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We report on the first measurements of J/ψ production at very low transverse momentum (pT< 0.2 GeV/c) in hadronic Au+Au collisions at √sNN = 200 GeV and U+U collisions at √sNN = 193 GeV. Remarkably, the inferred nuclear modification factor of J/ψ at mid-rapidity in Au+Au (U+U) collisions reaches about 24 (52) for pT< 0.05 GeV/c in the 60-80% collision centrality class. This noteworthy enhancement cannot be explained by hadronic production accompanied by cold and hot medium effects. In addition, the dN/dt distribution of J/ψ for the very low pT range is presented for the first time. The distribution is consistent with that expected from the Au nucleus and shows a hint of interference. Comparison of the measurements to theoretical calculations of coherent production shows that the excess yield can be described reasonably well and reveals a partial disruption of coherent production in semi-central collisions, perhaps due to the violent hadronic interactions. Incorporating theoretical calculations, the results strongly suggest that the dramatic enhancement of J/ψ yield observed at extremely low pT originates from coherent photon-nucleus interactions. In particular, coherently produced J/ψ's in violent hadronic collisions may provide a novel probe of the quark-gluon-plasma.
Wilhelm Hoegner, 1887–1980
(2022)
Marie Holzman : Manuskripte
(2020)
We present measurements of the differential cross sections of inclusive J/ψ meson production as a function of transverse momentum (pJ/ψT) using the μ+μ− and e+e− decay channels in proton+proton collisions at center-of-mass energies of 510 and 500 GeV, respectively, recorded by the STAR detector at the Relativistic Heavy Ion Collider. The measurement from the μ+μ− channel is for 0 <pJ/ψT< 9 GeV/c and rapidity range |yJ/ψ|< 0.4, and that from the e+e− channel is for 4 <pJ/ψT< 20 GeV/c and |yJ/ψ|< 1.0. The ψ(2S) to J/ψ ratio is also measured for 4 <pmesonT< 12 GeV/c through the e+e− decay channel. Model calculations, which incorporate different approaches toward the J/ψ production mechanism, are compared with experimental results and show reasonable agreement within uncertainties.
We report the differential yields at mid-rapidity of the Breit-Wheeler process (γγ→e+e−) in peripheral Au+Au collisions at sNN−−−√= 54.4 GeV and 200 GeV with the STAR experiment at RHIC, as a function of energy sNN−−−√, e+e− transverse momentum pT, p2T, invariant mass Mee and azimuthal angle. In the invariant mass range of 0.4 < Mee < 2.6 GeV/c2 at low transverse momentum (pT <0.15 GeV/c), the yields increase while the pair ⟨p2T⟩−−−−√ decreases with increasing sNN−−−√, a feature is correctly predicted by the QED calculation. The energy dependencies of the measured quantities are sensitive to the nuclear form factor, infrared divergence and photon polarization. The data are compiled and used to extract the charge radius of the Au nucleus.
We report multi-differential measurements of strange hadron production ranging from mid- to target-rapidity in Au+Au collisions at a center-of-momentum energy per nucleon pair of sNN−−−√=3 GeV with the STAR experiment at RHIC. K0S meson and Λ hyperon yields are measured via their weak decay channels. Collision centrality and rapidity dependences of the transverse momentum spectra and particle ratios are presented. Particle mass and centrality dependence of the average transverse momenta of Λ and K0S are compared with other strange particles, providing evidence of the development of hadronic rescattering in such collisions. The 4π yields of each of these strange hadrons show a consistent centrality dependence. Discussions on radial flow, the strange hadron production mechanism, and properties of the medium created in such collisions are presented together with results from hadronic transport and thermal model calculations.
A comprehensive checklist and host plants of Aphididae (Aphidomorpha: Hemiptera) from Pakistan
(2024)
The family Aphididae (Hemiptera) represents one of the most diverse groups of sap-sucking insect pests referred to as aphids or plant-lice, with 366 species reported in Pakistan, associated with wide array of agricultural and horticultural crops, including fruit and forest trees, weeds, grasses, shrubs, and vines. This work aims to provide an updated checklist of aphids and their associated host plants documented across various regions of Pakistan. The checklist consolidates information from various published literature sources, including annotated checklists, regional distribution data, and host plant records from Pakistan. In this study, we present an annotated checklist of 366 aphid species, belonging to 134 genera and 11 subfamilies, associated with a total of 359 host plant species stretched over 84 families in Pakistan.
We report the beam energy and collision centrality dependence of fifth and sixth order cumulants (C5, C6) and factorial cumulants (κ5, κ6) of net-proton and proton distributions, from sNN−−−−√=3−200 GeV Au+Au collisions at RHIC. The net-proton cumulant ratios generally follow the hierarchy expected from QCD thermodynamics, except for the case of collisions at sNN−−−−√ = 3 GeV. C6/C2 for 0-40\% centrality collisions is increasingly negative with decreasing sNN−−−−√, while it is positive for the lowest sNN−−−−√ studied. These observed negative signs are consistent with QCD calculations (at baryon chemical potential, μB≤ 110 MeV) that include a crossover quark-hadron transition. In addition, for sNN−−−−√≥ 11.5 GeV, the measured proton κn, within uncertainties, does not support the two-component shape of proton distributions that would be expected from a first-order phase transition. Taken in combination, the hyper-order proton number fluctuations suggest that the structure of QCD matter at high baryon density, μB∼750 MeV (sNN−−−−√ = 3 GeV) is starkly different from those at vanishing μB∼20MeV (sNN−−−−√ = 200 GeV and higher).
We report the beam energy and collision centrality dependence of fifth and sixth order cumulants (C5, C6) and factorial cumulants (κ5, κ6) of net-proton and proton distributions, from sNN−−−−√=3−200 GeV Au+Au collisions at RHIC. The net-proton cumulant ratios generally follow the hierarchy expected from QCD thermodynamics, except for the case of collisions at sNN−−−−√ = 3 GeV. C6/C2 for 0-40\% centrality collisions is increasingly negative with decreasing sNN−−−−√, while it is positive for the lowest sNN−−−−√ studied. These observed negative signs are consistent with QCD calculations (at baryon chemical potential, μB≤ 110 MeV) that include a crossover quark-hadron transition. In addition, for sNN−−−−√≥ 11.5 GeV, the measured proton κn, within uncertainties, does not support the two-component shape of proton distributions that would be expected from a first-order phase transition. Taken in combination, the hyper-order proton number fluctuations suggest that the structure of QCD matter at high baryon density, μB∼750 MeV (sNN−−−−√ = 3 GeV) is starkly different from those at vanishing μB∼20MeV (sNN−−−−√ = 200 GeV and higher).
Production of protons and light nuclei in Au+Au collisions at √sNN = 3 GeV with the STAR detector
(2023)
We report the systematic measurement of protons and light nuclei production in Au+Au collisions at √sNN = 3 GeV by the STAR experiment at the Relativistic Heavy Ion Collider (RHIC). The transverse momentum (pT) spectra of protons (p), deuterons (d), tritons (t), 3He, and 4He are measured from mid-rapidity to target rapidity for different collision centralities. We present the rapidity and centrality dependence of particle yields (dN/dy), average transverse momentum (⟨pT⟩), yield ratios (d/p, t/p,3He/p, 4He/p), as well as the coalescence parameters (B2, B3). The 4π yields for various particles are determined by utilizing the measured rapidity distributions, dN/dy. Furthermore, we present the energy, centrality, and rapidity dependence of the compound yield ratios (Np×Nt/N2d) and compare them with various model calculations. The physics implications of those results on the production mechanism of light nuclei and on QCD phase structure are discussed.
We report on the charged-particle multiplicity dependence of net-proton cumulant ratios up to sixth order from √s = 200 GeV p+p collisions at the Relativistic Heavy Ion Collider (RHIC). The measured ratios C4/C2, C5/C1, and C6/C2 decrease with increased charged-particle multiplicity and rapidity acceptance. Neither the Skellam baselines nor PYTHIA8 calculations account for the observed multiplicity dependence. In addition, the ratios C5/C1 and C6/C2 approach negative values in the highest-multiplicity events. The negative ratios in the most central p+p collisions at 200 GeV, similar to those observed in central Au+Au 200 GeV collisions, imply the formation of thermalized QCD matter.
Jet-hadron correlations with respect to the event plane in √sNN = 200 GeV Au+Au collisions in STAR
(2024)
Angular distributions of charged particles relative to jet axes are studied in sNN−−−√ = 200 GeV Au+Au collisions as a function of the jet orientation with respect to the event plane. This differential study tests the expected path-length dependence of energy loss experienced by a hard-scattered parton as it traverses the hot and dense medium formed in heavy-ion collisions. A second-order event plane is used in the analysis as an experimental estimate of the reaction plane formed by the collision impact parameter and the beam direction. Charged-particle jets with 15<pT,jet< 20 and 20<pT,jet< 40 GeV/c were reconstructed with the anti-kT algorithm with radius parameter setting of (R=0.4) in the 20-50\% centrality bin to maximize the initial-state eccentricity of the interaction region. The reaction plane fit method is implemented to remove the flow-modulated background with better precision than prior methods. Yields and widths of jet-associated charged-hadron distributions are extracted in three angular bins between the jet axis and the event plane. The event-plane (EP) dependence is further quantified by ratios of the associated yields in different EP bins. No dependence on orientation of the jet axis with respect to the event plane is seen within the uncertainties in the kinematic regime studied. This finding is consistent with a similar experimental observation by ALICE in sNN−−−√ = 2.76 TeV Pb+Pb collision data.
Jet-hadron correlations with respect to the event plane in √sNN = 200 GeV Au+Au collisions in STAR
(2023)
Angular distributions of charged particles relative to jet axes are studied in sNN−−−√ = 200 GeV Au+Au collisions as a function of the jet orientation with respect to the event plane.This differential study tests the expected path-length dependence of energy loss experienced by a hard-scattered parton as it traverses the hot and dense medium formed in heavy-ion collisions.A second-order event plane is used in the analysis as an experimental estimate of the reaction plane formed by the collision impact parameter and the beam direction. Charged-particle jets with 15<pT,jet< 20 and 20<pT,jet< 40 GeV/c were reconstructed with the anti-kT algorithm with radius parameter setting of \(R=0.4\) in the 20-50\% centrality bin to maximize the initial-state eccentricity of the interaction region. The reaction plane fit method is implemented to remove the flow-modulated background with better precision than prior methods. Yields and widths of jet-associated charged-hadron distributions are extracted in three angular bins between the jet axis and the event plane. The event-plane (EP) dependence is further quantified by ratios of the associated yields in different EP bins. No dependence on orientation of the jet axis with respect to the event plane is seen within the uncertainties in the kinematic regime studied. This finding is consistent with a similar experimental observation by ALICE in sNN−−−√ = 2.76 TeV Pb-Pb collision data.
Jet-hadron correlations with respect to the event plane in √sNN = 200 GeV Au+Au collisions in STAR
(2023)
Angular distributions of charged particles relative to jet axes are studied in sNN−−−√ = 200 GeV Au+Au collisions as a function of the jet orientation with respect to the event plane. This differential study tests the expected path-length dependence of energy loss experienced by a hard-scattered parton as it traverses the hot and dense medium formed in heavy-ion collisions. A second-order event plane is used in the analysis as an experimental estimate of the reaction plane formed by the collision impact parameter and the beam direction. Charged-particle jets with 15<pT,jet< 20 and 20<pT,jet< 40 GeV/c were reconstructed with the anti-kT algorithm with radius parameter setting of \(R=0.4\) in the 20-50\% centrality bin to maximize the initial-state eccentricity of the interaction region. The reaction plane fit method is implemented to remove the flow-modulated background with better precision than prior methods. Yields and widths of jet-associated charged-hadron distributions are extracted in three angular bins between the jet axis and the event plane. The event-plane (EP) dependence is further quantified by ratios of the associated yields in different EP bins. No dependence on orientation of the jet axis with respect to the event plane is seen within the uncertainties in the kinematic regime studied. This finding is consistent with a similar experimental observation by ALICE in sNN−−−√ = 2.76 TeV Pb+Pb collision data.
