@article{ZuritaSanchezHenkel2012, author = {Zurita-Sanchez, Jorge R. and Henkel, Carsten}, title = {Acoustic waves from mechanical impulses due to fluorescence resonant energy (Forster) transfer Blowing a whistle with light}, series = {epl : a letters journal exploring the frontiers of physics}, volume = {97}, journal = {epl : a letters journal exploring the frontiers of physics}, number = {4}, publisher = {EDP Sciences}, address = {Mulhouse}, issn = {0295-5075}, doi = {10.1209/0295-5075/97/43002}, pages = {6}, year = {2012}, abstract = {We present a momentum transfer mechanism mediated by electromagnetic fields that originates in a system of two nearby molecules: one excited (donor D*) and the other in ground state (acceptor A). An intermolecular force related to fluorescence resonant energy or Forster transfer (FRET) arises in the unstable D* A molecular system, which differs from the equilibrium van der Waals interaction. Due to the its finite lifetime, a mechanical impulse is imparted to the relative motion in the system. We analyze the FRET impulse when the molecules are embedded in free space and find that its magnitude can be much greater than the single recoil photon momentum, getting comparable with the thermal momentum (Maxwell-Boltzmann distribution) at room temperature. In addition, we propose that this FRET impulse can be exploited in the generation of acoustic waves inside a film containing layers of donor and acceptor molecules, when a picosecond laser pulse excites the donors. This acoustic transient is distinguishable from that produced by thermal stress due to laser absorption, and may therefore play a role in photoacoustic spectroscopy. The effect can be seen as exciting a vibrating system like a string or organ pipe with light; it may be used as an opto-mechanical transducer.}, language = {en} } @article{ZurellGrimmRossmanithetal.2012, author = {Zurell, Damaris and Grimm, Volker and Rossmanith, Eva and Zbinden, Niklaus and Zimmermann, Niklaus E. and Schr{\"o}der-Esselbach, Boris}, title = {Uncertainty in predictions of range dynamics black grouse climbing the Swiss Alps}, series = {Ecography : pattern and diversity in ecology ; research papers forum}, volume = {35}, journal = {Ecography : pattern and diversity in ecology ; research papers forum}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0906-7590}, doi = {10.1111/j.1600-0587.2011.07200.x}, pages = {590 -- 603}, year = {2012}, abstract = {Empirical species distribution models (SDMs) constitute often the tool of choice for the assessment of rapid climate change effects on species vulnerability. Conclusions regarding extinction risks might be misleading, however, because SDMs do not explicitly incorporate dispersal or other demographic processes. Here, we supplement SDMs with a dynamic population model 1) to predict climate-induced range dynamics for black grouse in Switzerland, 2) to compare direct and indirect measures of extinction risks, and 3) to quantify uncertainty in predictions as well as the sources of that uncertainty. To this end, we linked models of habitat suitability to a spatially explicit, individual-based model. In an extensive sensitivity analysis, we quantified uncertainty in various model outputs introduced by different SDM algorithms, by different climate scenarios and by demographic model parameters. Potentially suitable habitats were predicted to shift uphill and eastwards. By the end of the 21st century, abrupt habitat losses were predicted in the western Prealps for some climate scenarios. In contrast, population size and occupied area were primarily controlled by currently negative population growth and gradually declined from the beginning of the century across all climate scenarios and SDM algorithms. However, predictions of population dynamic features were highly variable across simulations. Results indicate that inferring extinction probabilities simply from the quantity of suitable habitat may underestimate extinction risks because this may ignore important interactions between life history traits and available habitat. Also, in dynamic range predictions uncertainty in SDM algorithms and climate scenarios can become secondary to uncertainty in dynamic model components. Our study emphasises the need for principal evaluation tools like sensitivity analysis in order to assess uncertainty and robustness in dynamic range predictions. A more direct benefit of such robustness analysis is an improved mechanistic understanding of dynamic species responses to climate change.}, language = {en} } @misc{ZurellElithSchroederEsselbach2012, author = {Zurell, Damaris and Elith, Jane and Schr{\"o}der-Esselbach, Boris}, title = {Predicting to new environments tools for visualizing model behaviour and impacts on mapped distributions}, series = {Diversity \& distributions : a journal of biological invasions and biodiversity}, volume = {18}, journal = {Diversity \& distributions : a journal of biological invasions and biodiversity}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1366-9516}, doi = {10.1111/j.1472-4642.2012.00887.x}, pages = {628 -- 634}, year = {2012}, abstract = {Data limitations can lead to unrealistic fits of predictive species distribution models (SDMs) and spurious extrapolation to novel environments. Here, we want to draw attention to novel combinations of environmental predictors that are within the sampled range of individual predictors but are nevertheless outside the sample space. These tend to be overlooked when visualizing model behaviour. They may be a cause of differing model transferability and environmental change predictions between methods, a problem described in some studies but generally not well understood. We here use a simple simulated data example to illustrate the problem and provide new and complementary visualization techniques to explore model behaviour and predictions to novel environments. We then apply these in a more complex real-world example. Our results underscore the necessity of scrutinizing model fits, ecological theory and environmental novelty.}, language = {en} } @article{ZuoGandhiArndtetal.2012, author = {Zuo, Zhili and Gandhi, Neha S. and Arndt, Katja Maren and Mancera, Ricardo L.}, title = {Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein}, series = {Biopolymers}, volume = {97}, journal = {Biopolymers}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0006-3525}, doi = {10.1002/bip.22099}, pages = {899 -- 909}, year = {2012}, abstract = {The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.}, language = {en} } @article{ZobirMocek2012, author = {Zobir, Soraya Hadj and Mocek, Beate}, title = {Determination of the source rocks for the diatexites from the Edough Massif, Annaba, NE Algeria}, series = {Journal of African earth sciences}, volume = {69}, journal = {Journal of African earth sciences}, number = {13}, publisher = {Elsevier}, address = {Oxford}, issn = {1464-343X}, doi = {10.1016/j.jafrearsci.2012.04.004}, pages = {26 -- 33}, year = {2012}, abstract = {The crystalline Edough Massif is located in the oriental part of the Algerian coastline. It consists of two tectonically superposed units of gneisses, augen-gneisses and migmatitic gneisses in the lower unit and micaschists in the upper unit. The crystalline rocks underwent a low to moderate degree of metamorphism; the gneisses suffered partial melting. They display migmatitic features such as nebulitic structures with contorted leucosome layers and K-feldspar porphyroblasts and thus can be classified as diatexites. The mineralogical composition of these rocks is very homogenous and consists of K-feldspar, micas and quartz. The feldspar-rich, arkosic nature of the outcrop implies a granitic source rock. High K2O/Na2O ratios and high A/CNK > 1.1 indicate an S-type granite source and a peraluminous composition of the protolith respectively. Chondrite normalized REE distribution patterns of the Edough diatexites show gently inclined patterns with a minor negative Eu anomaly (Eu/Eu* = 0.36-0.49), which points to a very slightly differentiated granitic source. The REE pattern and trace element data of the diatexites are similar to those of average Proterozoic upper continental crust, which suggests that they are derived mainly from upper continental crust and were deposited in continental margins.