@article{1036, abstract = {We report on the control of interaction-induced dephasing of Bloch oscillations for an atomic Bose-Einstein condensate in an optical lattice. We quantify the dephasing in terms of the width of the quasimomentum distribution and measure its dependence on time for different interaction strengths which we control by means of a Feshbach resonance. For minimal interaction, the dephasing time is increased from a few to more than 20 thousand Bloch oscillation periods, allowing us to realize a BEC-based atom interferometer in the noninteracting limit.}, author = {Gustavsson, Mattias and Haller, Elmar and Mark, Manfred and Danzl, Johann G and Rojas Kopeinig, Gabriel and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Control of interaction-induced dephasing of bloch oscillations}}, doi = {10.1103/PhysRevLett.100.080404}, volume = {100}, year = {2008}, } @article{1037, abstract = {We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation threshold, which are stable against spontaneous decay on the time scale of 1s. An optically trapped sample of ultracold dimers is prepared in a high rotational state and magnetically tuned into a region with a negative binding energy. The metastable character of these molecules arises from the large centrifugal barrier in combination with negligible coupling to states with low rotational angular momentum. A sharp onset of dissociation with increasing magnetic field is mediated by a crossing with a lower rotational dimer state and facilitates dissociation on demand with a well-defined energy.}, author = {Knoop, Steven and Mark, Michael and Ferlaino, Francesca and Danzl, Johann G and Kraemer, Tobias and Nägerl, Hanns and Grimm, Rudolf}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Metastable feshbach molecules in high rotational states}}, doi = {10.1103/PhysRevLett.100.083002}, volume = {100}, year = {2008}, } @article{1039, abstract = {Molecular cooling techniques face the hurdle of dissipating translational as well as internal energy in the presence of a rich electronic, vibrational, and rotational energy spectrum. In our experiment, we create a translationally ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers in the electronic ground state. Specifically, we stimulate with 80% efficiency, a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein condensate of cesium atoms. In the process, the initial loose, long-range electrostatic bond of the Feshbach molecule is coherently transformed into a tight chemical bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and show that the molecular sample is not heated during the transfer. Our results show that the preparation of a quantum gas of molecules in specific rovibrational states is possible and that the creation of a Bose-Einstein condensate of molecules in their rovibronic ground state is within reach.}, author = {Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Hart, Russell and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Nägerl, Hanns}, journal = {Science}, number = {5892}, pages = {1062 -- 1066}, publisher = {American Association for the Advancement of Science}, title = {{Quantum gas of deeply bound ground state molecules}}, doi = {10.1126/science.1159909}, volume = {321}, year = {2008}, } @article{10392, abstract = {Protonated formylmetallocenes [M(C5H5)(C5H4-CHOH)]+ (M = Fe, Ru) and their isomers have been studied at the BP86 and B3LYP levels of density functional theory. Oxygen-protonated isomers are the most stable forms in each case, with a plethora of ring- or metal-protonated species at least ca. 14 and 10 kcal/mol higher in energy for M = Fe and Ru, respectively. The computed rotational barriers around the C−C bond connecting the cyclopentadienyl and protonated formyl moieties, ca. 18 kcal/mol, are indicative of substantial conjugation between these moieties. Some of the ring- and iron-protonated species are models for possible intermediates in Friedel–Crafts acylation of ferrocene, and the computations provide further evidence that exo attack is clearly favored over endo attack of the electrophile in this reaction. The structures of the most stable mono- and diprotonated formylferrocenes are corroborated by the good agreement between GIAO-B3LYP-computed and experimental NMR chemical shifts.}, author = {Šarić, Anđela and Vrček, Valerije and Bühl, Michael}, issn = {1520-6041}, journal = {Organometallics}, keywords = {Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry}, number = {3}, pages = {394--401}, publisher = {American Chemical Society}, title = {{Density functional study of protonated formylmetallocenes}}, doi = {10.1021/om700916f}, volume = {27}, year = {2008}, } @article{11111, abstract = {During mitosis in metazoans, segregated chromosomes become enclosed by the nuclear envelope (NE), a double membrane that is continuous with the endoplasmic reticulum (ER). Recent in vitro data suggest that NE formation occurs by chromatin-mediated reorganization of the tubular ER; however, the basic principles of such a membrane-reshaping process remain uncharacterized. Here, we present a quantitative analysis of nuclear membrane assembly in mammalian cells using time-lapse microscopy. From the initial recruitment of ER tubules to chromatin, the formation of a membrane-enclosed, transport-competent nucleus occurs within ∼12 min. Overexpression of the ER tubule-forming proteins reticulon 3, reticulon 4, and DP1 inhibits NE formation and nuclear expansion, whereas their knockdown accelerates nuclear assembly. This suggests that the transition from membrane tubules to sheets is rate-limiting for nuclear assembly. Our results provide evidence that ER-shaping proteins are directly involved in the reconstruction of the nuclear compartment and that morphological restructuring of the ER is the principal mechanism of NE formation in vivo.