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Model transformation is one of the key tasks in model-driven engineering and relies on the efficient matching and modification of graph-based data structures; its sibling graph rewriting has been used to successfully model problems in a variety of domains. Over the last years, a wide range of graph and model transformation tools have been developed all of them with their own particular strengths and typical application domains. In this paper, we give a survey and a comparison of the model and graph transformation tools that participated at the Transformation Tool Contest 2011. The reader gains an overview of the field and its tools, based on the illustrative solutions submitted to a Hello World task, and a comparison alongside a detailed taxonomy. The article is of interest to researchers in the field of model and graph transformation, as well as to software engineers with a transformation task at hand who have to choose a tool fitting to their needs. All solutions referenced in this article provide a SHARE demo. It supported the peer-review process for the contest, and now allows the reader to test the tools online.
Background: Post-traumatic stress disorder (PTSD) is one of the more commonly occurring mental disorders following potentially traumatizing events soldiers may encounter when deployed abroad. One of the first-line recommended treatment options is eye movement desensitization and reprocessing (EMDR). The number of studies assessing the effectiveness of EMDR in German soldiers under routine conditions is currently almost nil. Methods: A retrospective, quasi-experimental effectiveness study on EMDR in an inpatient setting is presented using a prepost design. The study compares symptom reduction in soldiers (N = 78) with a wait-list (N = 18). Effect sizes of EMDR were measured for PTSD, symptoms of depression, and general mental health. Results: Effect size for EMDR treatment of PTSD was d = 0.77; 95% confidence interval (CI): 0.51 to 1.36, for symptoms of depression d = 0.99; 95% CI: 0.31 to 1.36, and for general psychiatric symptoms d = 0.53; 95% CI: 0.17 to 1.21. The effects resulting from EMDR treatment were somewhat weaker than those reported in comparable studies in civilians. Conclusion: EMDR therapy is an effective treatment to reduce symptoms of PTSD and depression. However, in the military context it needs to be complemented by treatment options that specifically address further conditions perpetuating the disorders.
Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland
(2015)
Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition?
We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions.
At a fine spatial scale, environmental factors explained 18% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved.
The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.
YedY from Escherichia coil is a new member of the sulfite oxidase family of molybdenum cofactor (Moco)-containing oxidoreductases. We investigated the atomic structure of the molybdenum site in YedY by X-ray absorption spectroscopy, in comparison to human sulfite oxidase (hSO) and to a Mo(IV) model complex. The K-edge energy was indicative of Mo(V) in YedY, in agreement with X- and Q-band electron paramagnetic resonance results, whereas the hSO protein contained Mo(VI). In YedY and hSO, molybdenum is coordinated by two sulfur ligands from the molybdopterin ligand of the Moco, one thiolate sulfur of a cysteine (average Mo-S bond length of similar to 2.4 angstrom), and one (axial) oxo ligand (Mo=O, similar to 1.7 angstrom). hSO contained a second oxo group at Mo as expected, but in YedY, two species in about a 1:1 ratio were found at the active site, corresponding to an equatorial Mo-OH bond (similar to 2.1 angstrom) or possibly to a shorter M-O(-) bond. Yet another oxygen (or nitrogen) at a similar to 2.6 angstrom distance to Mo in YedY was identified, which could originate from a water molecule in the substrate binding cavity or from an amino acid residue close to the molybdenum site, i.e., Glu104, that is replaced by a glycine in hSO, or Asn45. The addition of the poor substrate dimethyl sulfoxide to YedY left the molybdenum coordination unchanged at high pH. In contrast, we found indications that the better substrate trimethylamine N-oxide and the substrate analogue acetone were bound at a similar to 2.6 angstrom distance to the molybdenum, presumably replacing the equatorial oxygen ligand. These findings were used to interpret the recent crystal structure of YedY and bear implications for its catalytic mechanism.
Ten square-based pyramidal molybdenum complexes with different sulfur donor ligands, that is, a variety of dithiolenes and sulfides, were prepared, which mimic coordination motifs of the molybdenum cofactors of molybdenum-dependent oxidoreductases. The model compounds were investigated by Mo K-edge X-ray absorption spectroscopy (XAS) and (with one exception) their molecular structures were analyzed by X-ray diffraction to derive detailed information on bond lengths and geometries of the first coordination shell of molybdenum. Only small variations in Mo=O and Mo-S bond lengths and their respective coordination angles were observed for all complexes including those containing Mo(CO)(2) or Mo(mu-S)(2)Mo motifs. XAS analysis (edge energy) revealed higher relative oxidation levels in the molybdenum ion in compounds with innocent sulfur-based ligands relative to those in dithiolene complexes, which are known to exhibit noninnocence, that is, donation of substantial electron density from ligand to metal. In addition, longer average Mo-S and Mo=O bonds and consequently lower.(Mo=O) stretching frequencies in the IR spectra were observed for complexes with dithiolene-derived ligands. The results emphasize that the noninnocent character of the dithiolene ligand influences the electronic structure of the model compounds, but does not significantly affect their metal coordination geometry, which is largely determined by the Mo(IV) or (V) ion itself. The latter conclusion also holds for the molybdenum site geometries in the oxidized Mo-VI cofactor of DMSO reductase and the reduced Mo-IV cofactor of arsenite oxidase. The innocent behavior of the dithiolene molybdopterin ligands observed in the enzymes is likely to be related to cofactor-protein interactions.