}, language = {en} } @article{ZiolkowskiBleekTwamleyetal.2012, author = {Ziolkowski, Bartosz and Bleek, Katrin and Twamley, Brendan and Fraser, Kevin J. and Byrne, Robert and Diamond, Dermot and Taubert, Andreas}, title = {Magnetic ionogels (MagIGs) based on iron oxide nanoparticles, poly(N-isopropylacrylamide), and the ionic liquid trihexyl(tetradecyl)phosphonium dicyanamide}, series = {European journal of inorganic chemistry : a journal of ChemPubSoc Europe}, journal = {European journal of inorganic chemistry : a journal of ChemPubSoc Europe}, number = {32}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1434-1948}, doi = {10.1002/ejic.201200597}, pages = {5245 -- 5251}, year = {2012}, abstract = {Magnetic ionogels (MagIGs) were prepared from organosilane-coated iron oxide nanoparticles, N-isopropylacrylamide, and the ionic liquid trihexyl(tetradecyl)phosphonium dicyanamide. The ionogels prepared with the silane-modified nanoparticles are more homogeneous than ionogels prepared with unmodified magnetite particles. The silane-modified particles are immobilized in the ionogel and are resistant tonanoparticle leaching. The modified particles also render the ionogels mechanically more stable than the ionogels synthesized with unmodified nanoparticles. The ionogels respond to external permanent magnets and are therefore prototypes of a new soft magnetic actuator.}, language = {en} } @article{ZinsmeisterSmolka2012, author = {Zinsmeister, Heike and Smolka, Eva}, title = {Corpus-based evidence for approximating semantic transparency of complex verbs}, series = {Potsdam cognitive science series}, journal = {Potsdam cognitive science series}, number = {3}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {2190-4545}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-62353}, pages = {45 -- 59}, year = {2012}, language = {en} } @article{ZimmermannThienel2012, author = {Zimmermann, Andreas and Thienel, Tobias}, title = {Yugoslavia, cases and proceedings before the ICJ}, isbn = {978-0-19-929168-7}, year = {2012}, language = {en} } @book{ZimmermannOellersFrahmTomuschatetal.2012, author = {Zimmermann, Andreas and Oellers-Frahm, Karin and Tomuschat, Christian and Tams, Christian J.}, title = {The statute of the international court of justice : a commentary}, edition = {2. ed.}, publisher = {Oxford Univ. Press}, address = {Oxford}, isbn = {978-0-19-969299-6}, pages = {1745 S.}, year = {2012}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {Amending the amendment provisions of the rome statute the kampala compromise on the crime of aggression and the law of treaties}, series = {Journal of international criminal justice}, volume = {10}, journal = {Journal of international criminal justice}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1478-1387}, doi = {10.1093/jicj/mqs002}, pages = {209 -- 227}, year = {2012}, abstract = {The adoption, in Kampala in June 2010, of amendments to the Rome Statute on the crime of aggression was hailed as a historic milestone in the development of the international Criminal Court (ICC). However, the manner in which these amendments are supposed to enter into force runs the risk of undermining the rules of the international law of treaties, as well as the legality and acceptability of the Kampala compromise itself The author examines the relevant amendment procedures provided for in the ICC Statute and the compatibility with them of the amendment procedure chosen in Kampala and ultimately warns of the legal consequences which may follow from the Review Conference's somewhat-Alexandrian solution.}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {Abiding by and enforcing international humanitarian law in asymmetric warfare : the case of "operation cast lead"}, issn = {0554-498x}, year = {2012}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {Amending the amendment provisions of the rome statute : the kampala compromise on the crime of aggression and the law of treaties}, year = {2012}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {State sucession in other matters than treaties}, isbn = {978-0-19-929168-7}, year = {2012}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {State sucession in treaties}, isbn = {978-0-19-929168-7}, year = {2012}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {Continuity of states}, isbn = {978-0-19-929168-7}, year = {2012}, language = {en} } @article{Zimmermann2012, author = {Zimmermann, Andreas}, title = {International courts and tribunals, intervention in proceedings}, isbn = {978-0-19-929168-7}, year = {2012}, language = {en} } @article{ZimmermannFranckeElsenbeer2012, author = {Zimmermann, Alexander and Francke, Till and Elsenbeer, Helmut}, title = {Forests and erosion: Insights from a study of suspended-sediment dynamics in an overland flow-prone rainforest catchment}, series = {Journal of hydrology}, volume = {428}, journal = {Journal of hydrology}, number = {7}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0022-1694}, doi = {10.1016/j.jhydrol.2012.01.039}, pages = {170 -- 181}, year = {2012}, abstract = {Forests seem to represent low-erosion systems, according to most, but not all, studies of suspended-sediment yield. We surmised that this impression reflects an accidental bias in the selection of monitoring sites towards those with prevailing vertical hydrological flowpaths, rather than a tight causal link between vegetation cover and erosion alone. To evaluate this conjecture, we monitored, over a 2-year period, a 3.3 ha old-growth rainforest catchment prone to frequent and widespread overland flow. We sampled stream flow at two and overland flow at three sites in a nested arrangement on a within-event basis, and monitored the spatial and temporal frequency of overland flow. Suspended-sediment concentrations were modeled with Random Forest and Quantile Regression Forest to be able to estimate the annual yields for the 2 years, which amounted to 1 t ha(-1) and 2 t ha(-1) in a year with below-average and with average precipitation, respectively. These estimates place our monitoring site near the high end of reported suspended-sediment yields and lend credence to the notion that low yields reflect primarily the dominance of vertical flowpaths and not necessarily and exclusively the kind of vegetative cover. Undisturbed forest and surface erosion are certainly no contradiction in terms even in the absence of mass movements.}, language = {en} } @article{ZiegeHennigeSchulzMueckschetal.2012, author = {Ziege, Madlen and Hennige-Schulz, Carmen and Muecksch, Frauke and Bierbach, David and Tiedemann, Ralph and Streit, Bruno and Plath, Martin}, title = {A comparison of two methods to assess audience-induced changes in male mate choice}, series = {Current zoology}, volume = {58}, journal = {Current zoology}, number = {1}, publisher = {Current Zoology}, address = {Beijing}, issn = {1674-5507}, pages = {84 -- 94}, year = {2012}, abstract = {Multidirectional communicative interactions in social networks can have a profound effect on mate choice behavior. Male Atlantic molly Poecilia mexicana exhibit weaker mating preferences when an audience male is presented. This could be a male strategy to reduce sperm competition risk: interacting more equally with different females may be advantageous because rivals might copy mate choice decisions. In line with this hypothesis, a previous study found males to show a strong audience effect when being observed while exercising mate choice, but not when the rival was presented only before the choice tests. Audience effects on mate choice decisions have been quantified in poeciliid fishes using association preference designs, but it remains unknown if patterns found from measuring association times translate into actual mating behavior. Thus, we created five audience treatments simulating different forms of perceived sperm competition risk and determined focal males' mating preferences by scoring pre-mating (nipping) and mating behavior (gonopodial thrusting). Nipping did not reflect the pattern that was found when association preferences were measured, while a very similar pattern was uncovered in thrusting behavior. The strongest response was observed when the audience could eavesdrop on the focal male's behavior. A reduction in the strength of focal males' preferences was also seen after the rival male had an opportunity to mate with the focal male's preferred mate. In comparison, the reduction of mating preferences in response to an audience was greater when measuring association times than actual mating behavior. While measuring direct sexual interactions between the focal male and both stimulus females not only the male's motivational state is reflected but also females' behavior such as avoidance of male sexual harassment.