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {5}, pages = {911--924}, publisher = {Rockefeller University Press}, title = {{Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope formation}}, doi = {10.1083/jcb.200805140}, volume = {182}, year = {2008}, } @article{11110, abstract = {Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, thereby connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures, the only function of which was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we discuss the most recent developments in the nuclear-pore-complex field, focusing on the assembly, disassembly, maintenance and function of this macromolecular structure.}, author = {D’Angelo, Maximiliano A. and HETZER, Martin W}, issn = {0962-8924}, journal = {Trends in Cell Biology}, keywords = {Cell Biology}, number = {10}, pages = {456--466}, publisher = {Elsevier}, title = {{Structure, dynamics and function of nuclear pore complexes}}, doi = {10.1016/j.tcb.2008.07.009}, volume = {18}, year = {2008}, } @article{11109, abstract = {The nuclear envelope (NE) provides a selective barrier between the nuclear interior and the cytoplasm and constitutes a central component of intracellular architecture. During mitosis in metazoa, the NE breaks down leading to the complete mixing of the nuclear content with the cytosol. Interestingly, many NE components actively participate in mitotic progression. After chromosome segregation, the NE is reassembled around decondensing chromatin and the nuclear compartment is reestablished in the daughter cells. Here, we summarize recent progress in deciphering the molecular mechanisms underlying NE dynamics during cell division.}, author = {Kutay, Ulrike and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {6}, pages = {669--677}, publisher = {Elsevier}, title = {{Reorganization of the nuclear envelope during open mitosis}}, doi = {10.1016/j.ceb.2008.09.010}, volume = {20}, year = {2008}, } @article{11112, abstract = {The nuclear envelope is a double-layered membrane that encloses the nuclear genome and transcriptional machinery. In dividing cells of metazoa, the nucleus completely disassembles during mitosis, creating the need to re-establish the nuclear compartment at the end of each cell division. Given the crucial role of the nuclear envelope in gene regulation and cellular organization, it is not surprising that its biogenesis and organization have become active research areas. We will review recent insights into nuclear membrane dynamics during the cell cycle.}, author = {Anderson, Daniel J and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {4}, pages = {386--392}, publisher = {Elsevier}, title = {{The life cycle of the metazoan nuclear envelope}}, doi = {10.1016/j.ceb.2008.03.016}, volume = {20}, year = {2008}, } @article{11113, abstract = {The nuclear envelope (NE), a double membrane enclosing the nucleus of eukaryotic cells, controls the flow of information between the nucleoplasm and the cytoplasm and provides a scaffold for the organization of chromatin and the cytoskeleton. In dividing metazoan cells, the NE breaks down at the onset of mitosis and then reforms around segregated chromosomes to generate the daughter nuclei. Recent data from intact cells and cell-free nuclear assembly systems suggest that the endoplasmic reticulum (ER) is the source of membrane for NE assembly. At the end of mitosis, ER membrane tubules are targeted to chromatin via tubule ends and reorganized into flat nuclear membrane sheets by specific DNA-binding membrane proteins. In contrast to previous models, which proposed vesicle fusion to be the principal mechanism of NE formation, these new studies suggest that the nuclear membrane forms by the chromatin-mediated reshaping of the ER.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1477-9137}, journal = {Journal of Cell Science}, keywords = {Cell Biology}, number = {2}, pages = {137--142}, publisher = {The Company of Biologists}, title = {{Shaping the endoplasmic reticulum into the nuclear envelope}}, doi = {10.1242/jcs.005777}, volume = {121}, year = {2008}, } @article{11114, abstract = {We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform a pull-down experiment.