20)). The applicability of the model to other taxonomic groups was demonstrated by recording and classifying the behaviour of a tagged bird and by simulating the effect of different types of vertebrate activity with the help of humans carrying transmitters. The random forest model successfully classified the activity states of bats as well as those of birds and humans, although the latter were not included in model training (F-score 0.96–0.98).
The utility of the model in tackling ecologically relevant questions was demonstrated in a study of the differences in the daily activity patterns of the two bat species. The analysis showed a pronounced bimodal activity distribution of N. leisleri over the course of the night while the night-time activity of M. bechsteinii was relatively constant. These results show that significant differences in the timing of species activity according to ecological preferences or seasonality can be distinguished using our method.
Our approach enables the assignment of VHF signal patterns to fundamental behavioural states with high precision and is applicable to different terrestrial and flying vertebrates. To encourage the broader use of our radio-tracking method, we provide the trained random forest models together with an R-package that includes all necessary data-processing functionalities. In combination with state-of-the-art open-source automated radio-tracking, this toolset can be used by the scientific community to investigate the activity patterns of small vertebrates with high temporal resolution, even in dense vegetation.