@article{GodecMetzler2013, author = {Godec, Aljaz and Metzler, Ralf}, title = {Finite-Time effects and ultraweak ergodicity breaking in superdiffusive dynamics}, series = {Physical review letters}, volume = {110}, journal = {Physical review letters}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.110.020603}, pages = {5}, year = {2013}, abstract = {We study the ergodic properties of superdiffusive, spatiotemporally coupled Levy walk processes. For trajectories of finite duration, we reveal a distinct scatter of the scaling exponents of the time averaged mean squared displacement (delta x(2)) over bar around the ensemble value 3 - alpha (1 < alpha < 2) ranging from ballistic motion to subdiffusion, in strong contrast to the behavior of subdiffusive processes. In addition we find a significant dependence of the average of (delta x(2)) over bar over an ensemble of trajectories as a function of the finite measurement time. This so-called finite-time amplitude depression and the scatter of the scaling exponent is vital in the quantitative evaluation of superdiffusive processes. Comparing the long time average of the second moment with the ensemble mean squared displacement, these only differ by a constant factor, an ultraweak ergodicity breaking.}, language = {en} } @article{LiuSiblyGrimmetal.2013, author = {Liu, Chun and Sibly, Richard M. and Grimm, Volker and Thorbek, Pernille}, title = {Linking pesticide exposure and spatial dynamics an individual-based model of wood mouse (Apodemus sylvaticus) populations in agricultural landscapes}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {248}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2012.09.016}, pages = {92 -- 102}, year = {2013}, abstract = {The wood mouse is a common and abundant species in agricultural landscape and is a focal species in pesticide risk assessment. Empirical studies on the ecology of the wood mouse have provided sufficient information for the species to be modelled mechanistically. An individual-based model was constructed to explicitly represent the locations and movement patterns of individual mice. This together with the schedule of pesticide application allows prediction of the risk to the population from pesticide exposure. The model included life-history traits of wood mice as well as typical landscape dynamics in agricultural farmland in the UK. The model obtains a good fit to the available population data and is fit for risk assessment purposes. It can help identify spatio-temporal situations with the largest potential risk of exposure and enables extrapolation from individual-level endpoints to population-level effects. Largest risk of exposure to pesticides was found when good crop growth in the "sink" fields coincided with high "source" population densities in the hedgerows.}, language = {en} } @article{MoskalikShainyanAstakhovaetal.2013, author = {Moskalik, Mikhail Yu and Shainyan, Bagrat A. and Astakhova, Vera V. and Schilde, Uwe}, title = {Oxidative addition of trifluoromethanesulfonamide to cycloalkadienes}, series = {Tetrahedron}, volume = {69}, journal = {Tetrahedron}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0040-4020}, doi = {10.1016/j.tet.2012.10.099}, pages = {705 -- 711}, year = {2013}, abstract = {In the oxidative system (t-BuOCl+NaI) trifluoromethanesulfonamide is regio- and stereoselectively added to only one double bond of cyclopentadiene and 1,3-cyclohexadiene giving rise to 1,1,1-trifluoro-N-(5-iodocyclopent-2-en-1-yl)methanesulfonamide 7 and trans-N,N'-cyclohex-3-en-1,2-diylbis(1,1,1-trifluoromethanesulfonamide) 8. The structure of 7 and 8 was determined by X-ray, NMR, and MS. With 1,4-cyclohexadiene, addition to both double bonds occurs with the formation of N,N'-(4-chloro-5-iodocyclohexan-1,2-diyl)bis(1,1,1-trifluoromethanesulfonamide) 9. Under the action of sodium iodide in acetone, the latter product undergoes halogenophilic attack with the reduction of the CHI group and elimination of HCl to give trans-N,N'-cyclohex-4-en-1,2-diylbis(1,1,1-trifluoromethanesulfonamide) 10, whose structure was also determined by X-ray analysis. 1,3,5-Cycloheptatriene under these conditions is oxidized to benzaldehyde and does not react with trifluoromethanesulfonamide.