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The argument that I tried to elaborate on in this paper is that the conceptual problem behind the traditional competence/performance distinction does not go away, even if we abandon its original Chomskyan formulation. It returns as the question about the relation between the model of the grammar and the results of empirical investigations – the question of empirical verification The theoretical concept of markedness is argued to be an ideal correlate of gradience. Optimality Theory, being based on markedness, is a promising framework for the task of bridging the gap between model and empirical world. However, this task not only requires a model of grammar, but also a theory of the methods that are chosen in empirical investigations and how their results are interpreted, and a theory of how to derive predictions for these particular empirical investigations from the model. Stochastic Optimality Theory is one possible formulation of a proposal that derives empirical predictions from an OT model. However, I hope to have shown that it is not enough to take frequency distributions and relative acceptabilities at face value, and simply construe some Stochastic OT model that fits the facts. These facts first of all need to be interpreted, and those factors that the grammar has to account for must be sorted out from those about which grammar should have nothing to say. This task, to my mind, is more complicated than the picture that a simplistic application of (not only) Stochastic OT might draw.
The regeneration of hadronic resonances is discussed for heavy ion collisions at SPS and SIS-300 energies. The time evolutions of Delta, rho and phi resonances are investigated. Special emphasize is put on resonance regeneration after chemical freeze-out. The emission time spectra of experimentally detectable resonances are explored.
We predict transverse and longitudinal momentum spectra and yields of rho 0 and omega mesons reconstructed from hadron correlations in C+C reactions at 2~AGeV. The rapidity and pT distributions for reconstructable rho 0 mesons differs strongly from the primary distribution, while the omega's distributions are only weakly modified. We discuss the temporal and spatial distributions of the particles emitted in the hadron channel. Finally, we report on the mass shift of the rho 0 due to its coupling to the N*(1520), which is observable in both the di-lepton and pi pi channel. Our calculations can be tested with the Hades experiment at GSI, Darmstadt.
The establishment and maintenance of protected areas(PAs) is viewed as a key action in delivering post-2020 biodiversity targets. PAs often need to meet a multitude of objectives, ranging from biodiversity protection to ecosystem service provision and climate change mitigation. As available land and conservation funding are limited, optimizing resources by selecting the most beneficial PAs is vital. Here we present a decision support tool that enables a flexible approach to PA selection on a global scale, allowing different conservation objectives to be weighted and prioritized according to user-specified preferences. We apply the tool across 1347 terrestrial PAs and highlight frequent trade-offs among different objectives, e.g., between biodiversity protection and ecosystem integrity. These results indicate that decision makers must usually decide among conflicting objectives. To assist this our decision support tool provides an explicitly value-based approach that can help resolve such conflicts by considering divergent societal and political demands and values.
The establishment and maintenance of protected areas (PAs) is viewed as a key action in delivering post-2020 biodiversity targets. PAs often need to meet multiple objectives, ranging from biodiversity protection to ecosystem service provision and climate change mitigation, but available land and conservation funding is limited. Therefore, optimizing resources by selecting the most beneficial PAs is vital. Here, we advocate for a flexible and transparent approach to selecting protected areas based on multiple objectives, and illustrate this with a decision support tool on a global scale. The tool allows weighting and prioritization of different conservation objectives according to user-specified preferences, as well as real-time comparison of the selected areas that result from such different priorities. We apply the tool across 1347 terrestrial PAs and highlight frequent trade-offs among different objectives, e.g., between species protection and ecosystem integrity. Outputs indicate that decision makers frequently face trade-offs among conflicting objectives. Nevertheless, we show that transparent decision-support tools can reveal synergies and trade-offs associated with PA selection, thereby helping to illuminate and resolve land-use conflicts embedded in divergent societal and political demands and values.
Ongoing climate change is a major threat to biodiversity and impacts on species distributions and abundances are already evident. Heterogenous responses of species due to varying abiotic tolerances and dispersal abilities have the potential to further amplify or ameliorate these impacts through changes in species assemblages. Here we investigate the impacts of climate change on terrestrial bird distributions and, subsequently, on species richness as well as on different aspects of phylogenetic diversity of species assemblages across the globe. We go beyond previous work by disentangling the potential impacts on assemblage phylogenetic diversity of species gains vs. losses under climate change and compare the projected impacts to randomized assemblage changes.
We show that climate change might not only affect species numbers and composition of global species assemblages but could also have profound impacts on assemblage phylogenetic diversity, which, across extensive areas, differ significantly from random changes. Both the projected impacts on phylogenetic diversity and on phylogenetic structure vary greatly across the globe. Projected increases in the evolutionary history contained within species assemblages, associated with either increasing phylogenetic diversification or clustering, are most frequent at high northern latitudes. By contrast, projected declines in evolutionary history, associated with increasing phylogenetic over-dispersion or homogenisation, are projected across all continents.
The projected widespread changes in the phylogenetic structure of species assemblages show that changes in species richness do not fully reflect the potential threat from climate change to ecosystems. Our results indicate that the most severe changes to the phylogenetic diversity and structure of species assemblages are likely to be caused by species range shifts rather than range reductions and extinctions. Our findings highlight the importance of considering diverse measures in climate impact assessments and the value of integrating species-specific responses into assessments of entire community changes.