Jet-hadron correlations with respect to the event plane in √sNN = 200 GeV Au+Au collisions in STAR
(2024)
Angular distributions of charged particles relative to jet axes are studied in sNN−−−√ = 200 GeV Au+Au collisions as a function of the jet orientation with respect to the event plane. This differential study tests the expected path-length dependence of energy loss experienced by a hard-scattered parton as it traverses the hot and dense medium formed in heavy-ion collisions. A second-order event plane is used in the analysis as an experimental estimate of the reaction plane formed by the collision impact parameter and the beam direction. Charged-particle jets with 15<pT,jet< 20 and 20<pT,jet< 40 GeV/c were reconstructed with the anti-kT algorithm with radius parameter setting of (R=0.4) in the 20-50\% centrality bin to maximize the initial-state eccentricity of the interaction region. The reaction plane fit method is implemented to remove the flow-modulated background with better precision than prior methods. Yields and widths of jet-associated charged-hadron distributions are extracted in three angular bins between the jet axis and the event plane. The event-plane (EP) dependence is further quantified by ratios of the associated yields in different EP bins. No dependence on orientation of the jet axis with respect to the event plane is seen within the uncertainties in the kinematic regime studied. This finding is consistent with a similar experimental observation by ALICE in sNN−−−√ = 2.76 TeV Pb+Pb collision data.
The first evaluation of an ultra-high granularity digital electromagnetic calorimeter prototype using 1.0–5.8 GeV/c electrons is presented. The 25 × 106 pixel detector consists of 24 layers of ALPIDE CMOS MAPS sensors, with a pitch of around 30 μm, and has a depth of almost 20 radiation lengths of tungsten absorber. Ultra-thin cables allow for a very compact design. The properties that are critical for physics studies are measured: electromagnetic shower response, energy resolution and linearity. The stochastic energy resolution is comparable with the state-of-the art resolution for a Si-W calorimeter, with data described well by a simulation model using Geant4 and Allpix2. The performance achieved makes this technology a good candidate for use in the ALICE FoCal upgrade, and in general demonstrates the strong potential for future applications in high-energy physics.
The first evaluation of an ultra-high granularity digital electromagnetic calorimeter prototype using 1.0-5.8 GeV/c electrons is presented. The 25×106 pixel detector consists of 24 layers of ALPIDE CMOS MAPS sensors, with a pitch of around 30~μm, and has a depth of almost 20 radiation lengths of tungsten absorber. Ultra-thin cables allow for a very compact design. The properties that are critical for physics studies are measured: electromagnetic shower response, energy resolution and linearity. The stochastic energy resolution is comparable with the state-of-the art resolution for a Si-W calorimeter, with data described well by a simulation model using GEANT and Allpix2. The performance achieved makes this technology a good candidate for use in the ALICE FoCal upgrade, and in general demonstrates the strong potential for future applications in high-energy physics.
The evolution of cell-free protein synthesis (CFPS) over recent decades has made it a widely used system for expressing membrane proteins (MPs). Unlike traditional methods, CFPS allows direct and translocon-independent expression of MPs within lipid membranes, such as liposomes or nanodiscs (NDs), without the need for detergent solubilization. This open nature of CF systems enables customization of the experimental environment, including expression conditions, choice of nanoparticles (NPs), lipid composition, and addition of stabilizing molecules.
Membrane scaffold protein (MSP)-based NDs emerged as a gold standard for cotranslational solubilization of MPs using the CF-system. This approach allowed not only biochemical characterization, but also structural studies of MPs and even GPCRs. However, to solubilize MPs inside nanoparticles via the traditional reconstitution route, apart from MSPs other scaffolds were successfully implemented, e.g. the saposin A (commercially known as Salipro) scaffold system or the synthetic styrene maleic acid lipid particles (SMALPs). In this study the potential of saposin A-based nanoparticles (SapNPs) was explored for cotranslational MP solubilization.
Three strategies for applying SapNPs in CF systems were investigated: preassembly, (i) coassembly (ii), and coexpression (iii). (i) Preassembly involved forming SapNPs before CF expression and adding them to the CF reaction. In coassembly mode SapA and lipids were mixed in the CF reaction for spontaneous assembly with the synthesized MP. In coexpression mode lipids were added to the CF reaction while coexpressing SapA with the MP target. Proteorhodopsin (PR) served as a model protein to evaluate these strategies due to its ability to oligomerize and straightforward quantification using the cofactor retinal. Preassembled SapNPs provided homogeneous, aggregate-free particles yielding up to 200 µM solubilized PR inside in the CF reaction. Coassembly was also successfully applied to produce PR/SapNP complexes at slightly lower yields, however the system was prone to produce soluble aggregates at too high PR template concentrations and overall needed more adjustments. Coexpression resulted in PR yields below 20 µM and was not considered viable for MP production. Finally, the preassembled SapNPs were used to produce functional G-protein coupled receptor probes. Despite lower overall performance compared to MSP-based systems, SapNPs showed potential as an alternative in CF systems for specific MPs.
The second optimization approach was directed at the CF lysate itself. CF synthesis for NMR analysis benefits from selective labeling schemes enabled by truncated amino acid (AA) metabolic pathways in lysates, reducing spectral ambiguity. However, residual enzymatic AA conversions persist, leading to label dilution and ambiguous NMR spectra. This study aimed to eliminate these residual activities in the E. coli A19 strain, generating optimized CF lysates for NMR applications.
The approach involved cumulative gene deletions of the most problematic scrambling enzymes. The new strain, “Stablelabel,” included deletions and modifications in genes asnA, ansA, ansB, glnA, aspC, and ilvE, effectively eliminating background activities of L-Asn, L-Asp, and conversions of L-Glu to L-Asp and L-Gln. However, residual conversion of L-Gln to L-Glu persisted due to glutaminase activity of several glutaminases using the inhibitor 6 diazo-5-oxo-L-norleucine (DON). Stablelabel showed a slightly slower growth than A19, and an overall good performance with 2.7 mg/mL GFP expressed in the reaction mixture (RM) compared to the parental A19 strain with 3.5 mg/mL. Furthermore, the strain was successfully applied to demonstrate methyl group labeling of MPs using preconverted L-val and L-leu from their respective precursors 2-ketoisovalerate and 4-methyl-2-oxovalerate.
In this study, lipid nanoparticle particle-and strain engineering vividly demonstrated the potential of CFPS systems and their versatility. While the SapNP system requires further engineering to potentially reach the efficiency of the well-studied MSP NDs, this study provides an example of nanoparticle characterization allowing new insights into NP behavior in CF systems. Furthermore, it was shown that strain engineering is a straightforward solution to tailor CF lysates to the individual requirements. After this thesis was submitted, Stablelabel in fact was successfully applied for backbone assignment of casein kinase 1, thereby demonstrating its suitability to express complex targets for NMR studies.
A prototype of a new type of calorimeter has been designed and constructed, based on a silicon-tungsten sampling design using pixel sensors with digital readout. It makes use of the Alpide MAPS sensor developed for the ALICE ITS upgrade. A binary readout is possible due to the pixel size of ≈30×30μm2. This prototype has been successfully tested with cosmic muons and with test beams at DESY and the CERN SPS. We report on performance results obtained at DESY, showing good energy resolution and linearity, and compare to detailed MC simulations. Also shown are preliminary results of the high-energy performance as measured at the SPS. The two-shower separation capabilities are discussed.
Using (10087±44)×106 J/ψ events collected with the BESIII detector, numerous Ξ− and Λ decay asymmetry parameters are simultaneously determined from the process J/ψ→Ξ−Ξ¯+→Λ(pπ−)π−Λ¯(n¯π0)π+ and its charge-conjugate channel. The precisions of α0 for Λ→nπ0 and α¯0 for Λ¯→n¯π0 compared to world averages are improved by factors of 4 and 1.7, respectively. The ratio of decay asymmetry parameters of Λ→nπ0 to that of Λ→pπ−, ⟨α0⟩/⟨αΛ−⟩, is determined to be 0.873±0.012+0.011−0.010, where the first and the second uncertainties are statistical and systematic, respectively. The ratio is smaller than unity more than 5σ, which signifies the existence of the ΔI=3/2 transition in Λ for the first time. Beside, we test for CP violation in Ξ−→Λπ− and in Λ→nπ0 with the best precision to date.
Using (10087±44)×106 J/ψ events collected with the BESIII detector, numerous Ξ− and Λ decay asymmetry parameters are simultaneously determined from the process J/ψ→Ξ−Ξ¯+→Λ(pπ−)π−Λ¯(n¯π0)π+ and its charge-conjugate channel. The precisions of α0 for Λ→nπ0 and α¯0 for Λ¯→n¯π0 compared to world averages are improved by factors of 4 and 1.7, respectively. The ratio of decay asymmetry parameters of Λ→nπ0 to that of Λ→pπ−, ⟨α0⟩/⟨αΛ−⟩, is determined to be 0.873±0.012+0.011−0.010, where the first and the second uncertainties are statistical and systematic, respectively. The ratio is smaller than unity, which is predicted by the ΔI=1/2 rule, with a statistical significance of more than 5σ. We test for CP violation in Ξ−→Λπ− and in Λ→nπ0 with the best precision to date.
Using (10087±44)×106 J/ψ events collected with the BESIII detector, numerous Ξ− and Λ decay asymmetry parameters are simultaneously determined from the process J/ψ→Ξ−Ξ¯+→Λ(pπ−)π−Λ¯(n¯π0)π+ and its charge-conjugate channel. The precisions of α0 for Λ→nπ0 and α¯0 for Λ¯→n¯π0 compared to world averages are improved by factors of 4 and 1.7, respectively. The ratio of decay asymmetry parameters of Λ→nπ0 to that of Λ→pπ−, ⟨α0⟩/⟨αΛ−⟩, is determined to be 0.873±0.012+0.011−0.010, where the first and the second uncertainties are statistical and systematic, respectively. The ratio is smaller than unity more than 5σ, which signifies the existence of the ΔI=3/2 transition in Λ for the first time. Beside, we test for CP violation in Ξ−→Λπ− and in Λ→nπ0 with the best precision to date.
By analyzing e+e− annihilation da ta corresponding to an integrated luminosity of 2.93 fb−1 collected at a center-of-mass energy of 3.773 GeV with the \text{BESIII} detector, the first observation of the semileptonic decays D0→K0Sπ−π0e+νe and D+→K0Sπ+π−e+νe is reported. With a dominant hadronic contribution from K1(1270), the branching fractions are measured to be B(D0→K1(1270)−(→K0Sπ−π0)e+νe) = (1.69+0.53−0.46±0.15)×10−4 and B(D+→K¯1(1270)0(→K0Sπ+π−)e+νe) = (1.47+0.45−0.40±0.20)×10−4 with statistical significance of 5.4σ and 5.6σ, respectively. When combined with measurements of the K1(1270)→K+π−π decays, the absolute branching fractions are determined to be B(D0→K1(1270)−e+νe) = (1.05+0.33−0.28±0.12±0.12)×10−3 and B(D+→K¯1(1270)0e+νe) = (1.29+0.40−0.35±0.18±0.15)×10−3. The first and second uncertainties are statistical and systematic, respectively, and the third uncertainties originate from the assumed branching fractions of the K1(1270)→Kππ decays.
Using e+e− collision data, corresponding to an integrated luminosity of 892pb−1 collected at center-of-mass energies from 4.84 to 4.95\,GeV with the BESIII detector, we search for the process e+e−→K+K−ψ(3770) by reconstructing two charged kaons and one D meson from ψ(3770). No significant signal of e+e−→K+K−ψ(3770) is found and the upper limits of the Born cross sections are reported at 90\% confidence level.
Using e+e− collision data, corresponding to an integrated luminosity of 892pb−1 collected at center-of-mass energies from 4.84 to 4.95\,GeV with the BESIII detector, we search for the process e+e−→K+K−ψ(3770) by reconstructing two charged kaons and one D meson from ψ(3770). No significant signal of e+e−→K+K−ψ(3770) is found and the upper limits of the Born cross sections are reported at 90\% confidence level.
Using a sample of 448.1×106 ψ(2S) events collected with the BESIII detector, we perform a study of the decay J/ψ→K+K− via ψ(2S)→π+π−J/ψ.
The branching fraction of J/ψ→K+K− is determined to be BK+K−=(3.072±0.023(stat.)±0.050(syst.))×10−4, which is consistent with previous measurements but with significantly improved precision.