}, author = {Schulte, Roberta and Talamas, Jessica and Doucet, Christine and HETZER, Martin W}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {Multidisciplinary}, number = {4}, publisher = {Public Library of Science}, title = {{Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions}}, doi = {10.1371/journal.pone.0002061}, volume = {3}, year = {2008}, } @article{11878, abstract = {Given only the URL of a web page, can we identify its language? This is the question that we examine in this paper. Such a language classifier is, for example, useful for crawlers of web search engines, which frequently try to satisfy certain language quotas. To determine the language of uncrawled web pages, they have to download the page, which might be wasteful, if the page is not in the desired language. With URL-based language classifiers these redundant downloads can be avoided. We apply a variety of machine learning algorithms to the language identification task and evaluate their performance in extensive experiments for five languages: English, French, German, Spanish and Italian. Our best methods achieve an F-measure, averaged over all languages, of around .90 for both a random sample of 1,260 web page from a large web crawl and for 25k pages from the ODP directory. For 5k pages of web search engine results we even achieve an F-measure of .96. The achieved recall for these collections is .93, .88 and .95 respectively. Two independent human evaluators performed considerably worse on the task, with an F-measure of .75 and a typical recall of a mere .67. Using only country-code top-level domains, such as .de or .fr yields a good precision, but a typical recall of below .60 and an F-measure of around .68.}, author = {Baykan, Eda and Henzinger, Monika H and Weber, Ingmar}, issn = {2150-8097}, journal = {Proceedings of the VLDB Endowment}, number = {1}, pages = {176--187}, publisher = {Association for Computing Machinery}, title = {{Web page language identification based on URLs}}, doi = {10.14778/1453856.1453880}, volume = {1}, year = {2008}, } @article{12656, abstract = {We use meteorological data from two automatic weather stations (AWS) on Juncal Norte Glacier, central Chile, to investigate the glacier–climate interaction and to test ablation models of different complexity. The semi-arid Central Andes are characterized by dry summers, with precipitation close to zero, low relative humidity and intense solar radiation. We show that katabatic forcing is dominant both on the glacier tongue and in the fore field, and that low humidity and absence of clouds cause strong radiative cooling of the glacier surface. Surface albedo is basically constant for snow and ice, because of the scarcity of solid precipitation. The energy balance of the glacier is simulated for a 2-month period in austral summer using two models of different complexity, which differ in the inclusion of the heat conduction flux into the snowpack and in the parameterization of the incoming longwave radiation. Net shortwave radiation is the dominant component of the energy balance. The sensible heat flux is always positive, while both the net longwave radiation and latent heat flux are negative. Neglecting the subsurface heat flux and corresponding variations in surface temperature leads to an overestimation of ablation of 2% over a total of 3695 mm water equivalent (w.e.) at the end of the season. Correct modelling of incoming longwave radiation is crucial, and we suggest that parameterizations based on vapour pressure and air temperature should be used rather than on computed cloud amount. We also used an enhanced temperature-index model incorporating the shortwave radiation flux, which has two empirical parameters. We apply it both with values of parameters obtained for Alpine glaciers and recalibrated on Juncal Norte. The model recalibrated against the correct energy balance simulations performs very well. The model parameters respond to the meteorological conditions typical of this climatic setting.}, author = {Pellicciotti, Francesca and Helbing, Jakob and Rivera, Andrés and Favier, Vincent and Corripio, Javier and Araos, José and Sicart, Jean-Emmanuel and Carenzo, Marco}, issn = {1099-1085}, journal = {Hydrological Processes}, keywords = {Water Science and Technology}, number = {19}, pages = {3980--3997}, publisher = {Wiley}, title = {{A study of the energy balance and melt regime on Juncal Norte Glacier, semi-arid Andes of central Chile, using melt models of different complexity}}, doi = {10.1002/hyp.7085}, volume = {22}, year = {2008}, } @article{1296, abstract = {The crystalline-like structure of the optic lobes of the fruit fly Drosophila melanogaster has made them a model system for the study of neuronal cell-fate determination, axonal path finding, and target selection. For functional studies, however, the small size of the constituting visual interneurons has so far presented a formidable barrier. We have overcome this problem by establishing in vivo whole-cell recordings [1] from genetically targeted visual interneurons of Drosophila. Here, we describe the response properties of six motion-sensitive large-field neurons in the lobula plate that form a network consisting of individually identifiable, directionally selective cells most sensitive to vertical image motion (VS cells [2, 3]). Individual VS cell responses to visual motion stimuli exhibit all the characteristics that are indicative of presynaptic input from elementary motion detectors of the correlation type [4, 5]. Different VS cells possess distinct receptive fields that are arranged sequentially along the eye's azimuth, corresponding to their characteristic cellular morphology and position within the retinotopically organized lobula plate. In addition, lateral connections between individual VS cells cause strongly overlapping receptive fields that are wider than expected from their dendritic input. Our results suggest that motion vision in different dipteran fly species is accomplished in similar circuitries and according to common algorithmic rules. The underlying neural mechanisms of population coding within the VS cell network and of elementary motion detection, respectively, can now be analyzed by the combination of electrophysiology and genetic intervention in Drosophila.