}, language = {en} } @article{ZhuKolloscheLuetal.2012, author = {Zhu, Jian and Kollosche, Matthias and Lu, Tongqing and Kofod, Guggi and Suo, Zhigang}, title = {Two types of transitions to wrinkles in dielectric elastomers}, series = {Soft matter}, volume = {8}, journal = {Soft matter}, number = {34}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, doi = {10.1039/c2sm26034d}, pages = {8840 -- 8846}, year = {2012}, abstract = {A membrane of a dielectric elastomer coated with compliant electrodes may form wrinkles as the applied voltage is ramped up. We present a combination of experiment and theory to investigate the transition to wrinkles using a clamped membrane subject to a constant force and a voltage ramp. Two types of transitions are identified. In type-I transition, the voltage-stretch curve is N-shaped, and flat and wrinkled regions coexist in separate areas of the membrane. The type-I transition progresses by nucleation of small wrinkled regions, followed by the growth of the wrinkled regions at the expense of the flat regions, until the entire membrane is wrinkled. By contrast, in type-II transition, the voltage-stretch curve is monotonic, and the entire flat membrane becomes wrinkled with no nucleation barrier. The two types of transitions are analogous to the first and the second order phase transitions. While the type-I transition is accompanied by a jump in the vertical displacement, type-II transition is accompanied by a continuous change in the vertical displacement. Such transitions may enable applications in muscle-like actuation and energy harvesting, where large deformation and large energy of conversion are desired.}, language = {en} } @article{ZhongMetwalliKauneetal.2012, author = {Zhong, Qi and Metwalli, Ezzeldin and Kaune, Gunar and Rawolle, Monika and Bivigou Koumba, Achille Mayelle and Laschewsky, Andr{\´e} and Papadakis, Christine M. and Cubitt, Robert and M{\"u}ller-Buschbaum, Peter}, title = {Switching kinetics of thin thermo-responsive hydrogel films of poly(monomethoxy-diethyleneglycol-acrylate) probed with in situ neutron reflectivity}, series = {Soft matter}, volume = {8}, journal = {Soft matter}, number = {19}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, doi = {10.1039/c2sm25401h}, pages = {5241 -- 5249}, year = {2012}, abstract = {The switching kinetics of thin thermo-responsive hydrogel films of poly(monomethoxy-diethyleneglycol-acrylate) (PMDEGA) are investigated. Homogeneous and smooth PMDEGA films with a thickness of 35.9 nm are prepared on silicon substrates by spin coating. As probed with white light interferometry, PMDEGA films with a thickness of 35.9 nm exhibit a phase transition temperature of the lower critical solution temperature (LCST) type of 40 degrees C. In situ neutron reflectivity is performed to investigate the thermo-responsive behavior of these PMDEGA hydrogel films in response to a sudden thermal stimulus in deuterated water vapor atmosphere. The collapse transition proceeds in a complex way which can be seen as three steps. The first step is the shrinkage of the initially swollen film by a release of water. In the second step the thickness remains constant with water molecules embedded in the film. In the third step, perhaps due to a conformational rearrangement of the collapsed PMDEGA chains, water is reabsorbed from the vapor atmosphere, thereby giving rise to a relaxation process. Both the shrinkage and relaxation processes can be described by a simple model of hydrogel deswelling.}, language = {en} } @article{ZhangWielandReicheetal.2012, author = {Zhang, Zhuodong and Wieland, Ralf and Reiche, Matthias and Funk, Roger and Hoffmann, Carsten and Li, Yong and Sommer, Michael}, title = {Identifying sensitive areas to wind erosion in the xilingele grassland by computational fluid dynamics modelling}, series = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, volume = {8}, journal = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, number = {5}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1574-9541}, doi = {10.1016/j.ecoinf.2011.12.002}, pages = {37 -- 47}, year = {2012}, abstract = {In order to identify the areas in the Xilingele grassland which are sensitive to wind erosion, a computational fluid dynamics model (CFD-WEM) was used to simulate the wind fields over a region of 37 km(2) which contains different topography and land use types. Previous studies revealed the important influences of topography and land use on wind erosion in the Xilingele grassland. Topography influences wind fields at large scale, and land use influences wind fields near the ground. Two steps were designed to implement the CFD wind simulation, and they were respectively to simulate the influence of topography and surface roughness on the wind. Digital elevation model (DEM) and surface roughness length were the key inputs for the CFD simulation. The wind simulation by CFD-WEM was validated by a wind data set which was measured simultaneously at six positions in the field. Three scenarios with different wind velocities were designed based on observed dust storm events, and wind fields were simulated according to these scenarios to predict the sensitive areas to wind erosion. General assumptions that cropland is the most sensitive area to wind erosion and heavily and moderately grazed grasslands are both sensitive etc. can be refined by the modelling of CFD-WEM. Aided by the results of this study, the land use planning and protection measures against wind erosion can be more efficient. Based on the case study in the Xilingele grassland, a method of regional wind erosion assessment aided by CFD wind simulation is summarized. The essence of this method is a combination of CFD wind simulation and determination of threshold wind velocity for wind erosion. Because of the physically-based simulation and the flexibility of the method, it can be generalised to other regions.}, language = {en} } @article{ZhangWielandReicheetal.2012, author = {Zhang, Zhuo-dong and Wieland, Ralf and Reiche, Matthias and Funk, Roger and Hoffmann, Carsten and Li, Yong and Sommer, Michael}, title = {A computational fluid dynamics model for wind simulation: model implementation and experimental validation}, series = {Journal of Zhejiang University : an international journal ; Science A, Applied physics \& engineering : an international applied physics \& engineering journal}, volume = {13}, journal = {Journal of Zhejiang University : an international journal ; Science A, Applied physics \& engineering : an international applied physics \& engineering journal}, number = {4}, publisher = {Zhejiang University Press}, address = {Hangzou}, issn = {1673-565X}, doi = {10.1631/jzus.A1100231}, pages = {274 -- 283}, year = {2012}, abstract = {To provide physically based wind modelling for wind erosion research at regional scale, a 3D computational fluid dynamics (CFD) wind model was developed. The model was programmed in C language based on the Navier-Stokes equations, and it is freely available as open source. Integrated with the spatial analysis and modelling tool (SAMT), the wind model has convenient input preparation and powerful output visualization. To validate the wind model, a series of experiments was conducted in a wind tunnel. A blocking inflow experiment was designed to test the performance of the model on simulation of basic fluid processes. A round obstacle experiment was designed to check if the model could simulate the influences of the obstacle on wind field. Results show that measured and simulated wind fields have high correlations, and the wind model can simulate both the basic processes of the wind and the influences of the obstacle on the wind field. These results show the high reliability of the wind model. A digital elevation model (DEM) of an area (3800 m long and 1700 m wide) in the Xilingele grassland in Inner Mongolia (autonomous region, China) was applied to the model, and a 3D wind field has been successfully generated. The clear implementation of the model and the adequate validation by wind tunnel experiments laid a solid foundation for the prediction and assessment of wind erosion at regional scale.