Understanding how epigenetic variation in non-coding regions is involved in distal gene-expression regulation is an important problem. Regulatory regions can be associated to genes using large-scale datasets of epigenetic and expression data. However, for regions of complex epigenomic signals and enhancers that regulate many genes, it is difficult to understand these associations. We present StitchIt, an approach to dissect epigenetic variation in a gene-specific manner for the detection of regulatory elements (REMs) without relying on peak calls in individual samples. StitchIt segments epigenetic signal tracks over many samples to generate the location and the target genes of a REM simultaneously. We show that this approach leads to a more accurate and refined REM detection compared to standard methods even on heterogeneous datasets, which are challenging to model. Also, StitchIt REMs are highly enriched in experimentally determined chromatin interactions and expression quantitative trait loci. We validated several newly predicted REMs using CRISPR-Cas9 experiments, thereby demonstrating the reliability of StitchIt. StitchIt is able to dissect regulation in superenhancers and predicts thousands of putative REMs that go unnoticed using peak-based approaches suggesting that a large part of the regulome might be uncharted water.
Highlights
• Single nucleotide variants (SNVs) may affect transcription factor (TF) binding
• Fast statistical approach to assess significance of differential TF binding for SNVs
• Validate new approach on in vitro and in vivo TF binding assays
• Applications on GWAS SNVs and large eQTL studies illustrate utility
Summary
Non-coding variants located within regulatory elements may alter gene expression by modifying transcription factor (TF) binding sites, thereby leading to functional consequences. Different TF models are being used to assess the effect of DNA sequence variants, such as single nucleotide variants (SNVs). Often existing methods are slow and do not assess statistical significance of results. We investigated the distribution of absolute maximal differential TF binding scores for general computational models that affect TF binding. We find that a modified Laplace distribution can adequately approximate the empirical distributions. A benchmark on in vitro and in vivo datasets showed that our approach improves upon an existing method in terms of performance and speed. Applications on eQTLs and on a genome-wide association study illustrate the usefulness of our statistics by highlighting cell type-specific regulators and target genes. An implementation of our approach is freely available on GitHub and as bioconda package.
Human 5-lipoxygenase (5-LO) is the key enzyme of leukotriene biosynthesis, mostly expressed in leukocytes and thus a crucial component of the innate immune system.
In this study, we show that 5-LO, besides its canonical function as an arachidonic acid metabolizing enzyme, is a regulator of gene expression associated with euchromatin. By Crispr-Cas9-mediated 5-LO knockout (KO) in MonoMac6 (MM6) cells and subsequent RNA-Seq analysis, we identified 5-LO regulated genes which could be clustered to immune/defense response, cell adhesion, transcription and growth/developmental processes. Analysis of differentially expressed genes identified cyclooxygenase-2 (COX2, PTGS2) and kynureninase (KYNU) as strongly regulated 5-LO target genes. 5-LO knockout affected MM6 cell adhesion and tryptophan metabolism via inhibition of the degradation of the immunoregulator kynurenine. By subsequent FAIRE-Seq and 5-LO ChIP-Seq analyses, we found an association of 5-LO with euchromatin, with prominent 5-LO binding to promoter regions in actively transcribed genes. By enrichment analysis of the ChIP-Seq results, we identified potential 5-LO interaction partners. Furthermore, 5-LO ChIP-Seq peaks resemble patterns of H3K27ac histone marks, suggesting that 5-LO recruitment mainly takes place at acetylated histones.>
In summary, we demonstrate a noncanonical function of 5-LO as transcriptional regulator in monocytic cells.
Samples of Crustacea and Annelida (Polychaeta, Sipuncula, and Hirudinea) were collected in the Bering Sea and the northwestern Pacific Ocean during scientific cruise SO-249 BERING in 2016. Biological samples were collected from 32 locations by the team on-board RV Sonne using a chain bag dredge at depths ranging between 330–5,070 m, and preserved in 96% ethanol. Specimens were morphologically identified to the lowest taxonomic level possible using a Leica M60 stereomicroscope. The generated data here comprise taxonomic information as well as annotated bathymetric and biogeographic information from a total of 78 samples (26 Crustacea, 47 Polychaeta, 4 Sipuncula, and 1 Hirudinea). The dataset was prepared following Darwin Core Biodiversity standards for FAIR data sharing based on Ocean Biodiversity Information System (OBIS) and Global Biodiversity Facility (GBIF) guidelines. The standardised digitised data were then mobilised to both OBIS and GBIF under CC BY 4.0 licence to publicly share and adopt the data. As records of these important marine taxa from bathyal and abyssal depths are sparse, especially from the deep Bering Sea, the herein generated and digitised data aid in filling existing knowledge gaps on their diversity and distribution in that region. As part of the “Biogeography of the NW Pacific deep-sea fauna and their possible future invasions into the Arctic Ocean” (BENEFICIAL) project, this dataset thus not only increases our knowledge in re-assessing and uncovering the deep-sea diversity of these taxa, but also serves policy and management sectors by providing first-hand data for global report assessments.
The hepatitis B virus is one of the most common causes of virus-related chronic liver disease and remains a major global health problem affecting 296 million people worldwide. Despite an available and highly effective vaccination, hepatitis B infections lead to an annual mortality rate of approximately 0.8 million people. The global prevalence is heterogeneously distributed and reflects a high infections and chronicity, particularly in low-income countries, due to a lack of vaccination strategies, underdiagnosis and low treatment rates. A complete cure remains undiscovered to this day. Based on their genetic makeup, the virus is categorized into nine genotypes with a genetic difference of more than 8% within the sequence. In addition to their geographical distribution, hepatitis B virus genotypes also differ in terms of their clinical outcome, pathogenesis and treatment response.
The viral protein HBx is known to interact with several cellular signaling pathways and is thereby accounted as the driving force in the development of hepatitis B virus-associated pathogenesis and progression of hepatocellular carcinoma. In particular, HBx interacts with mitochondria and induces profound alterations in the mitochondrial morphology and function with a severe impact on the liver’s physiology and with an emerging role in liver-related disease progression.
This study aims to investigate the genotype-related impact of HBx with regard to their interaction with cellular signaling pathways. A particular focus was placed on mitochondria-dependent interactions and signaling pathways in order to broaden the understanding of the genetic diversity of the genotypes.
Differences between genotypes of HBx were examined and compared through in vitro experiments based on a cell culture-based system. Plasmid DNA encoding the HBx protein of the different genotypes was transiently transfected into Huh7 or HepG2 cells and examined for molecular and protein-biochemical effects on the host cell, usually 72 hours after transfection. This study focused on the most common genotypes A, B, C, D, E and G worldwide.
Based on initial kinome profiling analyses, it was found that HBx differs greatly within their genetic variants and suggests different effects on overall cell function and in particular on mitochondrial kinases. Furthermore, confocal laser scanning microscopy reveals profound HBx-mediated changes in the mitochondrial network structure, however with major differences among the different genotypes. In particular, HBx of genotypes A and G causes enormous fragmentation of mitochondrial structures, accompanied by emergent changes in mitochondrial function. Due to an increased interaction with the voltage-dependent anion channel 3, a significant loss of mitochondrial membrane potential was also observed, together with an increased radial oxygen stress level and an induction of central mitochondria-dependent inflammatory mediators. In contrast, the contribution of HBx-genotype B and E reveals only moderate effects in these regards. Using a pH-sensitive reporter system, HBx genotypes which previously indicated a strong distribution in the mitochondrial morphology and function, also showed an elevated mitophagy through the PINK1/Parkin-mediated pathway. This study provides direct evidence that HBx-mediated changes in host cell signaling pathways, especially in mitochondrial-associated pathways, fundamentally dependent on the different genotypes. In addition, the results also indicate an important role of HBx in the process of genotype-dependent liver pathogenesis and provide insight into the underlying cellular mechanisms and signaling pathways.
The monophyly of Theraphosinae is supported by both morphological and molecular phylogenies. However, intergeneric relationships often show polytomies and branches with low support. A previous phylogenetic study proposed an intergeneric relationship for the subfamily based on molecular data and divided it into three tribes: Grammostolini, Hapalopini and Theraphosini. However, not all genera of Theraphosinae were sampled, and some relationships were inferred based on morphological similarities. Regarding the Hapalopini from Brazil, the relationships of some genera are still uncertain, such as Kochiana, Catanduba, and Munduruku. In this paper, we describe four new species of Hapalopini from Brazil: Cyriocosmus paresi sp. nov., Hapalopus akroa sp. nov., H. guidonae sp. nov., and K. fukushimae sp. nov. In addition, we propose an updated diagnosis for these three genera and for the species K. brunnipes and M. bicoloratum.
Ophioderma teres (Lyman, 1860), an ophiuroid previously believed to have a wide distribution in the eastern Pacific, has been found to have an unclear taxonomic identity. While considered a well-known species, recent studies have revealed that O. teres lacks a holotype and has vague boundaries with its congeners Ophioderma teres unicolor H.L. Clark, 1940 and Ophioderma sodipallaresi Caso, 1986, as well as with two additional new morphotypes detected in Mexico and Nicaragua, causing continuous misidentifications. This study utilized an integrative taxonomy approach based on morphologic, morphometric, and molecular evidence to clarify the taxonomic status of O. teres, O. sodipallaresi, O. teres unicolor, and the two new morphotypes. Data integration led to the following results: 1) the neotype designation and redescription of O. teres; 2) the proposal of O. sodipallaresi as a junior synonym of O. teres; 3) the status change of O. unicolor stat. nov. from subspecies to species, and 4) the description of the morphotypes as the new species Ophioderma aija sp. nov. and Ophioderma bichi sp. nov. An identification key to the eastern Pacific species of Ophioderma was also developed. This work contributes to the knowledge of Ophioderma in the region, increasing the number of described species and providing resources for their accurate identification.
In this study, we describe two new species of Mesobiotus based on morphological data collected through light and scanning electron microscopy. Descriptions include DNA sequences of four commonly used molecular markers (18S rDNA, 28S rDNA, ITS-2, and COI). Mesobiotus efa sp. nov. was discovered in North-West Russia and belongs to the group of species with smooth cuticle, harmsworthi-type OCA, typical Mesobiotus claws IV with unindented lunules, and egg chorion with reticulated processes in form of ‘sharp wide cones’ or ‘cones with long slender endings’, egg process bases with well-developed crone of dark thickenings without finger-like projections, and egg shell surface between the processes with ridges without reticulation, areolation or semi-areolation. It can be distinguished from all know species of this group by a unique combination of morphological and morphometric characters. Mesobiotus vulpinus sp. nov. was found in the Russian Far East, and is similar to Mesobiotus mauccii by having an egg chorion with polygonal relief. The new species can be distinguished from M. mauccii by having a narrower buccal tube, by details of oral cavity armature, and by longer egg chorion processes. Furthermore, we provide results of the phylogenetic analyses of the genus Mesobiotus conducted in this study.
Although semi-aquatic cockroaches have been known for a long time, these insects remain little studied and their diversity underestimated. While a few species are known from Asia or South America, only a single one is known to be associated with water in Africa. Here, we report two species of semi-aquatic cockroaches of the subfamily Epilamprinae from Cameroon. One of these species is new: Rhabdoblatta fotoi Nyame Mbia, Legendre & Biram à Ngon sp. nov. Africalolampra camerunensis (Borg, 1902) comb. nov. was also found associated to these streams and we provide an extended description of this species, as well as for Africalolampra stipata comb. nov., also known from streams in West Africa. Another species was found in Cameroonian streams and is described here, although only identified at the family level (Blattellidae). The descriptions are based on morpho-anatomic characters, including male genitalia. Because nymphs were found primarily associated with water – more than adults – we provide a description of nymphs whenever possible. We provide molecular data (12S rRNA marker) for two of these water-associated species that we compared with published and unpublished sequences of Epilamprinae in a Maximum Likelihood approach. We also illustrate all but one species from continental Africa in the genera Africalolampra and Rhabdoblatta, including R. punctipennis (Saussure, 1895) which we reinstate. We provide a map and list of localities for Africalolampra and Rhabdoblatta spp. from continental Africa and Madagascar, as well as an identification key for species of Africalolampra. We finally discuss putative adaptations of semi-aquatic cockroaches.