}, author = {Maximilian Jösch and Plett, Johannes and Borst, Alexander and Reiff, Dierk F}, journal = {Current Biology}, number = {5}, pages = {368 -- 374}, publisher = {Cell Press}, title = {{Response properties of motion sensitive visual interneurons in the Lobula plate of Drosophila melanogaster}}, doi = {10.1016/j.cub.2008.02.022}, volume = {18}, year = {2008}, } @article{1460, abstract = {We calculate the E-polynomials of certain twisted GL(n,ℂ)-character varieties Mn of Riemann surfaces by counting points over finite fields using the character table of the finite group of Lie-type GL(n, q) and a theorem proved in the appendix by N. Katz. We deduce from this calculation several geometric results, for example, the value of the topological Euler characteristic of the associated PGL(n,ℂ)-character variety. The calculation also leads to several conjectures about the cohomology of Mn: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable representations of a certain quiver. We prove these conjectures for n=2.}, author = {Tamas Hausel and Rodríguez Villegas, Fernando}, journal = {Inventiones Mathematicae}, number = {3}, pages = {555 -- 624}, publisher = {Springer}, title = {{Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz}}, doi = {10.1007/s00222-008-0142-x}, volume = {174}, year = {2008}, } @article{1719, abstract = {We study the mechanics of tissue growth via cell division and cell death (apoptosis). The rearrangements of cells can on large scales and times be captured by a continuum theory which describes the tissue as an effective viscous material with active stresses generated by cell division. We study the effects of anisotropies of cell division on cell rearrangements and show that average cellular trajectories exhibit anisotropic scaling behaviors. If cell division and apoptosis balance, there is no net growth, but for anisotropic cell division the tissue undergoes spontaneous shear deformations. Our description is relevant for the study of developing tissues such as the imaginal disks of the fruit fly Drosophila melanogaster, which grow anisotropically.}, author = {Bittig, Thomas and Wartlick, Ortrud and Anna Kicheva and González-Gaitárr, Marcos and Julicher, Frank}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Dynamics of anisotropic tissue growth}}, doi = {10.1088/1367-2630/10/6/063001}, volume = {10}, year = {2008}, } @article{1717, abstract = {Two key processes are in the basis of morphogenesis: the spatial allocation of cell types in fields of naïve cells and the regulation of growth. Both are controlled by morphogens, which activate target genes in the growing tissue in a concentration-dependent manner. Thus the morphogen model is an intrinsically quantitative concept. However, quantitative studies were performed only in recent years on two morphogens: Bicoid and Decapentaplegic. This review covers quantitative aspects of the formation and precision of the Decapentaplegic morphogen gradient. The morphogen gradient concept is transitioning from a soft definition to a precise idea of what the gradient could really do.}, author = {Anna Kicheva and González-Gaitán, Marcos A}, journal = {Current Opinion in Cell Biology}, number = {2}, pages = {137 -- 143}, publisher = {Elsevier}, title = {{The Decapentaplegic morphogen gradient a precise definition}}, doi = {10.1016/j.ceb.2008.01.008}, volume = {20}, year = {2008}, } @article{1751, abstract = {When strained Stranski-Krastanow islands are used as "self-assembled quantum dots," a key goal is to control the island position. Here we show that nanoscale grooves can control the nucleation of epitaxial Ge islands on Si(001), and can drive lateral motion of existing islands onto the grooves, even when the grooves are very narrow and shallow compared to the islands. A position centered on the groove minimizes energy. We use as prototype grooves the trenches which form naturally around islands. During coarsening, the shrinking islands move laterally to sit directly astride that trench. In subsequent growth, we demonstrate that islands nucleate on the "empty trenches" which remain on the surface after complete dissolution of the original islands.}, author = {Georgios Katsaros and Tersoff, Jerry and Stoffel, Mathieu and Rastelli, Armando and Acosta-Diaz, P and Kar, Gouranga S and Costantini, Giovanni and Schmidt, Oliver G and Kern, Klaus}, journal = {Physical Review Letters}, number = {9}, publisher = {American Physical Society}, title = {{Positioning of strained islands by interaction with surface nanogrooves}}, doi = {10.1103/PhysRevLett.101.096103}, volume = {101}, year = {2008}, } @article{1749, abstract = {Scanning probe microscopy; Semiconductor quantum dots; Composition gradients; Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional (3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology; nanotechnology; optical tomography; scanning probe microscopy; three dimensional imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe; Nanotechnology; Quantum Dots; Tomography,}, author = {Rastelli, Armando and Stoffel, Mathieu and Malachias, Ângelo S and Merdzhanova, Tsvetelina and Georgios Katsaros and Kern, Klaus and Metzger, Till H and Schmidt, Oliver G}, journal = {Nano Letters}, number = {5}, pages = {1404 -- 1409}, publisher = {American Chemical Society}, title = {{Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography}}, doi = {10.1021/nl080290y}, volume = {8}, year = {2008}, } @article{1763, abstract = {The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.