}, language = {en} } @article{HeckmannSchwanghart2013, author = {Heckmann, Tobias and Schwanghart, Wolfgang}, title = {Geomorphic coupling and sediment connectivity in an alpine catchment - Exploring sediment cascades using graph theory}, series = {Geomorphology : an international journal on pure and applied geomorphology}, volume = {182}, journal = {Geomorphology : an international journal on pure and applied geomorphology}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0169-555X}, doi = {10.1016/j.geomorph.2012.10.033}, pages = {89 -- 103}, year = {2013}, abstract = {Through their relevance for sediment budgets and the sensitivity of geomorphic systems, geomorphic coupling and (sediment) connectivity represent important topics in geomorphology. Since the introduction of the systems perspective to physical geography by Chorley and Kennedy (1971), a catchment has been perceived as consisting of landscape elements (e.g. landforms, subcatchments) that are coupled by geomorphic processes through sediment transport. In this study, we present a novel application of mathematical graph theory to explore the network structure of coarse sediment pathways in a central alpine catchment. Numerical simulation models for rockfall, debris flows, and (hillslope and channel) fluvial processes are used to establish a spatially explicit graph model of sediment sources, pathways and sinks. The raster cells of a digital elevation model form the nodes of this graph, and simulated sediment trajectories represent the corresponding edges. Model results are validated by visual comparison with the field situation and aerial photos. The interaction of sediment pathways, i.e. where the deposits of a geomorphic process form the sources of another process, forms sediment cascades, represented by paths (a succession of edges) in the graph model. We show how this graph can be used to explore upslope (contributing area) and downslope (source to sink) functional connectivity by analysing its nodes, edges and paths. The analysis of the spatial distribution, composition and frequency of sediment cascades yields information on the relative importance of geomorphic processes and their interaction (however regardless of their transport capacity). In the study area, the analysis stresses the importance of mass movements and their interaction, e.g. the linkage of large rockfall source areas to debris flows that potentially enter the channel network. Moreover, it is shown that only a small percentage of the study area is coupled to the channel network which itself is longitudinally disconnected by natural and anthropogenic barriers. Besides the case study, we discuss the methodological framework and alternatives for node and edge representations of graph models in geomorphology. We conclude that graph theory provides an excellent methodological framework for the analysis of geomorphic systems, especially for the exploration of quantitative approaches towards sediment connectivity.}, language = {en} } @article{KahmenSchefussSachse2013, author = {Kahmen, Ansgar and Schefuss, Enno and Sachse, Dirk}, title = {Leaf water deuterium enrichment shapes leaf wax n-alkane delta D values of angiosperm plants I experimental evidence and mechanistic insights}, series = {Geochimica et cosmochimica acta : journal of the Geochemical Society and the Meteoritical Society}, volume = {111}, journal = {Geochimica et cosmochimica acta : journal of the Geochemical Society and the Meteoritical Society}, publisher = {Elsevier}, address = {Oxford}, issn = {0016-7037}, doi = {10.1016/j.gca.2012.09.003}, pages = {39 -- 49}, year = {2013}, abstract = {Leaf wax n-alkanes of terrestrial plants are long-chain hydrocarbons that can persist in sedimentary records over geologic timescales. Since meteoric water is the primary source of hydrogen used in leaf wax synthesis, the hydrogen isotope composition (delta D value) of these biomarkers contains information on hydrological processes. Consequently, leaf wax n-alkane delta D values have been advocated as powerful tools for paleohydrological research. The exact kind of hydrological information that is recorded in leaf wax n-alkanes remains, however, unclear because critical processes that determine their delta D values have not yet been resolved. In particular the effects of evaporative deuterium (D)-enrichment of leaf water on the delta D values of leaf wax n-alkanes have not yet been directly assessed and quantified. Here we present the results of a study where we experimentally tested if and by what magnitude evaporative D-enrichment of leaf water affects the delta D of leaf wax n-alkanes in angiosperm C3 and C4 plants. Our study revealed that n-alkane delta D values of all plants that we investigated were affected by evaporative D-enrichment of leaf water. For dicotyledonous plants we found that the full extent of leaf water evaporative D-enrichment is recorded in leaf wax n-alkane delta D values. For monocotyledonous plants we found that between 18\% and 68\% of the D-enrichment in leaf water was recorded in the delta D values of their n-alkanes. We hypothesize that the different magnitudes by which evaporative D-enrichment of leaf water affects the delta D values of leaf wax n-alkanes in monocotyledonous and dicotyledonous plants is the result of differences in leaf growth and development between these plant groups. Our finding that the evaporative D-enrichment of leaf water affects the delta D values of leaf wax n-alkanes in monocotyledonous and dicotyledonous plants albeit at different magnitudes - has important implications for the interpretation of leaf wax n-alkane delta D values from paleohydrological records. In addition, our finding opens the door to employ delta D values of leaf wax n-alkanes as new ecohydrological proxies for evapotranspiration that can be applied in contemporary plant and ecosystem research.