}, language = {en} } @article{ZhangFedyuninKirchneretal.2012, author = {Zhang, Gong and Fedyunin, Ivan and Kirchner, Sebastian and Xiao, Chuanle and Valleriani, Angelo and Ignatova, Zoya}, title = {FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads}, series = {Nucleic acids research}, volume = {40}, journal = {Nucleic acids research}, number = {11}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gks196}, pages = {11}, year = {2012}, abstract = {The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.}, language = {en} } @article{ZhangZhangFengetal.2012, author = {Zhang, Chengjun and Zhang, Wanyi and Feng, Zhaodong and Mischke, Steffen and Gao, Xiang and Gao, Dou and Sun, Feifei}, title = {Holocene hydrological and climatic change on the northern Mongolian Plateau based on multi-proxy records from Lake Gun Nuur}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {323}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, number = {6}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2012.01.032}, pages = {75 -- 86}, year = {2012}, abstract = {A multi-proxy study including analyses of delta C-13(org) for the lake sediment core GN-02 and grain size, TOC. CaCO3 content, delta C-13(carb) and delta O-18(carb) of bulk carbonate, and the mineralogy of the parallel core GN-04 from Gun Nuur was performed to reconstruct the Holocene hydrology and climate on the northern Mongolian Plateau. The chronology was established using 40 C-14 dates of bulk organic matter in addition to nine previously published radiocarbon dates for core GN-02, and further five C-14 dates for the new core GN-04. A lake reservoir effect of 1060 C-14 years was determined as the intercept of the high-resolution GN-02 age-depth model at the modern sediment surface. The size of the reservoir effect is supported by the age of the core-top sample (1200 +/- 40 C-14 years) and the determined difference between a wood-derived radiocarbon age from the GN-02 core base and the age-model inferred age for bulk organic matter at the same stratigraphic level (1000 C-14 years). Low lake level and prevailing aeolian sediment deposition at Gun Nuur under dry conditions were recorded during the earliest Holocene (> 10,800-10,300 cal a BP). Gun Nuur expanded under significantly wetter conditions between 10,300 and 7000 cal a BP. Unstable climate conditions existed in the mid Holocene (7000-2500 cal a BP) and three periods of low lake-levels and significantly drier conditions were recorded between 7000-5700, 4100-3600 and 3000-2500 cal a BP. Intermediate lake levels were inferred for the intervening periods. Around 2500 cal a BP, the climate change and wetter conditions were established again. As a consequence, the lake level of Gun Nuur rose again due to higher effective moisture and the relatively wet present conditions were achieved ca. 1600 cal a BP. Our results suggest that the initial Holocene climate change on the northern Mongolian Plateau was not accompanied by a rapid increase in precipitation as on the Tibetan Plateau. The establishment of wetter conditions in northern Mongolia lagged behind the early Holocene moisture increase on the Tibetan Plateau by ca. 1000 years. Subsiding dry air in the north of the Tibetan Plateau resulted from the strengthened summer monsoon on the Tibetan Plateau during the period of maximum summer insolation and probably inhibited a significant precipitation increase in Mongolia. The significant moisture increase in the Gun Nuur region at ca. 10.3 cal ka BP is probably not related to the northward shift of the present summer monsoon boundary or the moisture delivery from the northern Atlantic through the westerlies. Instead, water from melting snow, ice and frozen ground and the generation of precipitation from the local recycling of moisture are discussed as possible moisture source for the early onset of wetter conditions on the Mongolian Plateau.}, language = {en} } @misc{Zerbian2012, author = {Zerbian, Sabine}, title = {Variation in the grammar of black south African English}, series = {Southern African linguistics and applied language studies}, volume = {30}, journal = {Southern African linguistics and applied language studies}, number = {1}, publisher = {NISC}, address = {Grahamstown}, issn = {1607-3614}, doi = {10.2989/16073614.2012.693721}, pages = {131 -- 135}, year = {2012}, language = {en} } @article{ZenichowskiNacciFoelschetal.2012, author = {Zenichowski, Karl and Nacci, Ch and F{\"o}lsch, S. and Dokic, Jadranka and Klamroth, Tillmann and Saalfrank, Peter}, title = {STM-switching of organic molecules on semiconductor surfaces: an above threshold density matrix model for 1,5 cyclooctadiene on Si(100)}, series = {Journal of physics : Condensed matter}, volume = {24}, journal = {Journal of physics : Condensed matter}, number = {39}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0953-8984}, doi = {10.1088/0953-8984/24/39/394009}, pages = {11}, year = {2012}, abstract = {The scanning tunnelling microscope (STM)-induced switching of a single cyclooctadiene molecule between two stable conformations chemisorbed on a Si(100) surface is investigated using an above threshold model including a neutral ground state and an ionic excited state potential. Switching was recently achieved experimentally with an STM operated at cryogenic temperatures (Nacci et al 2008 Phys. Rev. B 77 121405(R)) and rationalized by a below threshold model using just a single potential energy surface (Nacci et al 2009 Nano Lett. 9 2997). In the present paper, we show that experimental key findings on the inelastic electron tunnelling (IET) switching can also be rationalized using an above threshold density matrix model, which includes, in addition to the neutral ground state potential, an anionic or cationic excited potential. We use one and two-dimensional potential energy surfaces. Furthermore, the influence of two key parameters of the density matrix description, namely the electronic lifetime of the ionic resonance and the vibrational lifetimes, on the ground state potential are discussed.}, language = {en} } @article{ZenichowskiDokicKlamrothetal.2012, author = {Zenichowski, Karl and Dokic, Jadranka and Klamroth, Tillmann and Saalfrank, Peter}, title = {Current versus temperature-induced switching of a single molecule - open-system density matrix theory for 1,5-cyclooctadiene on Si(100)}, series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, volume = {136}, journal = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, number = {9}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0021-9606}, doi = {10.1063/1.3692229}, pages = {13}, year = {2012}, abstract = {The switching of single cyclooctadiene molecules chemisorbed on a Si(100) surface between two stable conformations, can be achieved with a scanning tunneling microscope [Nacci , Phys. Rev. B 77, 121405(R) (2008)]. Recently, it was shown by quantum chemical and quantum dynamical simulations that major experimental facts can be explained by a single-mode model with switching enforced by inelastic electron tunneling (IET) excitations and perturbed by vibrational relaxation [Nacci , Nano Lett. 9, 2997 (2009)]. In the present paper, we extend the previous theoretical work in several respects: (1) The model is generalized to a two-mode description in which two C2H4 units of COD can move independently; (2) contributions of dipole and, in addition, (cation and anion) resonance-IET rates are considered; (3) the harmonic-linear vibrational relaxation model used previously is generalized to anharmonic vibrations. While the present models highlight generic aspects of IET-switching between two potential minima, they also rationalize specific experimental findings for COD/Si(100): (1) A single-electron excitation mechanism with a linear dependence of the switching rate on tunneling current I, (2) the capability to switch both at negative and positive sample biases, and (3) a crossover temperature around similar to 60 K from an IET-driven, T-independent atom tunneling regime, to classical over-the-barrier isomerization with exponential T-dependence at higher temperatures for a bias voltage of +1.5 V and an average tunneling current of 0.73 nA.