Abstract
The endoplasmic reticulum (ER) is a key organelle of membrane biogenesis and crucial for the folding of both membrane and secretory proteins. Sensors of the unfolded protein response (UPR) monitor the unfolded protein load in the ER and convey effector functions for maintaining ER homeostasis. Aberrant compositions of the ER membrane, referred to as lipid bilayer stress, are equally potent activators of the UPR. How the distinct signals from lipid bilayer stress and unfolded proteins are processed by the conserved UPR transducer Ire1 remains unknown. Here, we have generated a functional, cysteine-less variant of Ire1 and performed systematic cysteine crosslinking experiments in native membranes to establish its transmembrane architecture in signaling-active clusters. We show that the transmembrane helices of two neighboring Ire1 molecules adopt an X-shaped configuration independent of the primary cause for ER stress. This suggests that different forms of stress converge in a common, signaling-active transmembrane architecture of Ire1.
Summary
The endoplasmic reticulum (ER) is a hotspot of lipid biosynthesis and crucial for the folding of membrane and secretory proteins. The unfolded protein response (UPR) controls the size and folding capacity of the ER. The conserved UPR transducer Ire1 senses both unfolded proteins and aberrant lipid compositions to mount adaptive responses. Using a biochemical assay to study Ire1 in signaling-active clusters, Väth et al. provide evidence that the neighboring transmembrane helices of clustered Ire1 form an ‘X’ irrespectively of the primary cause of ER stress. Hence, different forms of ER stress converge in a common, signaling-active transmembrane architecture of Ire1.
Bisphenols and phthalates, chemicals frequently used in plastic products, promote obesity in cell and animal models. However, these well-known metabolism disrupting chemicals (MDCs) represent only a minute fraction of all compounds found in plastics. To gain a comprehensive understanding of plastics as a source of exposure to MDCs, we characterized all chemicals present in 34 everyday products using nontarget high-resolution mass spectrometry and analyzed their joint adipogenic activities by high-content imaging. We detected 55,300 chemical features and tentatively identified 629 unique compounds, including 11 known MDCs. Importantly, chemicals that induced proliferation, growth, and triglyceride accumulation in 3T3-L1 adipocytes were found in one third of the products. Since the majority did not target peroxisome proliferator-activated receptor γ, the effects are likely to be caused by unknown MDCs. Our study demonstrates that daily-use plastics contain potent mixtures of MDCs and can, therefore, be a relevant yet underestimated environmental factor contributing to obesity.
Teaser Plastics contain a potent mixture of chemicals promoting adipogenesis, a key process in developing obesity.
With the emergence of immunotherapies, the understanding of functional HLA class I antigen presentation to T cells is more relevant than ever. Current knowledge on antigen presentation is based on decades of research in a wide variety of cell types with varying antigen presentation machinery (APM) expression patterns, proteomes and HLA haplotypes. This diversity complicates the establishment of individual APM contributions to antigen generation, selection and presentation. Therefore, we generated a novel Panel of APM Knockout Cell lines (PAKC) from the same genetic origin. After CRISPR/Cas9 genome-editing of ten individual APM components in a human cell line, we derived clonal cell lines and confirmed their knockout status and phenotype. We then show how PAKC will accelerate research on the functional interplay between APM components and their role in antigen generation and presentation. This will lead to improved understanding of peptide-specific T cell responses in infection, cancer and autoimmunity.
CONCLUSION The analysis of the exposure measurement problem has shown that the proper measurement of counterparty exposure for portfolios of derivatives transactions is a complex task that cannot be performed without making a lot of simplifying assumptions. Because of the complicated interaction of correlation effects and offsettings from different transactions, the single transaction framework which is currently used by most banks is definitely not capable of accurately determining the portfolio credit risk. When simulation techniques are applied to estimate exposure, the accuracy of exposure estimations can be increased significantly. However, a lot of modelling choices has to be made concerning the valuation of transactions and the stochastic model of underlying market rates. Because the system has to make projections of market rates into the far future, the choice of an appropriate stochastic model for market rate dynamics is crucial in order to prevent unreasonable scenarios. The predominant application of models based on Brownian Motion in today’s bank risk management therefore leads to questionable results in respect to derivatives exposure evaluation.
The gradual heterogeneity of climatic factors pose varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift, and adaptation to non-clinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data, and population genetic modelling. Common-garden experiments revealed a positive correlation of population growth rates corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an FST outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in other studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.
The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different length, linkage-type and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying length, as well as, homotypic and heterotypic branched chains of the two most abundant linkage types – K48- and K63-linked Ub. We identified some of the first K48/K63 branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4 and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50 and p97-adaptor FAF1. Crucially, we compared datasets collected using two common DUB inhibitors – Chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.