}, language = {en} } @article{UnuabonahOluOwolabiTaubertetal.2013, author = {Unuabonah, Emmanuel Iyayi and Olu-Owolabi, Bamidele I. and Taubert, Andreas and Omolehin, Elizabeth B. and Adebowale, Kayode O.}, title = {SAPK a novel composite resin for water treatment with very high Zn2+, Cd2+, and Pb2+ adsorption capacity}, series = {Industrial \& engineering chemistry research}, volume = {52}, journal = {Industrial \& engineering chemistry research}, number = {2}, publisher = {American Chemical Society}, address = {Washington}, issn = {0888-5885}, doi = {10.1021/ie3024577}, pages = {578 -- 585}, year = {2013}, abstract = {A new sulfonated aniline-modified poly(vinyl alcohol)/K-feldspar (SAPK) composite was prepared. The cation-exchange capacity of the composite was found to be S times that of neat feldspar. The specific surface area and point of zero charge also changed significantly upon modification, from 15.6 +/- 0.1 m(2)/g and 2.20 (K-feldspar) to 73.6 +/- 0.3 m(2)/g and 1.91 (SAPK). Zn2+, Cd2+, and Pb2+ adsorption was found to be largely independent of pH, and the metal adsorption rate on SAPK was higher than that on neat feldspar. This particularly applies to the initial adsorption rates. The adsorption process involves both film and pore diffusion; film diffusion initially controls the adsorption. The Freundlich and Langmuir models were found to fit metal-ion adsorption on SAPK most accurately. Adsorption on neat feldspar was best fitted with a Langmuir model, indicating the formation of adsorbate monolayers. Both pure feldspar and SAPK showed better selectivity for Pb2+ than for Cd2+ or Zn2+.}, language = {en} } @article{SchubertPreisBlakesleyetal.2013, author = {Schubert, Marcel and Preis, Eduard and Blakesley, James C. and Pingel, Patrick and Scherf, Ullrich and Neher, Dieter}, title = {Mobility relaxation and electron trapping in a donor/acceptor copolymer}, series = {Physical review : B, Condensed matter and materials physics}, volume = {87}, journal = {Physical review : B, Condensed matter and materials physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {1098-0121}, doi = {10.1103/PhysRevB.87.024203}, pages = {12}, year = {2013}, abstract = {To address the nature of charge transport and the origin of severe (intrinsic) trapping in electron-transporting polymers, transient and steady-state charge transport measurements have been conducted on the prototype donor/acceptor copolymer poly[2,7-(9,9-dialkyl-fluorene)-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PFTBTT). A charge-generation layer technique is used to selectively address transport of the desired charge carrier type, to perform time-of-flight measurements on samples with < 200 nm thickness, and to combine the time-of-flight and the photocharge extraction by linearly increasing voltage (photo-CELIV) techniques to investigate charge carrier dynamics over a wide time range. Significant trapping of free electrons is observed in the bulk of dioctyl-substituted PFTBTT (alt-PF8TBTT), introducing a strong relaxation of the charge carrier mobility with time. We used Monte-Carlo simulation to simulate the measured transient data and found that all measurements can be modeled with a single parameter set, with the charge transport behavior determined by multiple trapping and detrapping of electrons in an exponential trap distribution. The influence of the concomitant mobility relaxation on the transient photocurrent characteristics in photo-CELIV experiments is discussed and shown to explain subtle features that were seen in former publications but were not yet assigned to electron trapping. Comparable studies on PFTBTT copolymers with chemical modifications of the side chains and backbone suggest that the observed electron trapping is not caused by a distinct chemical species but rather is related to interchain interactions.}, language = {en} } @article{BauerMetzler2013, author = {Bauer, Maximilian and Metzler, Ralf}, title = {In vivo facilitated diffusion model}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0053956}, pages = {8}, year = {2013}, abstract = {Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model.