Discoveries of new species often depend on one or a few specimens, leading to delays as researchers wait for additional context, sometimes for decades. There is currently little professional incentive for a single expert to publish a stand-alone species description. Additionally, while many journals accept taxonomic descriptions, even specialist journals expect insights beyond the descriptive work itself. The combination of these factors exacerbates the issue that only a small fraction of marine species are known and new discoveries are described at a slow pace, while they face increasing threats from accelerating global change. To tackle this challenge, this first compilation of Ocean Species Discoveries (OSD) presents a new collaborative framework to accelerate the description and naming of marine invertebrate taxa that can be extended across all phyla. Through a mode of publication that can be speedy, taxonomy-focused and generate higher citation rates, OSD aims to create an attractive home for single species descriptions. This Senckenberg Ocean Species Alliance (SOSA) approach emphasises thorough, but compact species descriptions and diagnoses, with supporting illustrations and with molecular data when available. Even basic species descriptions carry key data for distributions and ecological interactions (e.g., host-parasite relationships) besides universally valid species names; these are essential for downstream uses, such as conservation assessments and communicating biodiversity to the broader public.This paper presents thirteen marine invertebrate taxa, comprising one new genus, eleven new species and one re-description and reinstatement, covering wide taxonomic, geographic, bathymetric and ecological ranges. The taxa addressed herein span three phyla (Mollusca, Arthropoda, Echinodermata), five classes, eight orders and twelve families. Apart from the new genus, an updated generic diagnosis is provided for four other genera. The newly-described species of the phylum Mollusca are Placiphorella methanophila Vončina, sp. nov. (Polyplacophora, Mopaliidae), Lepetodrilus marianae Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Lepetodrilidae), Shinkailepas gigas Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Phenacolepadidae) and Lyonsiella illaesa Machado & Sigwart, sp. nov. (Bivalvia, Lyonsiellidae). The new taxa of the phylum Arthropoda are all members of the subphylum Crustacea: Lepechinella naces Lörz & Engel, sp. nov. (Amphipoda, Lepechinellidae), Cuniculomaera grata Tandberg & Jażdżewska, gen. et sp. nov. (Amphipoda, Maeridae), Pseudionella pumulaensis Williams & Landschoff, sp. nov. (Isopoda, Bopyridae), Mastigoniscus minimus Wenz, Knauber & Riehl, sp. nov. (Isopoda, Haploniscidae), Macrostylis papandreas Jonannsen, Riehl & Brandt, sp. nov. (Isopoda, Macrostylidae), Austroniscus indobathyasellus Kaiser, Kniesz & Kihara, sp. nov. (Isopoda, Nannoniscidae) and Apseudopsis daria Esquete & Tato, sp. nov. (Tanaidacea, Apseudidae). In the phylum Echinodermata, the reinstated species is Psychropotes buglossa E. Perrier, 1886 (Holothuroidea, Psychropotidae).The study areas span the North and Central Atlantic Ocean, the Indian Ocean and the North, East and West Pacific Ocean and depths from 5.2 m to 7081 m. Specimens of eleven free-living and one parasite species were collected from habitats ranging from an estuary to deep-sea trenches. The species were illustrated with photographs, line drawings, micro-computed tomography, confocal laser scanning microscopy and scanning electron microscopy images. Molecular data are included for nine species and four species include a molecular diagnosis in addition to their morphological diagnosis.The five new geographic and bathymetric distribution records comprise Lepechinella naces Lörz & Engel, sp. nov., Cuniculomaera grata Tandberg & Jażdżewska, sp. nov., Pseudionella pumulaensis Williams & Landschoff, sp. nov., Austroniscus indobathyasellus Kaiser, Kniesz & Kihara, sp. nov. and Psychropotes buglossa E. Perrier, 1886, with the novelty spanning from the species to the family level. The new parasite record is Pseudionella pumulaensis Williams & Landschoff, sp. nov., found in association with the hermit crab Pagurus fraserorum Landschoff & Komai, 2018.
Osteocalcin (auch Bone 6 la Protein [B G P] genannt), ein 49 Aminosäuren enthaltendes Knochenmatrixprotein, wird in den Osteoblasten synthetisiert und bei gesteigertem Knochenumsatz im Serum erhöht gefunden. Osteocalcin im Serum kann mittels eines Hadioimmunoassays gemessen werden. Die Werte steigen mit dem Lebensalter an und zeigen einen zirkadianen Rhythmus. Beim primären Hyperparathyreoidismus sind die Osteocalcinwerte erhöht. Bei Patienten mit Mammacarcinom zeigt ein Osteocalcinanstieg stets eine Metastasierung im Knochen an. Die Hyperthyreose geht mit erhöhten Osteocalcinwerten einher. Über den diagnostischen Wert einer Osteocalcinbestimmung beim Plasmozytom läßt sich zur Zeit noch keine sichere Aussage machen. Patienten mit einer histomorphometrisch gesicherten „low-turnover'"Osteoporose weisen niedrige Osteocalclnspiegel auf. Die stark erhöhten Osteocalcinwerte bei der renalen Osteopathie (sekundärer Hyperparathyreoidismus, Osteomalazie) sind z.T. auch au feine verminderte renale Elimination von Osteocalcin bei eingeschränkter glomerulärer Filtrationsrate zurückzuführen. Zusammenfassend stellt die Osteocalcinbestimmung eine Bereicherung der diagnostischen Möglichkeiten zur Beurteilung des Knochenumsatzes darf sollte vorerst jedoch noch vorwiegend wissenschaftlichen Fragestellungen vorbehalten sein.
Im Zeitraum von 1991 - 1992 wurden 2000 Stuhlproben von a) Tropenreisenden (n = 600), b) Patienten mit Durch fall (n = 500) und c) Patienten mit gastrointestinalen Symptomen, jedoch ohne Durchfall (n = 900) auf Campylobacter spp. untersucht Hierfür wurden drei Kultivierungsmethoden parallel eingesetzt: 7. eine Filtermembranmethode, 2. ein blutfreies Campylobacter-Selektivmedium und 3. ein Blutmedium mit Butzler-Supplement Zusätzlich wurde der Einfluß von Transportbedingungen untersucht mittels Vergleiches zwischen Nativ-Stuhlproben versus Stühlen, die in ein Transportnährmedium (Cary-Blair-Medium) gegeben worden waren (n = 517).
Insgesamt waren 54/2000 (2,7%) Stuhlproben positiv. Die Campylobacter-Auffindungsrate in flüssigen Stühlen (Gruppe B) lag dreifach höher im Vergleich zu nicht-durchfälligen Proben (p < 0.01). In den Gruppen b) und c) waren Patienten, die älter als 40 Jahre waren, signifikant seltener mit Campylobacter infiziert als jüngere Personen, während es bei den Tropenreisenden keinen Alterseffekt gab. Unter den drei Kultivierungsmethoden war das Filtermembranverfahren dasjenige mit der besten Campylobacter-Ausbeute (p < 0.01): Methode 1 ergab 57,5%, Methode 2 50% und Methode 3 40,7% positive Isolate. Durch den Einsatz von Cary-Blair-Transportmedium konnte die Campylobacter-Isolierungsrate um 25% gesteigert werden. Die am häufigsten isolierten Spezies waren C. jejuni und C. coli.
Das neue immunoluminometrische BeriLux® PSA - ein Test für das Routinelabor. Ein Methodenvergleich
(1993)
In dieser Studie wurde der immunoluminometrische BeriLux® PSA-Test mit zwei radio-immunologischen und einem fluorometrischen Verfahren verglichen. Für den BeriLux® PSA wurden an 150 gesunden Probanden (100 Männer und 50 Frauen) die Referenzbereiche ermittelt. Bei Männern lag die 95%-Perzentile bei 3,77 ng/ml, für Frauen lag die 95%-Perzentile bei0,1 ng/ml. Der Korrelationskoeffizient zwischen der immunoluminometrischen Methode und radioimmunologischen Methode liegt bei r = 0,99, die analytische Sensitivität von BeriLux9 PSA liegt bei 0,03 ng/ml. Die Stabilität der Serumproben bei Lagerungstemperaturen zwischen 2°C und 8°C ist über einen Tag garantiert. Über diesen Zeitraum hinaussollten Serumproben bei -20° C gelagert werden.
Using e+e− annihilation data sets corresponding to an integrated luminosity of 4.5 fb−1, collected with the BESIII detector at center-of-mass energies between 4.600 and 4.699 GeV, we report the first measurements of the absolute branching fractions B(Λ+c→pK0L)=(1.67±0.06±0.04)%, B(Λ+c→pK0Lπ+π−)=(1.69±0.10±0.05)%, and B(Λ+c→pK0Lπ0)=(2.02±0.13±0.05)%, where the first uncertainties are statistical and the second systematic. Combining with the known branching fractions of Λ+c→pK0S, Λ+c→pK0Sπ+π−, and Λ+c→pK0Sπ0, we present the first measurements of the K0S-K0L asymmetries R(Λ+c,K0S,LX)=B(Λ+c→K0SX)−B(Λ+c→K0LX)B(Λ+c→K0SX)+B(Λ+c→K0LX) in charmed baryon decays: R(Λ+c,pK0S,L)=−0.025±0.031, R(Λ+c,pK0S,Lπ+π−)=−0.027±0.048, and R(Λ+c,pK0S,Lπ0)=−0.015±0.046. No significant asymmetries within the uncertainties are observed.
Purpose: To assess the diagnostic precision of three different workstations for measuring thoracic aortic aneurysms (TAAs) in vivo and ex vivo using either pre-interventional computed tomography angiography scans (CTA) or a specifically designed phantom model.
Methods: This retrospective study included 23 patients with confirmed TAA on routinely performed CTAs. In addition to phantom tube diameters, one experienced blinded radiologist evaluated the dimensions of TAAs on three different workstations in two separate rounds. Precision was assessed by calculating measurement errors. In addition, correlation analysis was performed using Pearson correlation.
Results: Measurements acquired at the Siemens workstation deviated by 3.54% (range, 2.78–4.03%; p = 0.14) from the true size, those at General Electric by 4.05% (range, 1.46–7.09%; p < 0.0001), and at TeraRecon by 4.86% (range, 3.22–6.45%; p < 0.0001). Accordingly, Siemens provided the most precise workstation at simultaneously most fluctuating values (scattering of 4.46%). TeraRecon had the smallest fluctuation (scattering of 2.83%), but the largest deviation from the true size of the phantom. The workstation from General Electric showed a scattering of 2.94%. The highest overall correlation between the 1st and 2nd rounds was observed with measurements from Siemens (r = 0.898), followed by TeraRecon (r = 0.799), and General Electric (r = 0.703). Repetition of measurements reduced processing times by 40% when using General Electric, by 20% with Siemens, and by 18% with TeraRecon.
Conclusions: In conclusion, all three workstations facilitated precise assessment of dimensions in the majority of cases at simultaneously high reproducibility, ensuring accurate pre-interventional planning of thoracic endovascular aortic repair.
This study evaluates whether the short version of the German LITMUS quasi-universal nonword repetition task (LITMUS-QU-NWR) can be used as an index test for monolingual and early second language learners (eL2) of German aged 8 to 10 years. The NWR taps into quasi-universal phonological knowledge via the so-called language-independent part and into language-specific phonological knowledge via the language-dependent part. Thirty-six monolingual and thirty-three eL2 learners of German, typically developing (TD) and diagnosed as language-impaired (DLD), participated in the study. The effects of the language group (Mo vs. eL2) and the clinical status (TD vs. DLD) on repetition accuracy are investigated by a logistic mixed-model analysis. Receiver operating characteristics (ROC) and likelihood ratios are calculated to determine the diagnostic accuracy of the two parts. The group comparisons showed significant effects of the clinical status but not of the language group. The ROC analyses and the likelihood ratios reveal better diagnostic values for the language-dependent compared to the language-independent part and almost similar diagnostic values for the monolingual and the eL2 group. The results indicate that the LITMUS-QU-NWR helps to disentangle DLD and DLD in monolingual children and eL2 learners aged 8 to 10 years.
Background: Opsoclonus-myoclonus syndrome (OMS) is a rare, immune-mediated neurological disorder. In adults, the pathogenesis can be idiopathic, post-infectious or paraneoplastic, the latter etiology belonging to the ever-expanding group of defined paraneoplastic neurological syndromes (PNS). In contrast to other phenotypes of PNS, OMS cannot be ascribed to a single pathogenic autoantibody. Here, we report the first detailed case of paraneoplastic, antibody-negative OMS occurring in association with a pancreatic neuroendocrine tumor (pNET).