}, language = {en} } @phdthesis{Zenichowski2012, author = {Zenichowski, Karl}, title = {Quantum dynamical study of Si(100) surface-mounted, STM-driven switches at the atomic and molecular scale}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-62156}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {The aim of this thesis is the quantum dynamical study of two examples of scanning tunneling microscope (STM)-controllable, Si(100)(2x1) surface-mounted switches of atomic and molecular scale. The first example considers the switching of single H-atoms between two dangling-bond chemisorption sites on a Si-dimer of the Si(100) surface (Grey et al., 1996). The second system examines the conformational switching of single 1,5-cyclooctadiene molecules chemisorbed on the Si(100) surface (Nacci et al., 2008). The temporal dynamics are provided by the propagation of the density matrix in time via an according set of equations of motion (EQM). The latter are based on the open-system density matrix theory in Lindblad form. First order perturbation theory is used to evaluate those transition rates between vibrational levels of the system part. In order to account for interactions with the surface phonons, two different dissipative models are used, namely the bilinear, harmonic and the Ohmic bath model. IET-induced vibrational transitions in the system are due to the dipole- and the resonance-mechanism. A single surface approach is used to study the influence of dipole scattering and resonance scattering in the below-threshold regime. Further, a second electronic surface was included to study the resonance-induced switching in the above-threshold regime. Static properties of the adsorbate, e.g., potentials and dipole function and potentials, are obtained from quantum chemistry and used within the established quantum dynamical models.}, language = {en} } @phdthesis{Zeller2012, author = {Zeller, Carolin}, title = {Self-regulation and labour standards : an exemplary study investigating the emergence and strenghening of self- regulation regimes in the apparel industry}, publisher = {Lang Peter GmbH Internationaler Verlag der Wissenschaften}, address = {Frankfurt}, isbn = {978-3-631-62433-3}, pages = {261 S.}, year = {2012}, language = {en} } @phdthesis{Zarezadeh2012, author = {Zarezadeh, Aliakbar}, title = {Distributed smart cameras : architecture and communication protocols}, address = {Potsdam}, pages = {135 S.}, year = {2012}, language = {en} } @phdthesis{Zarafshani2012, author = {Zarafshani, Zoya}, title = {Chain-end functionalization and modification of polymers using modular chemical reactions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59723}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {Taking advantage of ATRP and using functionalized initiators, different functionalities were introduced in both α and ω chain-ends of synthetic polymers. These functionalized polymers could then go through modular synthetic pathways such as click cycloaddition (copper-catalyzed or copper-free) or amidation to couple synthetic polymers to other synthetic polymers, biomolecules or silica monoliths. Using this general strategy and designing these co/polymers so that they are thermoresponsive, yet bioinert and biocompatible with adjustable cloud point values (as it is the case in the present thesis), the whole generated system becomes "smart" and potentially applicable in different branches. The applications which were considered in the present thesis were in polymer post-functionalization (in situ functionalization of micellar aggregates with low and high molecular weight molecules), hydrophilic/hydrophobic tuning, chromatography and bioconjugation (enzyme thermoprecipitation and recovery, improvement of enzyme activity). Different α-functionalized co/polymers containing cholesterol moiety, aldehyde, t-Boc protected amine, TMS-protected alkyne and NHS-activated ester were designed and synthesized in this work.}, language = {en} } @article{ZamagniMuttiKosir2012, author = {Zamagni, Jessica and Mutti, Maria and Kosir, Adrijan}, title = {The evolution of mid paleocene-early eocene coral communities how to survive during rapid global warming}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {317}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2011.12.010}, pages = {48 -- 65}, year = {2012}, abstract = {Today, diverse communities of zooxanthellate corals thrive, but do not build reef, under a wide range of environmental conditions. In these settings they inhabit natural bottom communities, sometimes forming patch-reefs, coral carpets and knobs. Episodes in the fossil record, characterized by limited coral-reef development but widespread occurrence of coral-bearing carbonates, may represent the fossil analogs of these non-reef building, zooxanthellate coral communities. If so, the study of these corals could have valuable implications for paleoenvironmental reconstructions. Here we focus on the evolution of early Paleogene corals as a fossil example of coral communities mainly composed by zooxanthellate corals (or likely zooxanthellate), commonly occurring within carbonate biofacies and with relatively high diversity but with a limited bioconstructional potential as testified by the reduced record of coral reefs. We correlate changes of bioconstructional potential and community compositions of these fossil corals with the main ecological/environmental conditions at that time. The early Paleogene greenhouse climate was characterized by relatively short pulses of warming with the most prominent occurring at the Paleocene-Eocene boundary (PETM event), associated with high weathering rates, nutrient fluxes, and pCO(2) levels. A synthesis of coral occurrences integrated with our data from the Adriatic Carbonate Platform (SW Slovenia) and the Minervois region (SW France), provides evidence for temporal changes in the reef-building capacity of corals associated with a shift in community composition toward forms adapted to tolerate deteriorating sea-water conditions. During the middle Paleocene coral-algal patch reefs and barrier reefs occurred from shallow-water settings, locally with reef-crest structures. A first shift can be traced from middle Paleocene to late Paleocene, with small coral-algal patch reefs and coral-bearing mounds development in shallow to intermediate water depths. In these mounds corals were highly subordinated as bioconstructors to other groups tolerant to higher levels of trophic resources (calcareous red algae, encrusting foraminifera, microbes, and sponges). A second shift occurred at the onset of the early Eocene with a further reduction of coral framework-building capacity. These coral communities mainly formed knobs in shallow-water, turbid settings associated with abundant foraminiferal deposits. We suggest that environmental conditions other than high temperature determined a combination of interrelated stressors that limited the coral-reef construction. A continuous enhancement of sediment load/nutrients combined with geochemical changes of ocean waters likely displaced corals as the main bioconstructors during the late Paleocene-early Eocene times. Nonetheless, these conditions did not affect the capacity of some corals to colonize the substrate, maintain biodiversity, and act as locally important carbonate-sediment producers, suggesting broad environmental tolerance limits of various species of corals. The implications of this study include clues as to how both ancient and modern zooxanthellate corals could respond to changing climate.