}, language = {en} } @article{BertzWoehlBruhnMietheetal.2013, author = {Bertz, Andreas and W{\"o}hl-Bruhn, Stefanie and Miethe, Sebastian and Tiersch, Brigitte and Koetz, Joachim and Hust, Michael and Bunjes, Heike and Menzel, Henning}, title = {Encapsulation of proteins in hydrogel carrier systems for controlled drug delivery influence of network structure and drug size on release rate}, series = {Journal of biotechnology}, volume = {163}, journal = {Journal of biotechnology}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0168-1656}, doi = {10.1016/j.jbiotec.2012.06.036}, pages = {243 -- 249}, year = {2013}, abstract = {Novel hydrogels based on hydroxyethyl starch modified with polyethylene glycol methacrylate (HES-P(EG)(6)MA) were developed as delivery system for the controlled release of proteins. Since the drug release behavior is supposed to be related to the pore structure of the hydrogel network the pore sizes were determined by cryo-SEM, which is a mild technique for imaging on a nanometer scale. The results showed a decreasing pore size and an increase in pore homogeneity with increasing polymer concentration. Furthermore, the mesh sizes of the hydrogels were calculated based on swelling data. Pore and mesh size were significantly different which indicates that both structures are present in the hydrogel. The resulting structural model was correlated with release data for bulk hydrogel cylinders loaded with FITC-dextran and hydrogel microspheres loaded with FITC-IgG and FITC-dextran of different molecular size. The initial release depended much on the relation between hydrodynamic diameter and pore size while the long term release of the incorporated substances was predominantly controlled by degradation of the network of the much smaller meshes.}, language = {en} } @article{NeigenfindGrimbsNikoloski2013, author = {Neigenfind, Jost and Grimbs, Sergio and Nikoloski, Zoran}, title = {On the relation between reactions and complexes of (bio)chemical reaction networks}, series = {Journal of theoretical biology}, volume = {317}, journal = {Journal of theoretical biology}, number = {2}, publisher = {Elsevier}, address = {London}, issn = {0022-5193}, doi = {10.1016/j.jtbi.2012.10.016}, pages = {359 -- 365}, year = {2013}, abstract = {Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the stoichiometry of the underlying interrelated components, but also on the multitude of kinetic parameters. Invariant flux ratios, obtained within flux coupling analysis, as well as invariant complex ratios, derived within chemical reaction network theory, can characterize robust properties of a system at steady state. However, the existing formalisms for the description of these invariants do not provide full characterization as they either only focus on the flux-centric or the concentration-centric view. Here we develop a novel mathematical framework which combines both views and thereby overcomes the limitations of the classical methodologies. Our unified framework will be helpful in analyzing biologically important system properties.}, language = {en} } @article{HuebenerMariEisert2013, author = {Huebener, R. and Mari, Andrea and Eisert, Jens}, title = {Wick's theorem for matrix product states}, series = {Physical review letters}, volume = {110}, journal = {Physical review letters}, number = {4}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.110.040401}, pages = {5}, year = {2013}, abstract = {Matrix product states and their continuous analogues are variational classes of states that capture quantum many-body systems or quantum fields with low entanglement; they are at the basis of the density-matrix renormalization group method and continuous variants thereof. In this work we show that, generically, N-point functions of arbitrary operators in discrete and continuous translation invariant matrix product states are completely characterized by the corresponding two- and three-point functions. Aside from having important consequences for the structure of correlations in quantum states with low entanglement, this result provides a new way of reconstructing unknown states from correlation measurements, e. g., for one-dimensional continuous systems of cold atoms. We argue that such a relation of correlation functions may help in devising perturbative approaches to interacting theories.}, language = {en} } @article{AbramowskiAceroAharonianetal.2013, author = {Abramowski, Attila and Acero, F. and Aharonian, Felix A. and Akhperjanian, A. G. and Anton, Gisela and Balenderan, Shangkari and Balzer, Arnim and Barnacka, Anna and Becherini, Yvonne and Tjus, J. Becker and Bernl{\"o}hr, K. and Birsin, E. and Biteau, Jonathan and Bochow, A. and Boisson, Catherine and Bolmont, J. and Bordas, Pol and Brucker, J. and Brun, Francois and Brun, Pierre and Bulik, Tomasz and Carrigan, Svenja and Casanova, Sabrina and Cerruti, M. and Chadwick, Paula M. and Chaves, Ryan C. G. and Cheesebrough, A. and Colafrancesco, Sergio and Cologna, Gabriele and Conrad, Jan and Couturier, C. and Dalton, M. and Daniel, M. K. and Davids, I. D. and Degrange, B. and Deil, C. and deWilt, P. and Dickinson, H. J. and Djannati-Ata{\"i}, A. and Domainko, W. and Drury, L. O'C. and Dubus, G. and Dutson, K. and Dyks, J. and Dyrda, M. and Egberts, Kathrin and Eger, P. and Espigat, P. and Fallon, L. and Farnier, C. and Fegan, S. and Feinstein, F. and