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The STAR Collaboration at the Relativistic Heavy Ion Collider presents measurements of 𝐽/𝜓→𝑒+𝑒− at midrapidity and high transverse momentum (𝑝𝑇>5 GeV/𝑐) in 𝑝+𝑝 and central Cu+Cu collisions at √𝑠𝑁𝑁=200 GeV. The inclusive 𝐽/𝜓 production cross section for Cu+Cu collisions is found to be consistent at high 𝑝𝑇 with the binary collision-scaled cross section for 𝑝+𝑝 collisions. At a confidence level of 97%, this is in contrast to a suppression of 𝐽/𝜓 production observed at lower 𝑝𝑇. Azimuthal correlations of 𝐽/𝜓 with charged hadrons in 𝑝+𝑝 collisions provide an estimate of the contribution of 𝐵-hadron decays to 𝐽/𝜓 production of 13%±5%.
The STAR Collaboration reports measurements of back-to-back azimuthal correlations of di-π0s produced at forward pseudorapidities (2.6<η<4.0) in p+p, p+Al, and p+Au collisions at a center-of-mass energy of 200 GeV. We observe a clear suppression of the correlated yields of back-to-back π0 pairs in p+Al and p+Au collisions compared to the p+p data. The observed suppression of back-to-back pairs as a function of transverse momentum suggests nonlinear gluon dynamics arising at high parton densities. The larger suppression found in p+Au relative to p+Al collisions exhibits a dependence of the saturation scale, Q2s, on the mass number, A. A linear scaling of the suppression with A1/3 is observed with a slope of −0.09 ± 0.01.
The STAR Collaboration reports measurements of back-to-back azimuthal correlations of di-π0s produced at forward pseudorapidities (2.6<η<4.0) in p+p, p+Al, and p+Au collisions at a center-of-mass energy of 200 GeV. We observe a clear suppression of the correlated yields of back-to-back π0 pairs in p+Al and p+Au collisions compared to the p+p data. The observed suppression of back-to-back pairs as a function of event activity and transverse momentum suggests nonlinear gluon dynamics arising at high parton densities. The larger suppression found in p+Au relative to p+Al collisions exhibits a dependence of the saturation scale, Q2s, on the mass number, A. The suppression in high-activity p+Au collisions is consistent with theoretical predictions including gluon saturation effects.
The acceptance-corrected dielectron excess mass spectra, where the known hadronic sources have been subtracted from the inclusive dielectron mass spectra, are reported for the first time at mid-rapidity |yee|<1 in minimum-bias Au+Au collisions at sNN−−−−√ = 19.6 and 200 GeV. The excess mass spectra are consistently described by a model calculation with a broadened ρ spectral function for Mee<1.1 GeV/c2. The integrated dielectron excess yield at sNN−−−−√ = 19.6 GeV for 0.4<Mee<0.75 GeV/c2, normalized to the charged particle multiplicity at mid-rapidity, has a value similar to that in In+In collisions at sNN−−−−√ = 17.3 GeV. For sNN−−−−√ = 200 GeV, the normalized excess yield in central collisions is higher than that at sNN−−−−√ = 17.3 GeV and increases from peripheral to central collisions. These measurements indicate that the lifetime of the hot, dense medium created in central Au+Au collisions at sNN−−−−√ = 200 GeV is longer than those in peripheral collisions and at lower energies.
Partons traversing the strongly interacting medium produced in heavy-ion collisions are expected to lose energy depending on their color charge and mass. We measure the nuclear modification factors for charm- and bottom-decay electrons, defined as the ratio of yields, scaled by the number of binary nucleon-nucleon collisions, in sNN−−−√ = 200 GeV Au+Au collisions to p+p collisions (RAA), or in central to peripheral Au+Au collisions (RCP). We find the bottom-decay electron RAA and RCP to be significantly higher than that of charm-decay electrons. Model calculations including mass-dependent parton energy loss in a strongly coupled medium are consistent with the measured data. These observations provide clear evidence of mass ordering of charm and bottom quark energy loss when traversing through the strongly coupled medium created in heavy-ion collisions.
Partons traversing the strongly interacting medium produced in heavy-ion collisions are expected to lose energy depending on their color charge and mass. We measure the nuclear modification factors for charm- and bottom-decay electrons, defined as the ratio of yields, scaled by the number of binary nucleon-nucleon collisions, in sNN−−−√ = 200 GeV Au+Au collisions to p+p collisions (RAA), or in central to peripheral Au+Au collisions (RCP). We find the bottom-decay electron RAA and RCP to be significantly higher than that of charm-decay electrons. Model calculations including mass-dependent parton energy loss in a strongly coupled medium are consistent with the measured data. These observations provide clear evidence of mass ordering of charm and bottom quark energy loss when traversing through the strongly coupled medium created in heavy-ion collisions.