Case presentation: A 33-year-old female presented with a two-week history of severe ataxia of stance and gait, dysarthria, head tremor, myoclonus of the extremities and opsoclonus. Her past medical history was notable for a metastatic pancreatic neuroendocrine tumor, and she was subsequently diagnosed with paraneoplastic opsoclonus-myoclonus syndrome. Further workup did not reveal a paraneoplastic autoantibody. She responded well to plasmapheresis, as she was refractory to the first-line therapy with corticosteroids.
Conclusions: This case expands current knowledge on tumors associated with paraneoplastic opsoclonus-myoclonus syndrome and the age group in which it can occur. It further adds evidence to the effectiveness of plasmapheresis in severe cases of opsoclonus-myoclonus syndrome with a lack of response to first-line therapy.
The ALICE Collaboration measures the production of low-mass dielectrons in pp, p-Pb and Pb-Pb collisions at the LHC. The main detectors used in the analyses are the Inner Tracking System, Time Projection Chamber and Time-Of-Flight detector, all located around mid-rapidity. The production of virtual photons relative to the inclusive yield in pp collisions is determined by analyzing the dielectron excess with respect to the expected hadronic sources. The direct photon cross section is then calculated and found to be in agreement with NLO pQCD calculations. Results from the invariant mass analysis in p-Pb collisions show an overall agreement between data and hadronic cocktail. In Pb-Pb collisions, uncorrected background-subtracted yields have been extracted in two centrality classes. A feasibility study for LHC run 3 after the ALICE upgrade indicates the possibility for a future measurement of the early effective temperature.
Structured management programs have been developed for single diseases but rarely for patients with multiple medications. We conducted a qualitative study to investigate the views of stakeholders on the development and implementation of a polypharmacy management program in Germany. Overall, we interviewed ten experts in the fields of health policy and clinical practice. Using content analysis, we identified inclusion criteria for the selection of suitable patients, the individual elements that should make up such a program, healthcare providers and stakeholders that should be involved, and factors that may support or hinder the program’s implementation. All stakeholders were well aware of polypharmacy-related risks and challenges, as well as the urgent need for change. Intervention strategies should address all levels of care and include all concerned patients, caregivers, healthcare providers and stakeholders, and involved parties should agree on a joint approach.
We investigate the thermodynamic geometry of the quark-meson model at finite temperature, T, and quark number chemical potential, μ. We extend previous works by the inclusion of fluctuations exploiting the functional renormalization group approach. We use recent developments to recast the flow equation into the form of an advection-diffusion equation. We adopt the local potential approximation for the effective average action. We focus on the thermodynamic curvature, R, in the (μ,T) plane, in proximity of the chiral crossover, up to the critical point of the phase diagram. We find that the inclusion of fluctuations results in a smoother behavior of R near the chiral crossover. Moreover, for small μ, R remains negative, signaling the fact that bosonic fluctuations reduce the capability of the system to completely overcome the fermionic statistical repulsion of the quarks. We investigate in more detail the small μ region by analyzing a system in which we artificially lower the pion mass, thus approaching the chiral limit in which the crossover is actually a second order phase transition. On the other hand, as μ is increased and the critical point is approached, we find that R is enhanced and a sign change occurs, in agreement with mean field studies. Hence, we completely support the picture that R is sensitive to a crossover and a phase transition, and provides information about the effective behavior of the system at the phase transition.
We investigate the thermodynamic geometry of the quark-meson model at finite temperature, T, and quark number chemical potential, μ. We extend previous works by the inclusion of fluctuations exploiting the functional renormalization group approach. We use recent developments to recast the flow equation into the form of an advection-diffusion equation. We adopt the local potential approximation for the effective average action. We focus on the thermodynamic curvature, R, in the (μ,T) plane, in proximity of the chiral crossover, up to the critical point of the phase diagram. We find that the inclusion of fluctuations results in a smoother behavior of R near the chiral crossover. Moreover, for small μ, R remains negative, signaling the fact that bosonic fluctuations reduce the capability of the system to completely overcome the fermionic statistical repulsion of the quarks. We investigate in more detail the small μ region by analyzing a system in which we artificially lower the pion mass, thus approaching the chiral limit in which the crossover is actually a second order phase transition. On the other hand, as μ is increased and the critical point is approached, we find that R is enhanced and a sign change occurs, in agreement with mean field studies. Hence, we completely support the picture that R is sensitive to a crossover and a phase transition, and provides information about the effective behavior of the system at the phase transition.
Zielsetzung: Ziel der Studie ist die Frage, ob es möglich ist, einen Kommunikationskurs für ca. 400 Studierende erfolgreich in ein Blended Learning-Format (asynchrone Theorievermittlung/digitaler synchroner Praxisteil) umzustellen. Hauptfokus war dabei die Beurteilung des subjektiven Lernzuwachses und die Frage, inwiefern die Bedeutung des Themas Kommunikation und Gesprächsführung online abgebildet werden kann. Die Betrachtung erfolgt auf Basis von Evaluationsergebnissen der Studierenden und Dozierenden dieses Kurses.
Methodik: Die Studierenden des vierten vorklinischen Semesters aus dem Jahr 2020 wurden durch einen Selbsteinschätzungsbogen zu Beginn sowie durch eine Evaluation nach Abschluss des Kurses befragt. Zusätzlich wurden die Rückmeldungen der Dozierenden zum Kurs ausgewertet. Um die Ergebnisse vergleichen und mögliche Unterschiede feststellen zu können, wurden die entsprechenden Selbsteinschätzungs- und Evaluationsergebnisse der vorangegangenen zehn Jahre (in Form von Präsenzkursen) herangezogen.
Ergebnisse: Im Onlineformat wurde ein deutlicher subjektiver Lernzuwachs angegeben, der höher ausfiel als in den Vorjahren in Präsenz. Die Eignung des Onlineformats wurde von Studierenden sowie Dozierenden eher kritisch bewertet, während die Kursatmosphäre positiv gesehen wurde. Die Relevanz ärztlicher Gesprächsführung wurde im Onlineformat insgesamt besonders gut bewertet.
Schlussfolgerung: Aufgrund der Evaluationsergebnisse werden die Erfahrungen mit dem Blended Learning-Format auch in Zukunft in das Kommunikations-Curriculum des Medizinstudiums der Goethe-Universität Frankfurt einfließen. Die Ergebnisse haben gezeigt, dass das Erlernen ärztlicher Gesprächsführung online gut möglich ist. Daher kann dieses Format für zukünftige neue Konzepte empfohlen werden.
The photoelectric effect describes the ejection of an electron upon absorption of one or several photons. The kinetic energy of this electron is determined by the photon energy reduced by the binding energy of the electron and, if strong laser fields are involved, by the ponderomotive potential in addition. It has therefore been widely taken for granted that for atoms and molecules, the photoelectron energy does not depend on the electron’s emission direction, but theoretical studies have questioned this since 1990. Here, we provide experimental evidence that the energies of photoelectrons emitted against the light propagation direction are shifted toward higher values, while those electrons that are emitted along the light propagation direction are shifted to lower values. We attribute the energy shift to a nondipole contribution to the ponderomotive potential that is due to the interaction of the moving electrons with the incident photons.
The ALICE experiment at the LHC investigates the properties of the hot and dense nuclear matter created in heavy-ion collisions. By comparing the particle production in pp and p-Pb collisions, possible nuclear initial state effects can be isolated. Measurements of the ω meson pT-spectra in pp and p-Pb collisions not only allow for a determination of the nuclear modification factor RpPb, but also provide insight into the fragmentation process and serve as vital input for decay background simulations for direct photons. In this contribution, measurements of the ω meson production in pp and p-Pb collisions at √sNN=5.02 TeV are presented. This includes the signal extraction and various corrections of the ω meson yields, leading to their production cross sections and the first measured nuclear modification factor RpPb of the ω meson at LHC energies.
The ALICE experiment at the LHC investigates the properties of the hot and dense nuclear matter created in heavy-ion collisions. By comparing the particle production in pp and p-Pb collisions, possible nuclear initial state effects can be isolated. Measurements of the ω meson pT-spectra in pp and p-Pb collisions not only allow for a determination of the nuclear modification factor RpPb, but also provide insight into the fragmentation process and serve as vital input for decay background simulations for direct photons. In this contribution, measurements of the ω meson production in pp and p-Pb collisions at √sNN=5.02 TeV are presented. This includes the signal extraction and various corrections of the ω meson yields, leading to their production cross sections and the first measured nuclear modification factor RpPb of the ω meson at LHC energies.
Objectives: To assess the impact of noise-optimised virtual monoenergetic imaging (VMI+) on image quality and diagnostic evaluation in abdominal dual-energy CT scans with impaired portal-venous contrast.
Methods: We screened 11,746 patients who underwent portal-venous abdominal dual-energy CT for cancer staging between 08/2014 and 11/2019 and identified those with poor portal-venous contrast.
Standard linearly-blended image series and VMI+ image series at 40, 50, and 60 keV were reconstructed. Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of abdominal organs and vascular structures were calculated. Image noise, image contrast and overall image quality were rated by three radiologists using 5-point Likert scale.
Results: 452 of 11,746 (4%) exams were poorly opacified. We excluded 190 cases due to incomplete datasets or multiple exams of the same patient with a final study group of 262. Highest CNR values in all abdominal organs (liver, 6.4 ± 3.0; kidney, 17.4 ± 7.5; spleen, 8.0 ± 3.5) and vascular structures (aorta, 16.0 ± 7.3; intrahepatic vein, 11.3 ± 4.7; portal vein, 15.5 ± 6.7) were measured at 40 keV VMI+ with significantly superior values compared to all other series. In subjective analysis, highest image contrast was seen at 40 keV VMI+ (4.8 ± 0.4), whereas overall image quality peaked at 50 keV VMI+ (4.2 ± 0.5) with significantly superior results compared to all other series (p < 0.001).
Conclusions: Image reconstruction using VMI+ algorithm at 50 keV significantly improves image contrast and image quality of originally poorly opacified abdominal CT scans and reduces the number of non-diagnostic scans.
Advances in knowledge: We validated the impact of VMI+ reconstructions in poorly attenuated DECT studies of the abdomen in a big data cohort.
In the deep-sea, the interaction between benthic fauna and substrate mainly occurs through bioturbational processes which can be preserved as traces (i.e., lebensspuren). Lebensspuren are common features of deep seafloor landscapes and usually more abundant than the organism that produce them (i.e., tracemakers), rendering them promising proxies to infer biodiversity. The density and diversity relationships between lebensspuren and benthic fauna are to the present day unclear and contradicting hypotheses have been proposed suggesting negative, positive, or even null correlations. To test these hypotheses, in this study lebensspuren, tracemakers (specific epibenthic fauna that produce these traces), degrading fauna (benthic fauna that can erase lebensspuren), and fauna in general were characterized taxonomically at eight deep-sea stations in the Kuril Kamchatka Trench area. No general correlation (over-all study area) could be observed between diversities of lebensspuren, tracemakers, degrading fauna and fauna. However, a diversity correlation was observed between specific stations, showing both negative and positive correlations depending on: 1) the number of unknown tracemakers (especially significant for dwelling lebensspuren); and 2) the lebensspuren with multiple origins; and 3) tracemakers that can produce different lebensspuren. Lebensspuren and faunal density were not correlated. However, lebensspuren density was either positively or negatively correlated with tracemaker densities, depending on the lebensspuren morphotypes. A positive correlation was observed for resting lebensspuren (e.g., ophiuroid impressions, Actinaria circular impressions), while negative correlations were observed for locomotion-feeding lebensspuren (e.g., echinoid trails). In conclusion, lebensspuren diversity may be a good proxy for tracemaker biodiversity when the lebensspuren-tracemaker tandem can be reliable characterized; and lebensspuren-density correlations vary depending the specific lebensspuren residence time, tracemaker density and associated behaviour (rate of movement), but on a global scale abiotic and other biotic 42 factors may also play an important role.