Fernandes, M. V. and Fernandez, D. and Fiasson, A. and Fontaine, G. and Foerster, A. and Fussling, Matthias and Gajdus, M. and Gallant, Y. A. and Garrigoux, T. and Gast, H. and Giebels, B. and Glicenstein, J. F. and Glueck, B. and Goering, D. and Grondin, M. -H. and Haeffner, S. and Hague, J. D. and Hahn, J. and Hampf, D. and Harris, J. and Heinz, S. and Heinzelmann, G. and Henri, G. and Hermann, G. and Hillert, A. and Hinton, James Anthony and Hofmann, W. and Hofverberg, P. and Holler, M. and Horns, D. and Jacholkowska, A. and Jahn, C. and Jamrozy, M. and Jung, I. and Kastendieck, M. A. and Katarzynski, K. and Katz, U. and Kaufmann, S. and Khelifi, B. and Klepser, S. and Klochkov, D. and Kluzniak, W. and Kneiske, T. and Komin, Nu and Kosack, K. and Kossakowski, R. and Krayzel, F. and Krueger, P. P. and Laffon, H. and Lamanna, G. and Lefaucheur, J. and Lemoine-Goumard, M. and Lenain, J. -P. and Lennarz, D. and Lohse, T. and Lopatin, A. and Lu, C. -C. and Marandon, V. and Marcowith, Alexandre and Masbou, J. and Maurin, G. and Maxted, N. and Mayer, M. and McComb, T. J. L. and Medina, M. C. and Mehault, J. and Menzler, U. and Moderski, R. and Mohamed, M. and Moulin, Emmanuel and Naumann, C. L. and Naumann-Godo, M. and de Naurois, M. and Nedbal, D. and Nekrassov, D. and Nguyen, N. and Niemiec, J. and Nolan, S. J. and Ohm, S. and Awilhelmi, E. de Ona and Opitz, B. and Ostrowski, M. and Oya, I. and Panter, M. and Parsons, R. D. and Arribas, M. Paz and Pekeur, N. W. and Pelletier, G. and Perez, J. and Petrucci, P. -O. and Peyaud, B. and Pita, S. and Puehlhofer, G. and Punch, M. and Quirrenbach, A. and Raue, M. and Reimer, A. and Reimer, O. and Renaud, M. and de los Reyes, R. and Rieger, F. and Ripken, J. and Rob, L. and Rosier-Lees, S. and Rowell, G. and Rudak, B. and Rulten, C. B. and Sahakian, V. and Sanchez, David M. and Santangelo, Andrea and Schlickeiser, R. and Schulz, A. and Schwanke, U. and Schwarzburg, S. and Schwemmer, S. and Sheidaei, F. and Skilton, J. L. and Sol, H. and Spengler, G. and Stawarz, L. and Steenkamp, R. and Stegmann, Christian and Stinzing, F. and Stycz, K. and Sushch, Iurii and Szostek, A. and Tavernet, J. -P. and Terrier, R. and Tluczykont, M. and Trichard, C. and Valerius, K. and van Eldik, C. and Vasileiadis, G. and Venter, C. and Viana, A. and Vincent, P. and Voelk, H. J. and Volpe, F. and Vorobiov, S. and Vorster, M. and Wagner, S. J. and Ward, M. and White, R. and Wierzcholska, A. and Wouters, D. and Zacharias, M. and Zajczyk, A. and Zdziarski, A. A. and Zech, Alraune and Zechlin, H. -S.}, title = {Search for Photon-Linelike Signatures from Dark Matter Annihilations with H.E.S.S.}, series = {Physical review letters}, volume = {110}, journal = {Physical review letters}, number = {4}, publisher = {American Physical Society}, address = {College Park}, organization = {HESS Collaboration}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.110.041301}, pages = {6}, year = {2013}, abstract = {Gamma-ray line signatures can be expected in the very-high-energy (E-gamma > 100 GeV) domain due to self-annihilation or decay of dark matter (DM) particles in space. Such a signal would be readily distinguishable from astrophysical gamma-ray sources that in most cases produce continuous spectra that span over several orders of magnitude in energy. Using data collected with the H. E. S. S. gamma-ray instrument, upper limits on linelike emission are obtained in the energy range between similar to 500 GeV and similar to 25 TeV for the central part of the Milky Way halo and for extragalactic observations, complementing recent limits obtained with the Fermi-LAT instrument at lower energies. No statistically significant signal could be found. For monochromatic gamma-ray line emission, flux limits of (2 x 10(-7)-2 x 10(-5)) m(-2)s(-1)sr(-1) and (1 x 10(-8)- 2 x 10(-6)) m(-2)s(-1)sr(-1) are obtained for the central part of the Milky Way halo and extragalactic observations, respectively. For a DM particle mass of 1 TeV, limits on the velocity- averaged DM annihilation cross section (chi chi ->gamma gamma) reach similar to 10(-27)cm(3)s(-1), based on the Einasto parametrization of the Galactic DM halo density profile. DOI: 10.1103/PhysRevLett.110.041301}, language = {en} } @article{GeisslerStuflerLoehmannsroebenetal.2013, author = {Geissler, Daniel and Stufler, Stefan and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Hildebrandt, Niko}, title = {Six-color time-resolved forster resonance energy transfer for ultrasensitive multiplexed biosensing}, series = {Journal of the American Chemical Society}, volume = {135}, journal = {Journal of the American Chemical Society}, number = {3}, publisher = {American Chemical Society}, address = {Washington}, issn = {0002-7863}, doi = {10.1021/ja310317n}, pages = {1102 -- 1109}, year = {2013}, abstract = {Simultaneous monitoring of multiple molecular interactions and multiplexed detection of