Partons traversing the strongly interacting medium produced in heavy-ion collisions are expected to lose energy depending on their color charge and mass. We measure the nuclear modification factors for charm- and bottom-decay electrons, defined as the ratio of yields, scaled by the number of binary nucleon-nucleon collisions, in sNN−−−√ = 200 GeV Au+Au collisions to p+p collisions (RAA), or in central to peripheral Au+Au collisions (RCP). We find the bottom-decay electron RAA and RCP to be significantly higher than that of charm-decay electrons. Model calculations including mass-dependent parton energy loss in a strongly coupled medium are consistent with the measured data. These observations provide clear evidence of mass ordering of charm and bottom quark energy loss when traversing through the strongly coupled medium created in heavy-ion collisions.
Partons traversing the strongly interacting medium produced in heavy-ion collisions are expected to lose energy depending on their color charge and mass. We measure the nuclear modification factors for charm- and bottom-decay electrons, defined as the ratio of yields, scaled by the number of binary nucleon-nucleon collisions, in sNN−−−√ = 200 GeV Au+Au collisions to p+p collisions (RAA), or in central to peripheral Au+Au collisions (RCP). We find the bottom-decay electron RAA and RCP to be significantly higher than that of charm-decay electrons. Model calculations including mass-dependent parton energy loss in a strongly coupled medium are consistent with the measured data. These observations provide clear evidence of mass ordering of charm and bottom quark energy loss when traversing through the strongly coupled medium created in heavy-ion collisions.
Partons traversing the strongly interacting medium produced in heavy-ion collisions are expected to lose energy depending on their color charge and mass. We measure the nuclear modification factors for charm- and bottom-decay electrons, defined as the ratio of yields, scaled by the number of binary nucleon-nucleon collisions, in sNN−−−√ = 200 GeV Au+Au collisions to p+p collisions (RAA), or in central to peripheral Au+Au collisions (RCP). We find the bottom-decay electron RAA and RCP to be significantly higher than that of charm-decay electrons. Model calculations including mass-dependent parton energy loss in a strongly coupled medium are consistent with the measured data. These observations provide clear evidence of mass ordering of charm and bottom quark energy loss when traversing through the strongly coupled medium created in heavy-ion collisions.
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 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 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.
Particulate matter (PM) largely consists of secondary organic aerosol (SOA) that is formed via oxidation of biogenic and anthropogenic volatile organic compounds (VOCs). Unambiguous identification of SOA molecules and their assignment to their precursor vapors are challenges that have so far only succeeded for a few SOA marker compounds, which are now well characterized and (partly) available as authentic standards. In this work, we resolve the complex composition of SOA by means of a top-down approach based on the newly created Aerosolomics database, which is fed by non-target analysis results of filter samples from oxidation flow reactor experiments. We investigated the oxidation products from the five biogenic VOCs α-pinene, β-pinene, limonene, 3-carene, and trans-caryophyllene and from the four anthropogenic VOCs toluene, o-xylene, 1,2,4-trimethylbenzene, and naphthalene. Using ultrahigh-performance liquid chromatography coupled to a high-resolution (Orbitrap) mass spectrometer, we determine the molecular formula of 596 chromatographically separated compounds based on exact mass and isotopic pattern. We utilize retention time and fragmentation mass spectra as a basis for unambiguous attribution of the oxidation products to their parent VOCs. Based on the molecular-resolved application of the database, we are able to assign roughly half of the total signal of oxygenated hydrocarbons in ambient suburban PM2.5 to one of the nine studied VOCs. The application of the database enabled us to interpret the appearance of diurnal compound clusters that are formed by different oxidation processes. Furthermore, by performing a hierarchical cluster analysis (HCA) on the same set of filter samples, we identified compound clusters that depend on sulfur dioxide mixing ratio and temperature. This study demonstrates how Aerosolomics tools (database and HCA) applied to PM filter samples can improve our understanding of SOA sources, their formation pathways, and temperature-driven partitioning of SOA compounds.