In the deep sea, interactions between benthic fauna and seafloor sediment primarily occur through bioturbation that can be preserved as traces (i.e. lebensspuren). Lebensspuren are common features of deep-sea landscapes and are more abundant than the organisms that produce them (i.e. tracemakers), rendering lebensspuren promising proxies for inferring biodiversity. The density and diversity relationships between lebensspuren and benthic fauna remain unclear, and contradicting correlations have been proposed (i.e. negative, positive, or even null correlations). To approach these variable correlations, lebensspuren and benthic fauna were characterized taxonomically at eight deep-sea stations in the Kuril-Kamchatka Trench area, together with two novel categories: tracemakers (specific epibenthic fauna that produce these traces) and degrading fauna (benthic fauna that can erase lebensspuren). No general correlation (overall study area) was observed between diversities of lebensspuren, tracemakers, degrading fauna, and fauna. However, a diversity correlation was observed at specific stations, showing both negative and positive correlations depending on: (1) the number of unknown tracemakers (especially significant for dwelling lebensspuren); (2) the lebensspuren with multiple origins; and (3) tracemakers that can produce different lebensspuren. Lebensspuren and faunal density were not correlated. However, lebensspuren density was either positively or negatively correlated with tracemaker densities, depending on the lebensspuren morphotypes. A positive correlation was observed for resting lebensspuren (e.g. ophiuroid impressions, Actiniaria circular impressions), while negative correlations were observed for locomotion-feeding lebensspuren (e.g. echinoid trails). In conclusion, lebensspuren diversity may be a good proxy for tracemaker biodiversity when the lebensspuren–tracemaker relationship can be reliable characterized. Lebensspuren–density correlations vary depending on the specific lebensspuren residence time, tracemaker density, and associated behaviour (rate of movement). Overall, we suggest that lebensspuren density and diversity correlations should be studied with tracemakers rather than with general benthic fauna. On a global scale, abiotic (e.g. hydrodynamics, substrate consistency) and other biotic factors (e.g. microbial degradation) may also play an important role.
By analyzing (27.12±0.14)×108 ψ(3686) events accumulated with the BESIII detector, the decay ηc(2S)→K+K−η is observed for the first time with a significance of 6.2σ after considering systematic uncertainties. The product of the branching fractions of ψ(3686)→γηc(2S) and ηc(2S)→K+K−η is measured to be B(ψ(3686)→γηc(2S))×B(ηc(2S)→K+K−η)=(2.39±0.32±0.34)×10−6, where the first uncertainty is statistical, and the second one is systematic. The branching fraction of ηc(2S)→K+K−η is determined to be B(ηc(2S)→K+K−η)=(3.42±0.46±0.48±2.44)×10−3, where the third uncertainty is due to the branching fraction of ψ(3686)→γηc(2S). Using a recent BESIII measurement of B(ηc(2S)→K+K−π0), we also determine the ratio between the branching fractions of ηc(2S)→K+K−η and ηc(2S)→K+K−π0 to be 1.49±0.22±0.25, which is consistent with the previous result of BaBar at a comparable precision level.
Search for X(3872)→π⁰π⁰χc₁,₂
(2024)
Using 10.1 fb−1 of e+e− collision data collected by the BESIII detector with center-of-mass energies between 4.15 GeV and 4.30 GeV, we search for the decays X(3872)→π0π0χc1,2, where the X(3872) is produced in e+e−→γX(3872). No evidence above 3σ is found for either decay. Upper limits at the 90% C.L. on the branching fractions of X(3872)→π0π0χc1,2 normalized to the branching fraction of X(3872)→π+π−J/ψ are set to be B(X(3872)→π0π0χc1)/B(X(3872)→π+π−J/ψ)<1.1 and B(X(3872)→π0π0χc2)/B(X(3872)→π+π−J/ψ)<0.5, taking into account both statistical and systematic uncertainties.
We perform the first investigation of the process e+e−→K+K−ψ(2S) and report its Born cross sections over a range of center-of-mass energies from 4.699 to 4.951~GeV. The measurements are carried out using several partial reconstruction techniques using data samples collected by the BESIII detector with a total integrated luminosity of 2.5~fb−1. We search for new tetraquark candidates Z±cs in the decays Z±cs→K±ψ(2S). No significant Z±cs signals are observed.
Using (2.712±0.014)×109 ψ(3686) events collected with the BESIII detector operating at the BEPCII, we find an evidence of the ηc(2S)→K+K−η′ decay with a statistical significance of 3.1σ. Its decay branching fraction is measured to be (12.24±4.60(stat.)±2.37(syst.)±4.68(extr.))×10−4, where the first uncertainty is statistical, the second is systematic, and the third uncertainty is from the branching fraction of the ψ(3686)→γηc(2S) decay. The upper limit on the product branching fraction B[ψ(3686)→γηc(2S)]× B[ηc(2S)→K+K−η′] is set to be 1.14×10−6 at 90% confidence level. In addition, the branching fractions of χc1→K+K−η′ and χc2→K+K−η′ are updated to be (8.47±0.09(stat.)±0.47(syst.))×10−4 and (1.53±0.04(stat.)±0.08(syst.))×10−4, respectively. The precision is improved by twofold.
Der Artikel gibt einen Überblick über die unterschiedlichen Sammlungsbestände von Comics, Graphic Novels und Manga in wissenschaftlichen Bibliotheken in Deutschland. Im weiteren Verlauf wird ein Schwerpunkt auf die Herausforderungen und Probleme in Bezug auf Bestandsaufbau, Erschließung, Archivierung bzw. Verfügbarmachung sowie Findmittel gelegt.
Observation of χcJ → 3(K⁺K⁻)
(2024)
By analyzing (27.12±0.14)×108 𝜓(3686) events collected with the BESIII detector operating at the BEPCII collider, the decay processes 𝜒𝑐𝐽→3(𝐾+𝐾−) (𝐽=0, 1, 2) are observed for the first time with statistical significances of 8.2𝜎, 8.1𝜎, and 12.4𝜎, respectively. The product branching fractions of 𝜓(3686)→𝛾𝜒𝑐𝐽, 𝜒𝑐𝐽→3(𝐾+𝐾−) are presented and the branching fractions of 𝜒𝑐𝐽→3(𝐾+𝐾−) decays are determined to be ℬ𝜒𝑐0→3(𝐾+𝐾−)=(10.7±1.8±1.1)×10−6, ℬ𝜒𝑐1→3(𝐾+𝐾−)=(4.2±0.9±0.5)×10−6, and ℬ𝜒𝑐2→3(𝐾+𝐾−)=(7.2±1.1±0.8)×10−6, where the first uncertainties are statistical and the second are systematic.
Observation of χcJ → 3(K⁺K⁻)
(2023)
By analyzing (27.12±0.14)×108 ψ(3686) events collected with the BESIII detector operating at the BEPCII collider, the decay processes χcJ→3(K+K−) (J=0,1,2) are observed for the first time with statistical significances of 8.2σ, 8.1σ, and 12.4σ, respectively. The product branching fractions of ψ(3686)→γχcJ, χcJ→3(K+K−) are presented and the branching fractions of χcJ→3(K+K−) decays are determined to be Bχc0→3(K+K−)=(10.7±1.8±1.1)×10−6, Bχc1→3(K+K−)=(4.2±0.9±0.5)×10−6, and Bχc2→3(K+K−)=(7.2±1.1±0.8)×10−6, where the first uncertainties are statistical and the second are systematic.
Using data samples with an integrated luminosity of 6.4~fb−1 collected by the BESIII detector operating at the BEPCII storage ring, the process of e+e−→γϕJ/ψ is studied. The processes of e+e−→ϕχc1,c2, χc1,c2→γJ/ψ are observed with a significance of more than 10σ. The s√-dependent cross section of e+e−→ϕχc1,c2 is measured between 4.600 and 4.951~GeV, and evidence of a resonance structure is found for the first time in the ϕχc2 process. We also search for the processes of e+e−→γX(4140), γX(4274) and γX(4500) via the γϕJ/ψ final state, but no obvious structures are found. The upper limits on the production cross section times the branching fraction for these processes at the 90% confidence level are reported.
The cross section of the process e+e−→K+K− is measured at a number of center-of-mass energies s√ from 2.00 to 3.08 GeV with the BESIII detector at the Beijing Electron Positron Collider (BEPCII). The results provide the best precision achieved so far. A resonant structure around 2.2 GeV is observed in the cross section line shape. A Breit-Wigner fit yields a mass of M=2239.2±7.1±11.3~and a width of Γ=139.8±12.3±20.6 MeV, where the first uncertainties are statistical and the second ones are systematic. In addition, the time-like electromagnetic form factor of the kaon is determined at the individual center-of-mass energy points.
Using a 3.19 fb−1 data sample collected at an 𝑒+𝑒− center-of-mass energy of 𝐸cm=4.178 GeV with the BESIII detector, we measure the branching fraction of the leptonic decay 𝐷+𝑠→𝜇+𝜈𝜇 to be ℬ𝐷+𝑠→𝜇+𝜈𝜇=(5.49±0.16stat±0.15syst)×10−3. Combining our branching fraction with the masses of the 𝐷+𝑠 and 𝜇+ and the lifetime of the 𝐷+𝑠, we determine 𝑓𝐷+𝑠|𝑉𝑐𝑠|=246.2±3.6stat±3.5syst MeV. Using the 𝑐→𝑠 quark mixing matrix element |𝑉𝑐𝑠| determined from a global standard model fit, we evaluate the 𝐷+𝑠 decay constant 𝑓𝐷+𝑠=252.9±3.7stat±3.6syst MeV. Alternatively, using the value of 𝑓𝐷+𝑠 calculated by lattice quantum chromodynamics, we find |𝑉𝑐𝑠|=0.985±0.014stat±0.014syst. These values of ℬ𝐷+𝑠→𝜇+𝜈𝜇, 𝑓𝐷+𝑠|𝑉𝑐𝑠|, 𝑓𝐷+𝑠 and |𝑉𝑐𝑠| are each the most precise results to date.
Using a data sample of 448.1×106 𝜓(3686) events collected at √𝑠=3.686 GeV with the BESIII detector at the Beijing Electron-Positron Collider II, we search for the rare decay 𝐽/𝜓→𝜙𝑒+𝑒− via 𝜓(3686)→𝜋+𝜋−𝐽/𝜓. No signal events are observed and the upper limit on the branching fraction is set to be ℬ(𝐽/𝜓→𝜙𝑒+𝑒−)<1.2×10−7 at the 90% confidence level, which is still about one order of magnitude higher than the Standard Model prediction.
Using a data sample of 448.1×106 ψ(3686) events collected at s√= 3.686 GeV with the BESIII detector at the BEPCII, we search for the rare decay J/ψ→ϕe+e− via ψ(3686)→π+π−J/ψ. No signal events are observed and the upper limit on the branching fraction is set to be B(J/ψ→ϕe+e−)<1.2×10−7 at the 90\% confidence level, which is still about one order of magnitude higher than the Standard Model prediction.
Dielectrons are an excellent probe for the QCD matter created in created in ultra-relativistic heavy-ion collisions, since they are emitted during the whole evolution of the collision and do not interact strongly with the medium. To isolate the QGP signals, measurement of the dielectron production in vacuum and its modifications due to the presence of cold nuclear matter is necessary. We present and discuss results from a low magnetic field detector setup in proton-proton collisions at √s = 13 TeV, as well as the measurement of dielectron production in pp, p-Pb, and Pb-Pb collisions at √sNN = 5 TeV.
The attention on the protein PURA has increased recently following the discovery of the rare PURA Syndrome. This neurodevelopmental disorder is caused by de novo mutations in the PURA gene. Notably, our collaborators could show that the protein PURA can bind DNA and RNA in vitro. As a result, I was motivated to explore PURA's cellular RNAbinding activity. Furthermore, I inquired on the connection of PURA-RNA binding to the cellular effect of a reduction of functional PURA as present in PURA Syndrome patients.
To investigate the binding of PURA and the impact of PURA de ciency on cellular RNA and protein expression, I performed an integrative computational analysis of multimodal data from complementary high-throughput experiments. An essential component was the examination of UV Crosslinking and immunoprecipitation (CLIP) experiments, which can query the global RNA-binding behaviour of a given protein in a cellular context. As the processing and analysis of CLIP data are rather complex, I introduce an automated command line tool for the processing of CLIP data named racoon_clip as part of this dissertation. Therefore, this dissertation comprises two major segments. Firstly, I describe the implementation and usage of racoon clip for CLIP data analysis. Secondly, I discuss my research on the protein PURA, demonstrating its global RNA-binding properties, the effects of PURA depletion and its association with neuronal functions and P-bodies, among others.
racoon_clip is a command line application that I have developed for processing of individualnucleotide resolution CLIP (iCLIP) and enhanced CLIP (eCLIP) experiments - two of the most commonly used types of CLIP experiments - in a comparable and user-friendly way.