several diagnostic biomarkers at very low concentrations have become important issues in advanced biological and chemical sensing. Here we present an optically multiplexed six-color Forster resonance energy transfer (FRET) biosensor for simultaneous monitoring of five different individual binding events. We combined simultaneous FRET from one Tb complex to five different organic dyes measured in a filter-based time-resolved detection format with a sophisticated spectral crosstalk correction, which results in very efficient background suppression. The advantages and robustness of the multiplexed FRET sensor were exemplified by analyzing a 15-component lung cancer immunoassay involving 10 different antibodies and five different tumor markers in a single 50 mu L human serum sample. The multiplexed biosensor offers clinically relevant detection limits in the low picomolar (ng/mL) concentration range for all five markers, thus providing an effective early screening tool for lung cancer with the possibility of distinguishing small-cell from non-small-cell lung carcinoma. This novel technology will open new doors for multiple biomarker diagnostics as well as multiplexed real-time imaging and spectroscopy.}, language = {en} } @article{KrauseBekkeringLindemann2013, author = {Krause, Florian and Bekkering, Harold and Lindemann, Oliver}, title = {A feeling for numbers shared metric for symbolic and tactile numerosities}, series = {Frontiers in psychology}, volume = {4}, journal = {Frontiers in psychology}, number = {3}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2013.00007}, pages = {8}, year = {2013}, abstract = {Evidence for an approximate analog system of numbers has been provided by the finding that the comparison of two numerals takes longer and is more error-prone if the semantic distance between the numbers becomes smaller (so-called numerical distance effect). Recent embodied theories suggest that analog number representations are based on previous sensory experiences and constitute therefore a common magnitude metric shared by multiple domains. Here we demonstrate the existence of a cross-modal semantic distance effect between symbolic and tactile numerosities. Participants received tactile stimulations of different amounts of fingers while reading Arabic digits and indicated verbally whether the amount of stimulated fingers was different from the simultaneously presented digit or not. The larger the semantic distance was between the two numerosities, the faster and more accurate participants made their judgments. This cross-modal numerosity distance effect suggests a direct connection between tactile sensations and the concept of numerical magnitude. A second experiment replicated the interaction between symbolic and tactile numerosities and showed that this effect is not modulated by the participants' finger counting habits. Taken together, our data provide novel evidence for a shared metric for symbolic and tactile numerosities as an instance of an embodied representation of numbers.}, language = {en} } @article{KlingstromSoldatovaStevensetal.2013, author = {Klingstrom, Tomas and Soldatova, Larissa and Stevens, Robert and Roos, T. Erik and Swertz, Morris A. and M{\"u}ller, Kristian M. and Kalas, Matus and Lambrix, Patrick and Taussig, Michael J. and Litton, Jan-Eric and Landegren, Ulf and Bongcam-Rudloff, Erik}, title = {Workshop on laboratory protocol standards for the molecular methods database}, series = {New biotechnology}, volume = {30}, journal = {New biotechnology}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1871-6784}, doi = {10.1016/j.nbt.2012.05.019}, pages = {109 -- 113}, year = {2013}, abstract = {Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.}, language = {en} } @article{StoyanovKolloscheRisseetal.2013, author = {Stoyanov, Hristiyan and Kollosche, Matthias and Risse, Sebastian and Wache, Remi and Kofod, Guggi}, title = {Soft conductive elastomer materials for stretchable electronics and voltage controlled artificial muscles}, series = {Advanced materials}, volume = {25}, journal = {Advanced materials}, number = {4}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0935-9648}, doi = {10.1002/adma.201202728}, pages = {578 -- 583}, year = {2013}, abstract = {Block copolymer elastomer conductors (BEC) are mixtures of block copolymers grafted with conducting polymers, which are found to support very large strains, while retaining a high level of conductivity. These novel materials may find use in stretchable electronics. The use of BEC is demonstrated in a capacitive strain sensor and in an artificial muscle of the dielectric elastomer actuator type, supporting more than 100\% actuation strain and capacity strain sensitivity up to 300\%.