Adaptive teaching is considered fundamental to teaching quality and student learning. It describes teachers’ practices of adjusting their instruction to students’ diverse needs and levels of understanding. Adaptive teaching on a micro level has also been labeled as contingent support and has been shown to be effective in one-to-one and small-group settings. In the literature, the interplay of teachers’ diagnostic strategies and instructional prompts aiming at tailored support are emphasized. Our study adds to this research by presenting a reliable measurement approach to adaptive classroom discourse in elementary science which includes a global index and the single indices of diagnostic strategies, instructional support, and student understanding. Applying this coding scheme, we investigate whether N = 17 teachers’ adaptive classroom discourse predicts N = 341 elementary school students’ conceptual understanding of “floating and sinking” on two posttests. In multilevel regression analyses, adaptive classroom discourse was shown to be effective for long-term student learning in the final posttest, while no significant effects were found for the intermediate posttest. Further, the single index of diagnostic strategies in classroom discourse contributed to long-term conceptual restructuring. Overall, teachers rarely acted adaptively which points to the relevance of teacher professional development.
This article attempts to read the Transcendental Dialectic through Meillassoux’s model of the absolute contingency of being in order to rethink some of its central difficulties. Specifically, this concerns better understanding the role played by the categories of relation and modality in the empirical use of the ideas of reason, which underlies their regulative use that is directed at an absolute unity of reason. It will be discussed which questions are implied in the central claim of Meillassoux’s ontology, i.e., that it is possible to derive from the necessity of contingency the existence and noncontradictory being of the thing in itself. First, I will retrace basic points of Meillassoux’s critique of “correlationism”, by means of which he reconfigures the divisions between metaphysics, physics, and ontology. Second, against the background of the Kantian concept of hope, I will examine a relation between the Transcendental Dialectic and ethics, as, respectively, conceived of in Kant and in Meillassoux’s reinterpretation. Third, I will critically ask in how far absolute contingency can be understood as grounding a concept of experience and in which sense the idea of the antinomy chapter in the Transcendental Dialectic contains an argument more complex than Meillassoux’s model suggests.
We fabricated memristive devices using focused electron beam-induced deposition (FEBID) as a direct-writing technique employing a Pt/TiO2/Pt sandwich layer device configuration. Pinching in the measured current-voltage characteristics (i-v), the characteristic fingerprint of memristive behavior was clearly observed. The temperature dependence was measured for both high and low resistive states in the range from 290 K down to about 2 K, showing a stretched exponential behavior characteristic of Mott-type variable-range hopping. From this observation, a valence change mechanism of the charge transport inside the TiO2 layer can be deduced.
The strong force, as one of the four fundamental forces at work in the universe, governs interactions of quarks and gluons, and binds together the atomic nucleus. Notwithstanding decades of progress since Yukawa first developed a description of the force between nucleons in terms of meson exchange, a full understanding of the strong interaction remains a major challenge in modern science. One remaining difficulty arises from the non-perturbative nature of the strong force, which leads to the phenomenon of quark confinement at distance scales on the order of the size of the proton. Here we show that in relativistic heavy-ion collisions, where quarks and gluons are set free over an extended volume, two species of produced vector (spin-1) mesons, namely ϕ and K∗0, emerge with a surprising pattern of global spin alignment. In particular, the global spin alignment for ϕ is unexpectedly large, while that for K∗0 is consistent with zero. The observed spin-alignment pattern and magnitude for the ϕ cannot be explained by conventional mechanisms, while a model with strong force fields accommodates the current data. This is the first time that the strong force field is experimentally supported as a key mechanism that leads to global spin alignment. We extract a quantity proportional to the intensity of the field of the strong force. Within the framework of the Standard Model, where the strong force is typically described in the quark and gluon language of Quantum Chromodynamics, the field being considered here is an effective proxy description. This is a qualitatively new class of measurement, which opens a new avenue for studying the behaviour of strong force fields via their imprint on spin alignment.
The strong force, as one of the four fundamental forces at work in the universe, governs interactions of quarks and gluons, and binds together the atomic nucleus. Notwithstanding decades of progress since Yukawa first developed a description of the force between nucleons in terms of meson exchange, a full understanding of the strong interaction remains a major challenge in modern science. One remaining difficulty arises from the non-perturbative nature of the strong force, which leads to the phenomenon of quark confinement at distance scales on the order of the size of the proton. Here we show that in relativistic heavy-ion collisions, where quarks and gluons are set free over an extended volume, two species of produced vector (spin-1) mesons, namely ϕ and K∗0, emerge with a surprising pattern of global spin alignment. In particular, the global spin alignment for ϕ is unexpectedly large, while that for K∗0 is consistent with zero. The observed spin-alignment pattern and magnitude for the ϕ cannot be explained by conventional mechanisms, while a model with strong force fields accommodates the current data. This is the first time that the strong force field is experimentally supported as a key mechanism that leads to global spin alignment. We extract a quantity proportional to the intensity of the field of the strong force. Within the framework of the Standard Model, where the strong force is typically described in the quark and gluon language of Quantum Chromodynamics, the field being considered here is an effective proxy description. This is a qualitatively new class of measurement, which opens a new avenue for studying the behaviour of strong force fields via their imprint on spin alignment.