For this, I built racoon_clip as an automated work how that encompasses all CLIP processing steps from raw data to single-nucleotide resolution crosslink events. racoon_clip is available as a command line tool that users can run with a single command. The work how is implemented with Snakemake work how management providing computational advantage tages including parallelisation, scalability and portability of the work how. The main task of racoon_clip is to extract single-nucleotide crosslink events from iCLIP, iCLIP2, eCLIP and similar data types. To strike a balance between being highly customisable and easy to use, racoon_clip supplies pre-set options for the most common types of experiments.
Additionally, it is possible for users to create a custom setup of barcode and adapter architectures, which allows them to use the software for other types of CLIP data. While accounting for the different architectures in the reads, the performed central processing steps remain the same. This leads to a high degree of comparability between the different experiment types, which I demonstrate in the exemplary processing of U2AF2 iCLIP and eCLIP data. Taken together, I am confident that racoon_clip will be beneficial to numerous researchers interested in RNA-Protein interactions as it offers easily accessible processing for CLIP data and enhances the comparability of multiple CLIP datasets across di erent experiment types.
In the second part of this dissertation, I focus on the cellular function of the RNAbinding protein PURA. Through in-depth computational analysis of one iCLIP data set of endogenous PURA and two iCLIP data sets of overexpressed PURA in HeLa cells, I establish that PURA is a global RNA-binding protein. It preferentially binds RNAs in either the coding sequence (CDS) or the 3' untranslated region (3'UTR) of mature protein-coding transcripts by recognising a Purine-rich degenerated sequence motif. Even though overexpression of PURA results in less specific binding behaviour, the same overall binding patterns as from endogenous PURA persist. Overall characteristics of PURA binding remain similar in three distinct PURA iCLIP data sets with and without PURA overexpression.
To learn about the molecular consequences of a depletion of functional PURA in a cellular context, I used a 50% reduction of PURA in HeLa cells as a model for the heterozygous loss of PURA in PURA Syndrome and evaluated its impact on global RNA and protein expression. The results demonstrate that PURA depletion globally a ects RNA and protein expression. Additionally, I integrate PURA RNA binding with the changes in expression of RNAs and proteins in the context of PURA depletion. This reveals 234 targets of PURA that are bound by PURA and are impacted at both RNA and protein levels by the PURA protein. RNAs that are bound by PURA or change in abundance upon PURA depletion are enriched in neuronal development factors, RNA lifecycle regulators, and mitochondrial factors, among others. Consistent with a possible role of PURA in neuronal transport, there is considerable overlap between PURA bound transcripts and transcripts, that are transported to the dendritic end of neurons.
Notably, there is a link between PURA and P-bodies, as documented by the enrichment of PURA-bound RNAs in both the P-body and stress granule transcriptome. Further, PURA was found by our collaborators to be localised within P-bodies and P-body numbers were strongly reduced in cells that are depleted of PURA. This absence might be attributed to the downregulation of the proteins encoded by the PURA targets LSM14A and DDX6 as both of them were previously identified as essential for P-body formation.
Overall, the reduction of P-body numbers in PURA depletion, the neuronal function of PURA, and its association with mitochondria and RNA lifecycle regulation may indicate the cellular foundation of both PURA Syndrome and related neuronal diseases.
In summary, I present a versatile and user-friendly computational tool for the analysis of CLIP data. Subsequently, I conduct a thorough computational analysis of CLIP and other high-throughput data in the context of the RNA-binding protein PURA, which offers valuable insights into the cellular functions of PURA. These insights advance our understanding of the impact of PURA loss in PURA Syndrome and other disease contexts.
Stimulated emission depletion (STED) microscopy is a super-resolution technique that surpasses the diffraction limit and has contributed to the study of dynamic processes in living cells. However, high laser intensities induce fluorophore photobleaching and sample phototoxicity, limiting the number of fluorescence images obtainable from a living cell. Here, we address these challenges by using ultra-low irradiation intensities and a neural network for image restoration, enabling extensive imaging of single living cells. The endoplasmic reticulum (ER) was chosen as the target structure due to its dynamic nature over short and long timescales. The reduced irradiation intensity combined with denoising permitted continuous ER dynamics observation in living cells for up to 7 hours with a temporal resolution of seconds. This allowed for quantitative analysis of ER structural features over short (seconds) and long (hours) timescales within the same cell, and enabled fast 3D live-cell STED microscopy. Overall, the combination of ultra-low irradiation with image restoration enables comprehensive analysis of organelle dynamics over extended periods in living cells.
Five new species of the spider genus Heteropoda Latreille, 1804 (Araneae: Sparassidae) from China
(2024)
Five new species of Heteropoda (Araneae, Sparassidae, Heteropodinae) are described from China: H. bawanglingensis sp. nov. (female; Hainan), H. dulongensis sp. nov. (male, female; Yunnan), H. hainanensis sp. nov. (male, female; Hainan), H. longa sp. nov. (female; Guizhou), and H. vaginalis sp. nov. (female; Yunnan). We provide descriptions and illustrations for each species as well as a distribution map in the current paper.
Scalibregmatidae Malmgren, 1867 is a family of annelids, with only few taxa reported from Brazil. In this work, we describe two new species of Asclerocheilus Ashworth, 1901. The new species A. geiseae sp. nov. and A. blakei sp. nov. were collected during scientific expeditions to the Espírito Santo and Campos sedementary basins. These expeditions were coordinated by PETROBRAS/CENPES. The species A. geiseae sp. nov. is unique among its congeners by the presence of acicular spines with rounded and curved tips in two rows. The second species, A. blakei sp. nov., differs from its congeners by the combination of the presence of a trapezoidal prostomium, acicular spines on chaetigers 1–3, lyrate chaetae from chaetiger 3 on notopodia and 2 on neuropodia. Moreover, we report the species A. tropicus Blake, 1981 from the localities sampled on this study. We also provide an identification key to all species of Asclerocheilus of the world.
Sipunculans are a poorly studied group in the Tropical Eastern Pacific. For the Southern Mexican Pacific (SMP) there is only one record of a sipunculan species. The main objective of this work was to determine the species composition of the phylum Sipuncula present in the SMP. The study area covered three Mexican states: Guerrero, Oaxaca and Chiapas; specimens from 28 localities were examined from both intertidal and subtidal zones. A total of 551 specimens were reviewed, from which 11 species were identified. Five of them have previously been recorded in the Tropical Eastern Pacific (TEP): Apionsoma (A.) hespera comb. nov., A. (Edmondsius) pectinatum, Aspidosiphon (A.) elegans, Phascolosoma (P.) puntarenae and Themiste (T.) hennahi; four species are similar to nominal species: Sipunculus (S.) cf. polymyotus, Siphonosoma cf. vastum, Siphonosoma cf. cumanense and Phascolosoma (P.) cf. perlucens; and two new species are described: Aspidosiphon (Paraspidosiphon) cutleri sp. nov. and Aspidosiphon (Paraspidosiphon) pastori sp. nov. A checklist and an identification key for all sipunculan species from the TEP are presented. The checklist includes 53 taxa, 25 of which are questionable records. This work generated 11 new records of sipunculans in the SMP and five new records in the TEP.
A taxonomic study on the Afrotropical genera Afrepipona Giordani Soika, 1965 and Afrepsilon gen. nov. is presented. Twenty new species are described, of which 15 are in Afrepipona (Afrepipona anomala sp. nov., Afrepipona cellularis sp. nov., Afrepipona clonata sp. nov., Afrepipona cuprea sp. nov., Afrepipona lamellata sp. nov., Afrepipona lamptula sp. nov., Afrepipona lobulata sp. nov., Afrepipona meridionalis sp. nov., Afrepipona occidentalis sp. nov., Afrepipona orientalis sp. nov., Afrepipona punctatissima sp. nov., Afrepipona scabra sp. nov., Afrepipona segregata sp. nov., Afrepipona ulterior sp. nov., Afrepipona vulcanica sp. nov.) and five are in Afrepsilon (Afrepsilon aterrimum gen. et sp. nov., Afrepsilon ferrugineoaureum gen. et sp. nov., Afrepsilon hybridum gen. et sp. nov., Afrepsilon minor gen. et sp. nov., and Afrepsilon pictum gen. et sp. nov.). Afrepipona lamptoensis Giordani Soika, 1965 is withdrawn from synonymy with A. angusta (de Saussure, 1863) and subsequently revalidated. Afrepipona unifasciata Gusenleitner, 2012 is transferred to the genus Antodynerus de Saussure, 1855 (Antodynerus unifasciatus comb. nov.). Keys to all known species are provided.
Description of four new species of the Neotropical genus Scione Walker, 1850 (Diptera: Tabanidae)
(2024)
After 94 years after the last revision of the genus and after 22 years since the last species was named, we describe four new species of Scione from Ecuador and Peru: S. cooperi sp. nov., S. gertrudeae sp. nov., S. kroeberi sp. nov. and S. merianae sp. nov. We provide diagnoses, descriptions, photographs and discussions for each of the species.
Regelmäßig werden Debatten um Geschlecht geführt, auch mit dem Fokus auf Schule. So regt die PISA-Studie mit ihren Ergebnissen im Jahr 2000 einen Diskurs um Bildungserfolg und Geschlecht an. Jürgen Budde (2009) vermutet beispielsweise einen engen Zusammenhang vom Schulerfolg eines Jungen mit der jeweiligen Schulkultur und konstatiert in diesem Zusammenhang eine Forschungslücke. Die Studie zu GeschlechterSchulKulturen schließt hier in Bezug auf eine Beforschung von Schulkultur mit Fokus auf Geschlechter an.
Anhand eines gegenstandsverankerten Vorgehens in Form einer Kombination von ethnographischem Forschungsstil und Grounded Theory Methodologie werden Interaktionen und verbale Zuschreibungen im Arrangement zweier integrierter Gesamt- und Ganztagsschulen beforscht. Dabei liegen folgende Forschungsfragen zugrunde: Welche Geschlechterkonstruktionen lassen sich am Beispiel zweier Gesamt- und Ganztagsschulen rekonstruieren? Lassen sich über Geschlechterkonstruktionen im schulischen Kontext spezifische GeschlechterSchulKulturen analytisch fassen und unterscheiden sich die beiden Forschungsfelder darin? Im Rahmen dieser Fragestellungen steht insbesondere die Frage danach im Fokus, welche Geschlechterkonstruktionen die Schüler*innen fünfter Klassen selbst vornehmen. Denn den öffentlichen Diskurs um die Ausbildung von Geschlechtsidentität führen Erwachsene, aber wie konstruieren die Schüler*innen Geschlechtlichkeit in ihrem Schulalltag? Welche Geschlechterzuschreibungen nehmen sie vor und welche möglichen Zusammenhänge lassen sich mit den jeweiligen Schulen rekonstruieren?
In der Studie zu GeschlechterSchulKulturen werden verbale Schüler*innen-Zuschreibungen in den Blick genommen, die in einem zweiten Schritt über einen Vergleich der beiden beforschten Schulen betrachtet und darauf folgend mit den jeweiligen Geschlechter(vor)strukturierungen der Schulen kontextualisiert werden, um damit dem Begriff GeschlechterSchulKulturen analytisch auf die Spur zu kommen. Die Studie liefert dabei zahlreiche Einblicke in verbale Schüler*innen-Zuschreibungen. Daran schließt eine Erörterung möglicher Implikationen für die schulische Praxis an. Dabei liefert die Studie zu GeschlechterSchulKulturen Annahmen zu spezifischen schulischen Kulturen, die bestimmte Konstruktionsprozesse gegebenenfalls (be)fördern. Mit der Studie zu GeschlechterSchulKulturen werden zudem methodologische Fragen zu schulischer Geschlechterforschung bearbeitet und ein Beitrag zu der Darstellbarkeit reflexiver Forschung geleistet.