}, language = {en} } @article{ZamagniMuttiBallatoetal.2012, author = {Zamagni, Jessica and Mutti, Maria and Ballato, Paolo and Kosir, Adrijan}, title = {The Paleocene-Eocene thermal maximum (PETM) in shallow-marine successions of the Adriatic carbonate platform (SW Slovenia)}, series = {Geological Society of America bulletin}, volume = {124}, journal = {Geological Society of America bulletin}, number = {7-8}, publisher = {American Institute of Physics}, address = {Boulder}, issn = {0016-7606}, doi = {10.1130/B30553.1}, pages = {1071 -- 1086}, year = {2012}, abstract = {The Paleocene-Eocene thermal maximum represents one of the most rapid and extreme warming events in the Cenozoic. Shallow-water stratigraphic sections from the Adriatic carbonate platform offer a rare opportunity to learn about the nature of Paleocene-Eocene thermal maximum and the effects on shallow-water ecosystems. We use carbon and oxygen isotope stratigraphy, in conjunction with detailed larger benthic foraminiferal biostratigraphy, to establish a high-resolution paleoclimatic record for the Paleocene-Eocene thermal maximum. A prominent negative excursion in delta C-13 curves of bulk-rock (similar to 1 parts per thousand-3 parts per thousand), matrix (similar to 4 parts per thousand), and foraminifera (similar to 6 parts per thousand) is interpreted as the carbon isotope excursion during the Paleocene-Eocene thermal maximum. The strongly C-13-depleted delta(1)d(3)C record of our shallow-marine carbonates compared to open-marine records could result from organic matter oxidation, suggesting intensified weathering, runoff, and organic matter flux. The Ilerdian larger benthie foraminiferal turnover is documented in detail based on high-resolution correlation with the carbon isotopic excursion. The turnover is described as a two-step process, with the first step (early Ilerdian) marked by a rapid diversification of small alveolinids and nummulitids with weak adult dimorphism, possibly as adaptations to fluctuating Paleocene-Eocene thermal maximum nutrient levels, and a second step (middle Ilerdian) characterized by a further specific diversification, increase of shell size, and well-developed adult dimorphism. Within an evolutionary scheme controlled by long-term biological processes, we argue that high seawater temperatures could have stimulated the early Ilerdian rapid specific diversification. Together, these data help elucidate the effects of global warming and associated feedbacks in shallow-water ecosystems, and by inference, could serve as an assessment analog for future changes.}, language = {en} } @article{ZakrevskyyRichterZakrevskaetal.2012, author = {Zakrevskyy, Yuriy and Richter, Marcel and Zakrevska, Svitlana and Lomadze, Nino and von Klitzing, Regine and Santer, Svetlana}, title = {Light-controlled reversible manipulation of microgel particle size using azobenzene-containing surfactant}, series = {Advanced functional materials}, volume = {22}, journal = {Advanced functional materials}, number = {23}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1616-301X}, doi = {10.1002/adfm.201200617}, pages = {5000 -- 5009}, year = {2012}, abstract = {The light-induced reversible switching of the swelling of microgel particles triggered by photo-isomerization and binding/unbinding of a photosensitive azobenzene-containing surfactant is reported. The interactions between the microgel (N-isopropylacrylamide, co-monomer: allyl acetic acid, crosslinker: N,N'-methylenebisacrylamide) and the surfactant are studied by UV-Vis spectroscopy, dynamic and electrophoretic light scattering measurements. Addition of the surfactant above a critical concentration leads to contraction/collapse of the microgel. UV light irradiation results in trans-cis isomerization of the azobenzene unit incorporated into the surfactant tail and causes an unbinding of the more hydrophilic cis isomer from the microgel and its reversible swelling. The reversible contraction can be realized by blue light irradiation that transfers the surfactant back to the more hydrophobic trans conformation, in which it binds to the microgel. The phase diagram of the surfactant-microgel interaction and transitions (aggregation, contraction, and precipitation) is constructed and allows prediction of changes in the system when the concentration of one or both components is varied. Remote and reversible switching between different states can be realized by either UV or visible light irradiation.}, language = {en} } @article{ZakrevskyyRitschelDoscheetal.2012, author = {Zakrevskyy, Y. and Ritschel, T. and Dosche, C. and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Quantitative calibration - and reference-free wavelength modulation spectroscopy}, series = {Infrared physics \& technology}, volume = {55}, journal = {Infrared physics \& technology}, number = {2-3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1350-4495}, doi = {10.1016/j.infrared.2011.12.001}, pages = {183 -- 190}, year = {2012}, abstract = {A unified model for quantitative description of harmonic spectra of gases obtained by wavelength modulation spectroscopy (WMS) technique is presented. In the model, both intensity modulation (IM) and frequency modulation (FM) of the laser emission are taken into account using minimum number of parameters. For the first time, the static behavior of a laser is described as a limiting case of its dynamic response. Laser and its driver are considered as a single device converting applied bias to laser emission. This allows application of the model to any type of laser and the introduced parameters can be assigned to the corresponding laser and/or driver properties. The approach was tested using a distributed feedback (DFB) laser spectrometer. Correctness of the proposed model is justified by very good agreement between the measured and modeled/fitted spectra, which allowed evaluation of the setup performance and assessment of modulation parameters of the DFB laser. An algorithm to minimize the time of numerical calculation of harmonic spectra using numerically approximated Voigt lineshape function was developed. Absolute values of the absorption line parameters (line strength and line width) were obtained from a single calibration- and reference-free spectrum scan with accuracy better than 0.1\%.}, language = {en} } @article{ZaklanCullmannNeumannetal.2012, author = {Zaklan, Aleksandar and Cullmann, Astrid and Neumann, Anne and von Hirschhausen, Christian}, title = {The globalization of steam coal markets and the role of logistics an empirical analysis}, series = {Energy economics}, volume = {34}, journal = {Energy economics}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0140-9883}, doi = {10.1016/j.eneco.2011.03.001}, pages = {105 -- 116}, year = {2012}, abstract = {In this paper, we provide a comprehensive multivariate cointegration analysis of three parts of the steam coal value chain - export, transport and import prices. The analysis is based on a rich dataset of international coal prices: in particular, we combine data on steam coal prices with freight rates, covering the period December 2001 until August 2009 at weekly frequency. We then test whether the demand and supply side components of steam coal trade are consistently integrated with one another. In addition, export and import prices as well as freight rates for individual trading routes, across regions and globally are combined. We find evidence of significant yet incomplete integration. We also find heterogeneous short-term dynamics of individual markets. Furthermore, we examine whether logistics enter coal price dynamics through transportation costs, which are mainly determined by oil prices. Our results suggest that this is generally not the case.}, language = {en} } @phdthesis{Zakharova2012, author = {Zakharova, Anna}, title = {Bifurcations in deterministic and stochastic systems and applications to biology}, address = {Potsdam}, pages = {VI, 69 S.}, year = {2012}, language = {en} } @article{ZaccheusBroekerLundborgetal.2012, author = {Zaccheus, Mona V. and Br{\"o}ker, Nina Kristin and Lundborg, Magnus and Uetrecht, Charlotte and Barbirz, Stefanie and Widmalm, Goran}, title = {Structural studies of the O-antigen polysaccharide from Escherichia coli TD2158 having O18 serogroup specificity and aspects of its interaction with the tailspike endoglycosidase of the infecting bacteriophage HK620}, series = {Carbohydrate research}, volume = {357}, journal = {Carbohydrate research}, number = {8}, publisher = {Elsevier}, address = {Oxford}, issn = {0008-6215}, doi = {10.1016/j.carres.2012.05.022}, pages = {118 -- 125}, year = {2012}, abstract = {We have analyzed the O-antigen polysaccharide of the previously uncharacterized Escherichia coli strain TD2158 which is a host of bacteriophage HK620. This bacteriophage recognizes and cleaves the polysaccharide with its tailspike protein (TSP). The polysaccharide preparation as well as oligosaccharides obtained from HK620TSP endoglycosidase digests were analyzed with NMR spectroscopy. Additionally, sugar analysis was performed on the O-antigen polysaccharide and MALDI-TOF MS was used in oligosaccharide analysis. The present study revealed a heterogeneous polysaccharide with a hexasaccharide repeating unit of the following structure: alpha-D-Glcp-(1 -> 6) vertical bar vertical bar 2)-alpha-L-Rhap-(1 -> 6)-alpha-D-Glcp-(1 -> 4)-alpha-D-Galp-(1 -> 3)-alpha-D-GlcpNAc- (1 ->vertical bar beta-D-Glcp/beta-D-GlcpNAc-(1 -> 3) A repeating unit with a D-GlcNAc substitution of D-Gal has been described earlier as characteristic for serogroup O18A1. Accordingly, we termed repeating units with D-Glc substitution at D-Gal as O18A2. NMR analyses of the polysaccharide confirmed that O18A1- and O18A2-type repeats were present in a 1:1 ratio. However, HK620TSP preferentially bound the D-GlcNAc- substituted O18A1-type repeating units in its high affinity binding pocket with a dissociation constant of 140 mu M and disfavored the O18A2-type having a beta-D-Glcp-(1 -> 3)-linked group. As a result, in hexasaccharide preparations, O18A1 and O18A2 repeats were present in a 9: 1 ratio stressing the clear preference of O18A1- type repeats to be cleaved by HK620TSP.