Notwithstanding decades of progress since Yukawa first developed a description of the force between nucleons in terms of meson exchange, a full understanding of the strong interaction remains a major challenge in modern science. One remaining difficulty arises from the non-perturbative nature of the strong force, which leads to the phenomenon of quark confinement at distances on the order of the size of the proton. Here we show that in relativistic heavy-ion collisions, where quarks and gluons are set free over an extended volume, two species of produced vector (spin-1) mesons, namely ϕ and K∗0, emerge with a surprising pattern of global spin alignment. In particular, the global spin alignment for ϕ is unexpectedly large, while that for K∗0 is consistent with zero. The observed spin-alignment pattern and magnitude for the ϕ cannot be explained by conventional mechanisms, while a model with a connection to strong force fields, i.e. an effective proxy description within the Standard Model and Quantum Chromodynamics, accommodates the current data. This connection, if fully established, will open a potential new avenue for studying the behaviour of strong force fields.
Di-hadron correlations with identified leading hadrons in 200 GeV Au+Au and d+Au collisions at STAR
(2015)
The STAR collaboration presents for the first time two-dimensional di-hadron correlations with identified leading hadrons in 200 GeV central Au+Au and minimum-bias d+Au collisions to explore hadronization mechanisms in the quark gluon plasma. The enhancement of the jet-like yield for leading pions in Au+Au data with respect to the d+Au reference and the absence of such an enhancement for leading non-pions (protons and kaons) are discussed within the context of a quark recombination scenario. The correlated yield at large angles, specifically in the \emph{ridge region}, is found to be significantly higher for leading non-pions than pions. The consistencies of the constituent quark scaling, azimuthal harmonic model and a mini-jet modification model description of the data are tested, providing further constraints on hadronization.
A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at sNN−−−√=27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η|<1.0 and at forward rapidity 2.1<|η|<5.1. We compare the results based on the directed flow plane (Ψ1) at forward rapidity and the elliptic flow plane (Ψ2) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to Ψ1 than to Ψ2, while a flow driven background scenario would lead to a consistent result for both event planes. In 10-50\% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95\% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.
A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at sNN−−−√=27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η|<1.0 and at forward rapidity 2.1<|η|<5.1. We compare the results based on the directed flow plane (Ψ1) at forward rapidity and the elliptic flow plane (Ψ2) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to Ψ1 than to Ψ2, while a flow driven background scenario would lead to a consistent result for both event planes. In 10-50\% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95\% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.
A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at sNN−−−√=27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η|<1.0 and at forward rapidity 2.1<|η|<5.1. We compare the results based on the directed flow plane (Ψ1) at forward rapidity and the elliptic flow plane (Ψ2) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to Ψ1 than to Ψ2, while a flow driven background scenario would lead to a consistent result for both event planes[1,2]. In 10-50\% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95\% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.
Lilli Jergitsch, 1904–1988
(2024)
Hans Jacob : Bibliographie
(2024)
Hans Jacob, 1896–1961
(2024)
A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at sNN−−−√=27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η|<1.0 and at forward rapidity 2.1<|η|<5.1. We compare the results based on the directed flow plane (Ψ1) at forward rapidity and the elliptic flow plane (Ψ2) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to Ψ1 than to Ψ2, while a flow driven background scenario would lead to a consistent result for both event planes. In 10-50\% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95\% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.
Obwohl Therese Huber (geborene Heyne, verwitwete Forster) zeit ihres Lebens keine einzige Übersetzung unter ihrem Namen veröffentlicht hat - sieht man von einer Romanbearbeitung ab, die als ihr Originalwerk publiziert wurde - ist sie dennoch eine nicht zu vernachlässigende Figur in der Geschichte der Übersetzung an der Wende vom 18. zum 19. Jahrhundert.
Horbatsch übersetzte seit Ende 1940er Jahre Texte ukrainischer Schriftsteller ins Deutsche und engagierte sich für die Verbreitung ukrainischer Literatur in Westdeutschland. Sie machte sich einen Namen als Übersetzerin, nachdem von ihr zwei große Anthologien ukrainischer Literatur vorbereitet und herausgegeben wurden: "Blauer November. Ukrainische Erzähler unseres Jahrhunderts" (1959) und "Ein Brunnen für Durstige und andere ukrainische Erzählungen" (1970).
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.
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.