Correlative dynamic imaging of cellular landmarks, such as nuclei and nucleoli, cell membranes, nuclear envelope and lipid droplets is critical for systems cell biology and drug discovery, but challenging to achieve with molecular labels. Virtual staining of label-free images with deep neural networks is an emerging solution for correlative dynamic imaging. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining leaves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Current approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. We report training protocols for virtual staining of nuclei and membranes robust to variations in imaging parameters, cell states, and cell types. We describe a flexible and scalable convolutional architecture, UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including human cell lines, neuromasts of zebrafish and stem cell (iPSC)-derived neurons, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and cell membranes. The models rescue missing labels, non-uniform expression of labels, and photobleaching. We share three pre-trained models (VSCyto3D, VSNeuromast, and VSCyto2D) and a PyTorch-based pipeline (VisCy) for training, inference, and deployment that leverages current community standards for image data and metadata.
Snapshots of acetyl-CoA synthesis, the final step of CO₂ fixation in the Wood-Ljungdahl pathway
(2024)
In the ancient microbial Wood-Ljungdahl pathway, CO2 is fixed in a multi-step process with acetyl-CoA synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). Here, we present catalytic snapshots of the CODH/ACS from the gas-converting acetogen Clostridium autoethanogenum, characterizing the molecular choreography of the overall reaction including electron transfer to the CODH for CO2 reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme crucial for CO2 fixation in anaerobic organisms.
Members of the arginine–serine-rich protein family (SR proteins) are multifunctional RNA-binding proteins that have emerged as key determinants for mRNP formation, identity and fate. They bind to pre-mRNAs early during transcription in the nucleus and accompany bound transcripts until they are translated or degraded in the cytoplasm. SR proteins are mostly known for their essential roles in constitutive splicing and as regulators of alternative splicing. However, many additional activities of individual SR proteins, beyond splicing, have been reported in recent years. We will summarize the different functions of SR proteins and discuss how multifunctionality can be achieved. We will also highlight the difficulties of studying highly versatile SR proteins and propose approaches to disentangle their activities, which is transferrable to other multifunctional RBPs.
Cell-free (CF) synthesis with highly productive E. coli lysates is a convenient method to produce labeled proteins for NMR studies. Despite reduced metabolic activity in CF lysates, a certain scrambling of supplied isotope labels is still notable. Most problematic are conversions of 15N labels of the amino acids L-Asp, L-Asn, L-Gln, L-Glu and L-Ala, resulting in ambiguous NMR signals as well as in label dilution. Specific inhibitor cocktails suppress most undesired conversion reactions, while limited availability and potential side effects on CF system productivity need to be considered. As alternative route to address NMR label conversion in CF systems, we describe the generation of optimized E. coli lysates with reduced amino acid scrambling activity. Our strategy is based on the proteome blueprint of standardized CF S30 lysates of the E. coli strain A19. Identified lysate enzymes with suspected amino acid scrambling activity were eliminated by engineering corresponding single and cumulative chromosomal mutations in A19. CF lysates prepared from the mutants were analyzed for their CF protein synthesis efficiency and for residual scrambling activity. The A19 derivative “Stablelabel” containing the cumulative mutations asnA, ansA/B, glnA, aspC and ilvE yielded the most useful CF S30 lysates. We demonstrate the optimized NMR spectral complexity of selectively labeled proteins CF synthesized in “Stablelabel” lysates. By taking advantage of ilvE deletion in "Stablelabel", we further exemplify a new strategy for methyl group specific labeling of membrane proteins with the proton pump proteorhodopsin.
Measurements of vertical velocity from vertically pointing Doppler lidars are used to derive the profiles of vertical velocity variance. Observations were taken during the FESSTVaL (Field Experiment on Submesoscale Spatio-Temporal Variability in Lindenberg) campaign during the warm seasons of 2020 and 2021. Normalized by the square of convective velocity scale, the average vertical velocity variance profile follows the universal profile of Lenschow et al. (1980), however, daily profiles still show a high day-to-day variability. We found that moisture transport and the content of moisture in the boundary layer could explain the remaining variability of the normalized vertical velocity variance. The magnitude of the normalized vertical velocity variance is highest on clear-sky days, and decreases as the relative humidity increase and surface latent heat flux decrease in cloud-topped and rainy days. This suggests that moisture content and moisture transport are limiting factors for the intensity of turbulence in the convective boundary layer. We also found that the intensity of turbulence decreases with an increase in boundary layer cloud fraction during FESSTVaL, while the latent heating in the cloud layer was not a relevant source of turbulence in this case. We conclude that a new vertical velocity scale has to be defined that would take into account the moist processes in the convective boundary layer.
Measurements of vertical velocity from vertically pointing Doppler lidars are used to derive the profiles of normalized vertical velocity variance. Observations were taken during the FESSTVaL (Field Experiment on Submesoscale Spatio-Temporal Variability in Lindenberg) campaign during the warm seasons of 2020 and 2021. Normalized by the square of the convective velocity scale, the average vertical velocity variance profile follows the universal profile of Lenschow et al. (1980). However, daily profiles still show a high day-to-day variability. We found that moisture transport and the content of moisture in the boundary layer could explain the remaining variability of the normalized vertical velocity variance. The magnitude of the normalized vertical velocity variance is highest on clear-sky days and decreases as the absolute humidity increases and surface latent heat flux decreases on cloud-topped days. This suggests that moisture content and moisture transport are limiting factors for the intensity of turbulence in the convective boundary layer. We also found that the intensity of turbulence decreases with an increase in the boundary layer cloud fraction during FESSTVaL, while the latent heating in the cloud layer was not a relevant source of turbulence in this case. We conclude that a new vertical velocity scale has to be defined that would take into account the moist processes in the convective boundary layer.
Ziel der vorliegenden Untersuchung war es, die Analytik der Neurotransmitterbestimmung im Liquor zu etablieren und in das vorhandene Leistungsspektrum des Stoffwechsellabors zu integrieren. Die klinische Ausrichtung gilt sowohl der Detektion primärer Neurotransmitterdefekte als auch der Untersuchung der Ursachen und Auswirkungen sekundärer Neurotransmitterstörungen.
Die Messung der Biogenen Amine im Liquor mittels der Hochdruck-Flüssigkeits-Chromatographie in dem hier vorgestellten Verfahren konnte standardisiert und in das vorhandene Leistungsspektrum des Stoffwechsellabors des Zentrums für Kinderheilkunde und Jugendmedizin der J.W. Goethe-Universität, Frankfurt etabliert werden. Es ist nachgewiesenermaßen sensitiv, spezifisch und erlaubt eine schnelle und reproduzierbare Analyse bei minimaler Probenmenge und Probenaufarbeitung.
Meßtechnisch konnte durch den von unserer Arbeitsgruppe verwendeten ESA CoulArray® Detektor (Modell 5600) (im Gegensatz zu den bisher beschriebenen amperometrischen Detektoren) aufgrund seiner 16 einzelnen coulometrischen Sensoren eine enorme Verbesserung der Nachweisqualität der untersuchten Neurotransmittersubstanzen erreicht werden. Aufgrund verschiedener Potentialfelder ist eine spezifische Detektion über einen weiten Einsatzbereich aufgrund der elektrochemischen Unterschiede zu erzielen. Dies ermöglicht eine wesentlich größere Anzahl zu detektierender Substanzen eindeutig zu identifizieren und erlaubt damit nicht nur die eindeutige Zuordnung der zu messenden Endabbauprodukte HVA und 5HIAA, sondern auch des gesamten Spektrums der vorgeschalteten Metabolite. Somit ließ sich mit diesem aufgebauten Analysesystem die komplexe vollständige Abbildung des Stoffwechselwegs der zentralen biogenen Amine verwirklichen.
Die sehr sensible Messung der Parameter stellt große Anforderung an
Probengewinnung, Probenverarbeitung und Meßanalyse. Aufgrund der
Durchführung interner Qualitäskontrolluntersuchungen konnte der Nachweis einer sicheren reproduzierbaren Analytik erbracht werden. Insbesondere die Notwendigkeit der ausreichenden Unterdrückung der weiter ablaufenden chemischen Prozesse durch die unmittelbare Kühlung der Liquorproben auf eine Temperatur von -80°C wurde nachgewiesen. Zusätzlich konnte gezeigt werden, dass die Verwendung von handelsüblichen EDTA-Röhrchen einen ausreichenden antioxidativen Schutz bietet und wir somit eine anwenderfreundliche Probengewinnung empfehlen können. Die strikte Einhaltung des Protokolls zur Gewinnung und weiteren Verarbeitung der Liquorproben ist elementar und stellt insbesondere bei zur Zeit noch bestehenden uneinheitlichen altersabhängigen Referenzwerten die Grundlage zur diagnostischen Bewertung der gemessenen Werte dar. Eine Standardisierung der Referenzwerte auf internationaler Ebene ist unverzichtbar zur korrekten Interpretation der gemessenen Daten und sollte vorrangiges Streben aller beteiligten Laboratorien sein. Ein entsprechender Antrag auf ein erneutes, jährlich stattfindendes externes Qualitätskontrollprogramm (Ringversuch) wurde gestellt.
Mit der Bestimmung der Biogenen Amine im Liquor steht ein potentes Instrument zur Detektion pädiatrischer Neurotransmittererkrankungen zur Verfügung. Es gibt weltweit jedoch nur eine geringe Anzahl von Laboratorien mit diesem Analyseangebot. Somit trägt die Etablierung dieser Analytik im vorhandenen Leistungsspektrum des Stoffwechsellabors des Zentrums für Kinderheilkunde und Jugendmedizin der J.W. Goethe-Universität, Frankfurt dazu bei diese Lücke zu schließen. In der Mehrzahl sind Erkrankungen der zentralen Biogenen Amine ausschließlich nur über eine Messung der Metaboliten im Liquor diagnostizierbar, nur wenige angeborene Neurotransmitterdefekte fallen durch periphere Serumparameter, wie z.B. einer Hyperphenylalaninämie auf. Es ergibt sich der Verdacht, dass diese Erkrankungsformen unterdiagnostiziert sind und auch das Wissen um diese Erkrankungen nicht allgemein vorausgesetzt werden kann.
Mit den Neurotransmittervorstufen (z.B. L-Dopa oder 5OH-Tryptophan) steht betroffenen Patienten eine adäquate Therapieoption zur Verfügung, so dass die Aufdeckung eines spezifischen Defektes in der Synthese der Biogenen Amine vorrangiges Ziel sein müsste. Exemplarisch für die beeindruckende Effektivität der Therapie mittels L-Dopa und 5OH-Tryptophan sei auf den Erfahrungsbericht des von unserer Arbeitsgruppe betreuten Patienten mit 6-PTPS-Defekt verwiesen.
Zusätzlich konnte mit dieser Arbeit gezeigt werden, dass die wiederholenden Messungen dem Therapiemonitoring dienen und eine unverzichtbare Grundlage der individuellen Therapie betroffener Patienten darstellen. Sekundäre Veränderungen der Neurotransmission sind beschrieben, jedoch fehlen weitergehende Untersuchungen zur Einordnung ihrer klinischen Relevanz. Gerade diese große inhomogene Patientengruppe stellt eine zukünftige Herausforderung für weitere wissenschaftliche Anstrengungen in diesem Bereich dar. Wie anhand des Beispiels der Patienten mit mitochondrialer Enzephalopathie dargestellt, kann die vorhandene Analysemethode dazu beitragen das Wissen um die Pathophysiologie bekannter Erkrankungen zu erweitern. Da analog zu den primären Erkrankungen auch hier Therapieoptionen zur Verfügung stehen würden, ist es dringend notwendig die übliche Liquordiagnostik diesbezüglich auszudehnen. Aufgrund der auch im Rahmen dieser Arbeit erhobenen Daten kann gefolgert werden bei ungeklärten neuropädiatrischen Erkrankungen, besonders jenen, welche in der Neonatal- oder frühen Säuglingszeit beginnen und progredient verlaufen, und sich klinisch durch Dyskinesien, Krampfanfälle und Enzephalopathien äußern, eine Liquoruntersuchung auf Biogene Amine zu veranlassen.
Somit dient die erbrachte Arbeit zur Etablierung der Analytik der Neurotransmitterbestimmung im Liquor dem Erkenntnisgewinn neuer metabolischer Erkrankungen, erweitert das Grundlagenwissen bekannter Störungen und dient der Detektion seltener, jedoch oft schwerwiegender Erkrankungen.