}, language = {en} } @article{YinLinker2012, author = {Yin, Jian and Linker, Torsten}, title = {Recent advances in the stereoselective synthesis of carbohydrate 2-C-analogs}, series = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, volume = {10}, journal = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, number = {12}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1477-0520}, doi = {10.1039/c2ob06529k}, pages = {2351 -- 2362}, year = {2012}, abstract = {C-branched carbohydrates are of current interest for glycochemistry, are widely found in nature and serve as important subunits in many antibiotics, bacterial polysaccharides and macrolides. Among C-functionalized saccharides, 2-C-branched carbohydrates represent challenging structures for synthetic chemists, since in contrast to C-glycosides they are not easily accessible from glycosyl bromides or other simple precursors. In this perspective we want to summarize recent approaches to 2-C-branched carbohydrates over the past fifteen years. The two main strategies are based on ring-opening of 1,2-cyclopropanated carbohydrates by various reagents, as well as radical additions to glycals and further transformations, developed in our group. Both methods are characterized by high stereoselectivities and good yields and give access to a broad variety of functionalized carbohydrate 2-C-analogs.}, language = {en} } @article{YarmanGroebeNeumannetal.2012, author = {Yarman, Aysu and Gr{\"o}be, Glenn and Neumann, Bettina and Kinne, Mathias and Gajovic-Eichelmann, Nenad and Wollenberger, Ursula and Hofrichter, Martin and Ullrich, Rene and Scheibner, Katrin and Scheller, Frieder W.}, title = {The aromatic peroxygenase from Marasmius rutola-a new enzyme for biosensor applications}, series = {Analytical \& bioanalytical chemistry}, volume = {402}, journal = {Analytical \& bioanalytical chemistry}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-011-5497-y}, pages = {405 -- 412}, year = {2012}, abstract = {The aromatic peroxygenase (APO; EC 1.11.2.1) from the agraric basidomycete Marasmius rotula (MroAPO) immobilized at the chitosan-capped gold-nanoparticle-modified glassy carbon electrode displayed a pair of redox peaks with a midpoint potential of -278.5 mV vs. AgCl/AgCl (1 M KCl) for the Fe(2+)/Fe(3+) redox couple of the heme-thiolate-containing protein. MroAPO oxidizes aromatic substrates such as aniline, p-aminophenol, hydroquinone, resorcinol, catechol, and paracetamol by means of hydrogen peroxide. The substrate spectrum overlaps with those of cytochrome P450s and plant peroxidases which are relevant in environmental analysis and drug monitoring. In M. rotula peroxygenase-based enzyme electrodes, the signal is generated by the reduction of electrode-active reaction products (e.g., p-benzoquinone and p-quinoneimine) with electro-enzymatic recycling of the analyte. In these enzyme electrodes, the signal reflects the conversion of all substrates thus representing an overall parameter in complex media. The performance of these sensors and their further development are discussed.}, language = {en} } @phdthesis{Yarman2012, author = {Yarman, Aysu}, title = {Biomimetic sensors for substrates of peroxidases and cytochrome P450s}, address = {Potsdam}, pages = {121 S.}, year = {2012}, language = {en} } @article{YangDumasGarciaBanuelosetal.2012, author = {Yang, Yong and Dumas, Marlon and Garcia-Banuelos, Luciano and Polyvyanyy, Artem and Zhang, Liang}, title = {Generalized aggregate quality of service computation for composite services}, series = {The journal of systems and software}, volume = {85}, journal = {The journal of systems and software}, number = {8}, publisher = {Elsevier}, address = {New York}, issn = {0164-1212}, doi = {10.1016/j.jss.2012.03.005}, pages = {1818 -- 1830}, year = {2012}, abstract = {This article addresses the problem of estimating the Quality of Service (QoS) of a composite service given the QoS of the services participating in the composition. Previous solutions to this problem impose restrictions on the topology of the orchestration models, limiting their applicability to well-structured orchestration models for example. This article lifts these restrictions by proposing a method for aggregate QoS computation that deals with more general types of unstructured orchestration models. The applicability and scalability of the proposed method are validated using a collection of models from industrial practice.}, language = {en} } @article{YangBao2012, author = {Yang, Ling and Bao, Hongwei}, title = {Queerly intimate friends, fans and affective communication in a Super Girl fan fiction community}, series = {Cultural studies : theorizing politics, politicizing theory}, volume = {26}, journal = {Cultural studies : theorizing politics, politicizing theory}, number = {6}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0950-2386}, doi = {10.1080/09502386.2012.679286}, pages = {842 -- 871}, year = {2012}, abstract = {This article examines the rise of the Girls' Love (GL) fan fiction community in contemporary China. More specifically, we focus on the 'Pink Super Girl Bar', an online fan fiction community devoted to the pairing of the contestants of the 2006 season of Super Girl, an entertainment program featured on Hunan Satellite TV that enjoys great popularity in the Sinophone world. Through an ethnographic account of the formation, convention and performativity of identities and socialities in this community, we demonstrate how Super Girl GL fans mobilize their emotional capital to create artworks, to have fun and to enrich their everyday lives. We argue that the GL fan fiction community has become a space of female homosociality, intimacy and affect in which a new generation of young Chinese women actively enact friendship and female subjectivity in a way that refuses the normalization of gender, sexuality and social relations. Moreover, by linking fan studies to affect studies and emotional geography, and by paying particular attention to indigenous concepts and cultural practices in mainland China's fan communities, we wish to contribute to fan studies with feminist, queer and transnational perspectives.}, language = {en} } @article{YangWangYanetal.2012, author = {Yang, Jiongjiong and Wang, Aobing and Yan, Ming and Zhu, Zijian and Chen, Cheng and Wang, Yizhou}, title = {Distinct processing for pictures of animals and objects Evidence from eye movements}, series = {Emotion : a new journal from the American Psychological Association}, volume = {12}, journal = {Emotion : a new journal from the American Psychological Association}, number = {3}, publisher = {American Psychological Association}, address = {Washington}, issn = {1528-3542}, doi = {10.1037/a0026848}, pages = {540 -- 551}, year = {2012}, abstract = {Many studies have suggested that emotional stimuli orient and engage attention. There is also evidence that animate stimuli, such as those from humans and animals, cause attentional bias. However, categorical and emotional factors are usually mixed, and it is unclear to what extent human context influences attentional allocation. To address this issue, we tracked participants' eye movements while they viewed pictures with animals and inanimate images (i.e., category) as focal objects. These pictures had either negative or neutral emotional valence, and either human body parts or nonhuman parts were near the focal objects (i.e., context). The picture's valence, arousal, position, size, and most of the low-level visual features were matched across categories. The results showed that nonhuman animals were more likely to be attended to and to be attended to for longer times than inanimate objects. The same pattern held for the human contexts (vs. nonhuman contexts). The effects of emotional valence, category, and context interacted. Specifically, in images with a negative valence, focal animals and objects with human context had comparable numbers of gaze fixations and gaze duration. These results highlighted the attentional bias to animate parts of a picture and clarified that the effects of category, valence, and picture context interacted to influence attentional allocation.