By using the background field method of QCD in a path integral approach, we derive the equation of motion for the classical chromofield and for the gluon in a system containing the gluon and the classical chromofield simul- taneously. This inhomogeneous field equation contains a current term, which is the expectation value of a composite operator including linear, square and cubic terms of the gluon field. We also derive identities which the current should obey from the gauge invariance. We calculate the current at the leading order where the current induced by the gluon is opposite in sign to that induced by the quark. This is just the feature of the non-Abelian gauge field theory which has asymptotic freedom. Physically, the induced current can be treated as the displacement current in the polarized vacuum, and its e ect is equivalent to redefining the field and the coupling constant. PACS: 12.38.-t,12.38.Aw,11.15.-q,12.38.Mh
The non-equilibrium quantum field dynamics is usually described in the closed-time-path formalism. The initial state correlations are introduced into the generating functional by non-local source terms. We propose a functional approach to the Dyson-Schwinger equation, which treats the non-local and local source terms in the same way. In this approach, the generating functional is formulated for the connected Green functions and one-particle-irreducible vertices. The great advantages of our approach over the widely used two-particle-irreducible method are that it is much simpler and that it is easy to implement the procedure in a computer program to automatically generate the Feynman diagrams for a given process. The method is then applied to a pure gluon plasma to derive the gauge-covariant transport equation from the Dyson-Schwinger equation in the background covariant gauge. We discuss the structure of the kinetic equation and show its relationship with the classical one. We derive the gauge-covariant collision part and present an approximation in the vicinity of equilibrium. The role of the non-local source kernel in the non-equilibrium system is discussed in the context of a free scalar field. PACS numbers: 12.38.Mh, 25.75.-q, 24.85.+p, 11.15.Kc
We derive the kinetic equation for pure gluon QCD plasma in a general way, applying the background field method. We show that the quantum kinetic equation contains a term as in the classical case, that describes a color charge precession of partons moving in the gauge field. We emphasize that this new term is necessary for the gauge covariance of the resulting equation.
We derive the quantum kinetic equation for a pure gluon plasma, applying the background field and closed-time-path method. The derivation is more general and transparent than earlier works. A term in the equation is found which, as in the classical case, corresponds to the color charge precession for partons moving in the gauge field. PACS numbers: 12.38.Mh, 25.75.-q, 24.85.+p, 11.15.Kc
We calculate p, ±,K± and (+ 0) rapidity distributions and compare to experimental data from SIS to SPS energies within the UrQMD and HSD transport approaches that are both based on string, quark, diquark (q, ¯q, qq, ¯q ¯q) and hadronic degrees of freedom. The two transport models do not include any explicit phase transition to a quark-gluon plasma (QGP). It is found that both approaches agree rather well with each other and with the experimental rapidity distributions for protons, s, ± and K±. In- spite of this apparent agreement both transport models fail to reproduce the maximum in the excitation function for the ratio K+/ + found experimen- tally between 11 and 40 A·GeV. A comparison to the various experimental data shows that this failure is dominantly due to an insu cient description of pion rapidity distributions rather than missing strangeness . The modest di erences in the transport model results on the other hand can be attributed to di erent implementations of string formation and frag- mentation, that are not su ciently controlled by experimental data for the elementary reactions in vacuum.
We study central collision of Pb + Pb at 20, 40, 80 and 160 A·GeV within the UrQMD transport approach and compare rapidity distributions of ,K+,K and with the recent measurements from the NA49 Collaboration at 40, 80 and 160 A·GeV. It is found that the UrQMD model reasonably describes the data, however, systematically overpredicts the yield by < 20%, whereas the K+ yield is underestimated by < 15%. The K yields are in a good agreement with the experimental data, the yields are also in a reasonable correspondence with the data for all energies. We find that hadronic flavour exchange reactions largely distort the information about the initial strangeness production mechanism at all energies considered. PACS: 25.75.+r
We estimate the energy density epsilon pile-up at mid-rapidity in central Pb+Pb collisions from 2 200 GeV/nucleon. epsilon is decomposed into hadronic and partonic contributions. A detailed analysis of the collision dynamics in the framework of a microscopic transport model shows the importance of partonic degrees of freedom and rescattering of leading (di)quarks in the early phase of the reaction for Elab 30 GeV/nucleon. In Pb+Pb collisions at 160 GeV/nucleon the energy density reaches up to 4 GeV/fm3, 95% of which are contained in partonic degrees of freedom.
The amount of proton stopping in central Pb+Pb collisions from 20 160 A·GeV as well as hyperon and antihyperon rapidity distributions are calcu- lated within the UrQMD model in comparison to experimental data at 40, 80 and 160 A·GeV taken recently from the NA49 collaboration. Further- more, the amount of baryon stopping at 160 A·GeV for Pb + Pb collisions is studied as a function of centrality in comparison to the NA49 data. We find that the strange baryon yield is reasonably described for central colli- sions, however, the rapidity distributions are somewhat more narrow than the data. Moreover, the experimental antihyperon rapidity distributions at 40, 80 and 160 A·GeV are underestimated by up to factors of 3 - depending on the annihilation cross section employed - which might be addressed to missing multi-meson fusion channels in the UrQMD model. PACS 25.75.+r