}, language = {en} } @article{BeyeneKatohWoldeGabrieletal.2013, author = {Beyene, Yonas and Katoh, Shigehiro and Wolde Gabriel, Giday and Hart, William K. and Uto, Kozo and Sudo, Masafumi and Kondo, Megumi and Hyodo, Masayuki and Renne, Paul R. and Suwa, Gen and Asfaw, Berhane}, title = {The characteristics and chronology of the earliest. Acheulean at Konso, Ethiopia}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {5}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1221285110}, pages = {1584 -- 1591}, year = {2013}, abstract = {The Acheulean technological tradition, characterized by a large (>10 cm) flake-based component, represents a significant technological advance over the Oldowan. Although stone tool assemblages attributed to the Acheulean have been reported from as early as circa 1.6-1.75 Ma, the characteristics of these earliest occurrences and comparisons with later assemblages have not been reported in detail. Here, we provide a newly established chronometric calibration for the Acheulean assemblages of the Konso Formation, southern Ethiopia, which span the time period similar to 1.75 to <1.0 Ma. The earliest Konso Acheulean is chronologically indistinguishable from the assemblage recently published as the world's earliest with an age of similar to 1.75 Ma at Kokiselei, west of Lake Turkana, Kenya. This Konso assemblage is characterized by a combination of large picks and crude bifaces/unifaces made predominantly on large flake blanks. An increase in the number of flake scars was observed within the Konso Formation handaxe assemblages through time, but this was less so with picks. The Konso evidence suggests that both picks and handaxes were essential components of the Acheulean from its initial stages and that the two probably differed in function. The temporal refinement seen, especially in the handaxe forms at Konso, implies enhanced function through time, perhaps in processing carcasses with long and stable cutting edges. The documentation of the earliest Acheulean at similar to 1.75 Ma in both northern Kenya and southern Ethiopia suggests that behavioral novelties were being established in a regional scale at that time, paralleling the emergence of Homo erectus-like hominid morphology.}, language = {en} } @article{OhligerNesmeEisert2013, author = {Ohliger, Matthias and Nesme, V. and Eisert, J.}, title = {Efficient and feasible state tomography of quantum many-body systems}, series = {New journal of physics : the open-access journal for physics}, volume = {15}, journal = {New journal of physics : the open-access journal for physics}, number = {5}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/15/1/015024}, pages = {19}, year = {2013}, abstract = {We present a novel method for performing quantum state tomography for many-particle systems, which are particularly suitable for estimating the states in lattice systems such as of ultra-cold atoms in optical lattices. We show that the need to measure a tomographically complete set of observables can be overcome by letting the state evolve under some suitably chosen random circuits followed by the measurement of a single observable. We generalize known results about the approximation of unitary two-designs, i.e. certain classes of random unitary matrices, by random quantum circuits and connect our findings to the theory of quantum compressed sensing. We show that for ultra-cold atoms in optical lattices established experimental techniques such as optical super-lattices, laser speckles and time-of-flight measurements are sufficient to perform fully certified, assumption-free tomography. This is possible without the need to address single sites in any step of the procedure. Combining our approach with tensor network methods-in particular, the theory of matrix product states-we identify situations where the effort of reconstruction is even constant in the number of lattice sites, allowing, in principle, to perform tomography on large-scale systems readily available in present experiments.}, language = {en} } @article{HuangHattermannKrysanovaetal.2013, author = {Huang, Shaochun and Hattermann, Fred and Krysanova, Valentina and Bronstert, Axel}, title = {Projections of climate change impacts on river flood conditions in Germany by combining three different RCMs with a regional eco-hydrological model}, series = {Climatic change : an interdisciplinary, intern. journal devoted to the description, causes and implications of climatic change}, volume = {116}, journal = {Climatic change : an interdisciplinary, intern. journal devoted to the description, causes and implications of climatic change}, number = {3-4}, publisher = {Springer}, address = {Dordrecht}, issn = {0165-0009}, doi = {10.1007/s10584-012-0586-2}, pages = {631 -- 663}, year = {2013}, abstract = {A general increase in precipitation has been observed in Germany in the last century, and potential changes in flood generation and intensity are now at the focus of interest. The aim of the paper is twofold: a) to project the future flood conditions in Germany accounting for various river