}, language = {en} } @article{YanZhouShuetal.2012, author = {Yan, Ming and Zhou, Wei and Shu, Hua and Kliegl, Reinhold}, title = {Lexical and sublexical semantic preview benefits in chinese reading}, series = {Journal of experimental psychology : Learning, memory, and cognition}, volume = {38}, journal = {Journal of experimental psychology : Learning, memory, and cognition}, number = {4}, publisher = {American Psychological Association}, address = {Washington}, issn = {0278-7393}, doi = {10.1037/a0026935}, pages = {1069 -- 1075}, year = {2012}, abstract = {Semantic processing from parafoveal words is an elusive phenomenon in alphabetic languages, but it has been demonstrated only for a restricted set of noncompound Chinese characters. Using the gaze-contingent boundary paradigm, this experiment examined whether parafoveal lexical and sublexical semantic information was extracted from compound preview characters. Results generalized parafoveal semantic processing to this representative set of Chinese characters and extended the parafoveal processing to radical (sublexical) level semantic information extraction. Implications for notions of parafoveal information extraction during Chinese reading are discussed.}, language = {en} } @article{YanRisseZhouetal.2012, author = {Yan, Ming and Risse, Sarah and Zhou, Xiaolin and Kliegl, Reinhold}, title = {Preview fixation duration modulates identical and semantic preview benefit in Chinese reading}, series = {Reading and writing : an interdisciplinary journal}, volume = {25}, journal = {Reading and writing : an interdisciplinary journal}, number = {5}, publisher = {Springer}, address = {Dordrecht}, issn = {0922-4777}, doi = {10.1007/s11145-010-9274-7}, pages = {1093 -- 1111}, year = {2012}, abstract = {Semantic preview benefit from parafoveal words is critical for proposals of distributed lexical processing during reading. Semantic preview benefit has been demonstrated for Chinese reading with the boundary paradigm in which unrelated or semantically related previews of a target word N + 1 are replaced by the target word once the eyes cross an invisible boundary located after word N (Yan et al., 2009); for the target word in position N + 2, only identical compared to unrelated-word preview led to shorter fixation times on the target word (Yan et al., in press). A reanalysis of these data reveals that identical and semantic preview benefits depend on preview duration (i.e., the fixation duration on the preboundary word). Identical preview benefit from word N + 1 increased with preview duration. The identical preview benefit was also significant for N + 2, but did not significantly interact with preview duration. The previously reported semantic preview benefit from word N + 1 was mainly due to single- or first-fixation durations following short previews. We discuss implications for notions of serial attention shifts and parallel distributed processing of words during reading.}, language = {en} } @article{XieXuGessneretal.2012, author = {Xie, Zai-Lai and Xu, Hai-Bing and Gessner, Andre and Kumke, Michael Uwe and Priebe, Magdalena and Fromm, Katharina M. and Taubert, Andreas}, title = {A transparent, flexible, ion conductive, and luminescent PMMA ionogel based on a Pt/Eu bimetallic complex and the ionic liquid [Bmim][N(Tf)(2)]}, series = {Journal of materials chemistry}, volume = {22}, journal = {Journal of materials chemistry}, number = {16}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {0959-9428}, doi = {10.1039/c2jm15862k}, pages = {8110 -- 8116}, year = {2012}, abstract = {Transparent, ion-conducting, luminescent, and flexible ionogels based on the room temperature ionic liquid (IL) 1-butyl-3-methylimidazolium bis(trifluoromethane sulfonyl) imide [Bmim][N(Tf)(2)], a PtEu2 chromophore, and poly(methylmethacrylate) (PMMA) have been prepared. The thermal stability of the PMMA significantly increases with IL incorporation. In particular, the onset weight loss observed at ca. 229 degrees C for pure PMMA increases to 305 degrees C with IL addition. The ionogel has a high ionic conductivity of 10(-3) S cm(-1) at 373 K and exhibits a strong emission in the red with a long average luminescence decay time of tau = 890 mu s. The resulting material is a new type of soft hybrid material featuring useful thermal, optical, and ion transport properties.}, language = {en} } @phdthesis{Xie2012, author = {Xie, Zai-Lai}, title = {Functional materials in metal-containing ionic liquids}, address = {Potsdam}, pages = {108 S.}, year = {2012}, language = {en} } @article{XiaCaoDaietal.2012, author = {Xia, Haiyan and Cao, Yun and Dai, Xiaoman and Marelja, Zvonimir and Zhou, Di and Mo, Ran and Al-Mahdawi, Sahar and Pook, Mark A. and Leimk{\"u}hler, Silke and Rouault, Tracey A. and Li, Kuanyu}, title = {Novel Frataxin Isoforms May Contribute to the Pathological Mechanism of Friedreich Ataxia}, series = {PLOS ONE}, volume = {7}, journal = {PLOS ONE}, number = {10}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {SAN FRANCISCO}, issn = {1932-6203}, doi = {10.1371/journal.pone.0047847}, pages = {11}, year = {2012}, abstract = {Friedreich ataxia (FRDA) is an inherited neurodegenerative disease caused by frataxin (FXN) deficiency. The nervous system and heart are the most severely affected tissues. However, highly mitochondria-dependent tissues, such as kidney and liver, are not obviously affected, although the abundance of FXN is normally high in these tissues. In this study we have revealed two novel FXN isoforms (II and III), which are specifically expressed in affected cerebellum and heart tissues, respectively, and are functional in vitro and in vivo. Increasing the abundance of the heart-specific isoform III significantly increased the mitochondrial aconitase activity, while over-expression of the cerebellum-specific isoform II protected against oxidative damage of Fe-S cluster-containing aconitase. Further, we observed that the protein level of isoform III decreased in FRDA patient heart, while the mRNA level of isoform II decreased more in FRDA patient cerebellum compared to total FXN mRNA. Our novel findings are highly relevant to understanding the mechanism of tissue-specific pathology in FRDA.}, language = {en} } @article{WoehlBruhnBadarBertzetal.2012, author = {W{\"o}hl-Bruhn, Stefanie and Badar, Muhammad and Bertz, Andreas and Tiersch, Brigitte and Koetz, Joachim and Menzel, Henning and M{\"u}ller, Peter P. and Bunjes, Heike}, title = {Comparison of in vitro and in vivo protein release from hydrogel systems}, series = {Journal of controlled release}, volume = {162}, journal = {Journal of controlled release}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0168-3659}, doi = {10.1016/j.jconrel.2012.05.049}, pages = {127 -- 133}, year = {2012}, abstract = {Hydrogel systems based on hydroxyethyl starch-polyethylene glycol methacrylate (HES-P(EG)(6)MA) or hydroxyethyl starch methacrylate (HES-MA) were used to assess the protein release behavior. Here, we analyzed the in vitro release of FITC-anti-human antibodies incorporated in either HES-P(EG)(6)MA or HES-MA hydrogel delivery systems in PBS or human serum. In addition, hydrogel disks and microparticles prepared from the two polymers were subcutaneously implanted in BALB/c mice. The in vivo release of FITC-IgG was non-invasively monitored by an in vivo imaging system (IVIS 200) over a time period of up to 3 months. The imaging system allowed to asses individual animals over time, therefore only a small number of animals was required to obtain high quality data. The reduction in fluorescence intensity at the site of administration was compared to in vitro release profiles. These investigations demonstrated a sustained release from HES-MA hydrogel disks compared to rapidly degrading HES-P(EG)(6)MA disks and microparticles. The sustained release from HES-MA disks could be further optimized by using increased polymer concentrations. Human serum as in vitro release medium reflected better the in vivo release from HES-P(EG)(6)MA systems than PBS, suggesting that the presence of organic substances like proteins or lipids may play a significant role for the release kinetics.}, language = {en} }