Portal = Diversity
(2022)
In Europa herrscht Krieg, an unserer Universität diskutieren wir über Diversity. Passt das zusammen? Wir denken: ja. Fragen nach Gleichstellung, Diskriminierung und gesellschaftlicher Vielfalt sind irgendwie ständig präsent und doch scheint anderes immer wichtiger zu sein. Wenn wir aber darüber sprechen, wie Menschen unabhängig von ihrer Nationalität, ihrem Alter oder Geschlecht, ihrer Weltanschauung und Religion, ihrer sexuellen Orientierung, ihrem gesundheitlichen, ethnischen und sozialen Hintergrund, gleichberechtigt und ohne Hürden teilhaben können, sind wir mit Grundsatzfragen konfrontiert. Und zugleich mit dem Ursprung von (gewaltvollen) Konflikten überall auf der Welt. Es handelt sich um ein Kernthema des demokratischen Zusammenlebens, nicht nur in Europa. Dabei geht es nicht zuletzt um das zutiefst Persönliche, um Fragen der Identität – doch das Private ist immer auch politisch.
Wie „schwarz“ ist eigentlich mein Seminarplan? Warum lerne ich im Studium der Literaturgeschichte so viel über Schiller und Goethe und so wenig über Bettina von Arnim oder Charlotte von Stein? Weshalb bin ich der einzige Doktorand im Kolloquium, dessen Eltern kein Abitur haben? Wieso finde ich viele Informationen an der Uni nur auf Deutsch? Wo ist der Fahrstuhl, der mich zum Hörsaal bringt? Spricht die jüngere Generation eine Sprache, die ich nicht mehr verstehe?
All diese Fragen zeigen auch, dass sich unsere Gesellschaft wandelt. Das, was früher als „normal“ galt, ist es heute nicht mehr – und eine Hochschule muss dem Rechnung tragen: in Lehre und Forschung, in der Studierendenbetreuung und als Arbeitgeberin. Und tatsächlich machen sich an der Universität Potsdam bereits viele Menschen über solche und ähnliche Fragen Gedanken. Das zeigt die große Vielfalt an Projekten, Forschungsthemen und Lehrveranstaltungen zu Diversität, mit denen sich Studierende und Beschäftigte befassen – meist aus eigener Initiative. Und mit dem Diversity Audit, das die Hochschule derzeit durchläuft, könnte sie dem Ziel einer diversitätssensiblen und diskriminierungsfreien Einrichtung ein Stück näherkommen. Nicht zuletzt ist das Audit die Chance, dass Gleichstellung Teil der Marke „Uni Potsdam“ wird.
Wie immer bieten wir Ihnen über das Titelthema hinaus Einblicke in das, was Forschende, Studierende und Beschäftigte umtreibt: wie sie mit Astronauten über das Leben in einer Weltraumstation ins Gespräch kommen, die Haut von Buckelwalen untersuchen, um deren unsichtbare Bewohner besser kennenzulernen, die elitäre Literaturszene in Berlin-Brandenburg aufmischen oder sich für bessere Arbeitsbedingungen an der Hochschule ins Zeug legen.
Nun noch ein Hinweis: Uns beschäftigt alle sehr, wie der Krieg in der Ukraine ein schnelles Ende finden kann. In Interviews versuchen wir mit Forschenden der Uni Potsdam eine Antwort auf diese Frage zu finden. In diesem Heft beschreibt der Slavist Prof. Dr. Alexander Wöll den Kampf der ukrainischen Bevölkerung um ihre Unabhängigkeit. Außerdem stellen wir Ihnen die Denkfabrik „Translating Eastern Europe“ vor, die an der Universität entstehen soll. Weitere Interviews finden sich auf den Seiten des Referats für Presse- und Öffentlichkeitsarbeit.
Wir wünschen Ihnen eine anregende Lektüre und neue Perspektiven.