regimes (from pluvial to nival-pluvial regimes) and under different climate scenarios (the high, A2, low, B1, and medium, A1B, emission scenarios) and b) to investigate sources of uncertainty generated by climate input data and regional climate models. Data of two dynamical Regional Climate Models (RCMs), REMO (REgional Model) and CCLM (Cosmo-Climate Local Model), and one statistical-empirical RCM, Wettreg (Wetterlagenbasierte Regionalisierungsmethode: weather-type based regionalization method), were applied to drive the eco-hydrological model SWIM (Soil and Water Integrated Model), which was previously validated for 15 gauges in Germany. At most of the gauges, the 95 and 99 percentiles of the simulated discharge using SWIM with observed climate data had a good agreement with the observed discharge for 1961-2000 (deviation within +/- 10 \%). However, the simulated discharge had a bias when using RCM climate as input for the same period. Generalized Extreme Value (GEV) distributions were fitted to the annual maximum series of river runoff for each realization for the control and scenario periods, and the changes in flood generation over the whole simulation time were analyzed. The 50-year flood values estimated for two scenario periods (2021-2060, 2061-2100) were compared to the ones derived from the control period using the same climate models. The results driven by the statistical-empirical model show a declining trend in the flood level for most rivers, and under all climate scenarios. The simulations driven by dynamical models give various change directions depending on region, scenario and time period. The uncertainty in estimating high flows and, in particular, extreme floods remains high, due to differences in regional climate models, emission scenarios and multi-realizations generated by RCMs.}, language = {en} } @article{GechevBeninaObataetal.2013, author = {Gechev, Tsanko S. and Benina, Maria and Obata, Toshihiro and Tohge, Takayuki and Neerakkal, Sujeeth and Minkov, Ivan and Hille, Jacques and Temanni, Mohamed-Ramzi and Marriott, Andrew S. and Bergstr{\"o}m, Ed and Thomas-Oates, Jane and Antonio, Carla and M{\"u}ller-R{\"o}ber, Bernd and Schippers, Jos H. M. and Fernie, Alisdair R. and Toneva, Valentina}, title = {Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis}, series = {Cellular and molecular life sciences}, volume = {70}, journal = {Cellular and molecular life sciences}, number = {4}, publisher = {Springer}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-012-1155-6}, pages = {689 -- 709}, year = {2013}, abstract = {Haberlea rhodopensis is a resurrection plant with remarkable tolerance to desiccation. Haberlea exposed to drought stress, desiccation, and subsequent rehydration showed no signs of damage or severe oxidative stress compared to untreated control plants. Transcriptome analysis by next-generation sequencing revealed a drought-induced reprogramming, which redirected resources from growth towards cell protection. Repression of photosynthetic and growth-related genes during water deficiency was concomitant with induction of transcription factors (members of the NAC, NF-YA, MADS box, HSF, GRAS, and WRKY families) presumably acting as master switches of the genetic reprogramming, as well as with an upregulation of genes related to sugar metabolism, signaling, and genes encoding early light-inducible (ELIP), late embryogenesis abundant (LEA), and heat shock (HSP) proteins. At the same time, genes encoding other LEA, HSP, and stress protective proteins were constitutively expressed at high levels even in unstressed controls. Genes normally involved in tolerance to salinity, chilling, and pathogens were also highly induced, suggesting a possible cross-tolerance against a number of abiotic and biotic stress factors. A notable percentage of the genes highly regulated in dehydration and subsequent rehydration were novel, with no sequence homology to genes from other plant genomes. Additionally, an extensive antioxidant gene network was identified with several gene families possessing a greater number of antioxidant genes than most other species with sequenced genomes. Two of the transcripts most abundant during all conditions encoded catalases and five more catalases were induced in water-deficient samples. Using the pharmacological inhibitor 3-aminotriazole (AT) to compromise catalase activity resulted in increased sensitivity to desiccation. Metabolome analysis by GC or LC-MS revealed accumulation of sucrose, verbascose, spermidine, and gamma-aminobutyric acid during drought, as well as particular secondary metabolites accumulating during rehydration. This observation, together with the complex antioxidant system and the constitutive expression of stress protective genes suggests that both constitutive and inducible mechanisms contribute to the extreme desiccation tolerance of H. rhodopensis.}, language = {en} }