@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} } @article{NazeOskinovaGosset2013, author = {Naze, Yael and Oskinova, Lida and Gosset, Eric}, title = {A detailed x-ray investigation of zeta puppis - II. the variability on short and long timescales}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, volume = {763}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, number = {2}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0004-637X}, doi = {10.1088/0004-637X/763/2/143}, pages = {21}, year = {2013}, abstract = {Stellar winds are a crucial component of massive stars, but their exact properties still remain uncertain. To shed some light on this subject, we have analyzed an exceptional set of X-ray observations of zeta Puppis, one of the closest and brightest massive stars. The sensitive light curves that were derived reveal two major results. On the one hand, a slow modulation of the X-ray flux (with a relative amplitude of up to 15\% over 16 hr in the 0.3-4.0 keV band) is detected. Its characteristic timescale cannot be determined with precision, but amounts from one to several days. It could be related to corotating interaction regions, known to exist in zeta Puppis from UV observations. Hour-long changes, linked to flares or to the pulsation activity, are not observed in the last decade covered by the XMM observations; the 17 hr tentative period, previously reported in a ROSAT analysis, is not confirmed either and is thus transient, at best. On the other hand, short-term changes are surprisingly small (<1\% relative amplitude for the total energy band). In fact, they are compatible solely with the presence of Poisson noise in the data. This surprisingly low level of short-term variability, in view of the embedded wind-shock origin, requires a very high fragmentation of the stellar wind, for both absorbing and emitting features (>10(5) parcels, comparing with a two-dimensional wind model). This is the first time that constraints have been placed on the number of clumps in an O-type star wind and from X-ray observations.}, language = {en} } @article{TrinhEllisBlandHawthornetal.2013, author = {Trinh, Christopher Q. and Ellis, Simon C. and Bland-Hawthorn, Joss and Lawrence, Jon S. and Horton, Anthony J. and Leon-Saval, Sergio G. and Shortridge, Keith and Bryant, Julia and Case, Scott and Colless, Matthew and Couch, Warrick and Freeman, Kenneth and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Gers, Luke and Glazebrook, Karl and Haynes, Roger and Lee, Steve and O'Byrne, John and Miziarski, Stan and Roth, Martin M. and Schmidt, Brian and Tinney, Christopher G. and Zheng, Jessica}, title = {Gnosis - the first instrument to use fiber bragg gratings for OH suppression}, series = {The astronomical journal}, volume = {145}, journal = {The astronomical journal}, number = {2}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0004-6256}, doi = {10.1088/0004-6256/145/2/51}, pages = {13}, year = {2013}, abstract = {The near-infrared is an important part of the spectrum in astronomy, especially in cosmology because the light from objects in the early universe is redshifted to these wavelengths. However, deep near-infrared observations are extremely difficult to make from ground-based telescopes due to the bright background from the atmosphere. Nearly all of this background comes from the bright and narrow emission lines of atmospheric hydroxyl (OH) molecules. The atmospheric background cannot be easily removed from data because the brightness fluctuates unpredictably on short timescales. The sensitivity of ground-based optical astronomy far exceeds that of near-infrared astronomy because of this long-standing problem. GNOSIS is a prototype astrophotonic instrument that utilizes "OH suppression fibers" consisting of fiber Bragg gratings and photonic lanterns to suppress the 103 brightest atmospheric emission doublets between 1.47 and 1.7 mu m. GNOSIS was commissioned at the 3.9 m Anglo-Australian Telescope with the IRIS2 spectrograph to demonstrate the potential of OH suppression fibers, but may be potentially used with any telescope and spectrograph combination. Unlike previous atmospheric suppression techniques GNOSIS suppresses the lines before dispersion and in a manner that depends purely on wavelength. We present the instrument design and report the results of laboratory and on-sky tests from commissioning. While these tests demonstrated high throughput (approximate to 60\%) and excellent suppression of the skylines by the OH suppression fibers, surprisingly GNOSIS produced no significant reduction in the interline background and the sensitivity of GNOSIS+IRIS2 is about the same as IRIS2. It is unclear whether the lack of reduction in the interline background is due to physical sources or systematic errors as the observations are detector noise dominated. OH suppression fibers could potentially impact ground-based astronomy at the level of adaptive optics or greater. However, until a clear reduction in the interline background and the corresponding increasing in sensitivity is demonstrated optimized OH suppression fibers paired with a fiber-fed spectrograph will at least provide a real benefit at low resolving powers.}, language = {en} }