}, author = {Johannes Fink and Göppl, M and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Nature}, number = {7202}, pages = {315 -- 318}, publisher = {Nature Publishing Group}, title = {{Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system}}, doi = {10.1038/nature07112}, volume = {454}, year = {2008}, } @article{1765, abstract = {High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.}, author = {Göppl, M and Fragner, A and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Johannes Fink and Leek, Peter J and Puebla, G and Steffen, L. Kraig and Wallraff, Andreas}, journal = {Journal of Applied Physics}, number = {11}, publisher = {American Institute of Physics}, title = {{Coplanar waveguide resonators for circuit quantum electrodynamics}}, doi = {10.1063/1.3010859}, volume = {104}, year = {2008}, } @article{1764, abstract = {Quantum theory predicts that empty space is not truly empty. Even in the absence of any particles or radiation, in pure vacuum, virtual particles are constantly created and annihilated. In an electromagnetic field, the presence of virtual photons manifests itself as a small renormalization of the energy of a quantum system, known as the Lamb shift. We present an experimental observation of the Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition frequency. The qubit is also observed to couple more strongly to the vacuum field than to a single photon inside the cavity, an effect that is explained by taking into account the limited anharmonicity of the higher excited qubit states.}, author = {Fragner, A and Göppl, M and Johannes Fink and Baur, Matthias P and Bianchetti, R and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Science}, number = {5906}, pages = {1357 -- 1360}, publisher = {American Association for the Advancement of Science}, title = {{Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift}}, doi = {10.1126/science.1164482}, volume = {322}, year = {2008}, } @article{1826, abstract = {Proliferating cell populations at steady-state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by asymptotic analysis of the population balance equation. We show that the steady-state distribution tail is determined by a combination of protein production and cell division and is insensitive to other model details. Under general conditions this tail is exponential with a dependence on parameters consistent with experiment. We discuss the conditions for this effect to be dominant over other sources of variation and the relation to experiments.}, author = {Tamar Friedlander and Brenner, Naama}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Cellular properties and population asymptotics in the population balance equation}}, doi = {10.1103/PhysRevLett.101.018104}, volume = {101}, year = {2008}, } @article{1967, abstract = {Complex I of respiratory chains transfers electrons from NADH to ubiquinone, coupled to the translocation of protons across the membrane. Two alternative coupling mechanisms are being discussed, redox-driven or conformation-driven. Using "zero-length" cross-linking reagent and isolated hydrophilic domains of complex I from Escherichia coli and Thermus thermophilus, we show that the pattern of cross-links between subunits changes significantly in the presence of NADH. Similar observations were made previously with intact purified E. coli and bovine complex I. This indicates that, upon reduction with NADH, similar conformational changes are likely to occur in the intact enzyme and in the isolated hydrophilic domain (which can be used for crystallographic studies). Within intact E. coli complex I, the cross-link between the hydrophobic subunits NuoA and NuoJ was abolished in the presence of NADH, indicating that conformational changes extend into the membrane domain, possibly as part of a coupling mechanism. Unexpectedly, in the absence of any chemical cross-linker, incubation of complex I with NADH resulted in covalent cross-links between subunits Nqo4 (NuoCD) and Nqo6 (NuoB), as well as between Nqo6 and Nqo9. Their formation depends on the presence of oxygen and so is likely a result of oxidative damage via reactive oxygen species (ROS) induced cross-linking. In addition, ROS- and metal ion-dependent proteolysis of these subunits (as well as Nqo3) is observed. Fe-S cluster N2 is coordinated between subunits Nqo4 and Nqo6 and could be involved in these processes. Our observations suggest that oxidative damage to complex I in vivo may include not only side-chain modifications but also protein cross-linking and degradation.}, author = {Berrisford, John M and Thompson, Christopher J and Leonid Sazanov}, journal = {Biochemistry}, number = {39}, pages = {10262 -- 10270}, publisher = {ACS}, title = {{Chemical and NADH-induced, ROS-dependent, cross-linking between sublimits of complex I from Escherichia coli and Thermus thermophilus}}, doi = {10.1021/bi801160u}, volume = {47}, year = {2008}, } @article{1968, abstract = { Complex I (NADH:ubiquinone oxidoreductase) is the largest protein complex of bacterial and mitochondrial respiratory chains. The first three-dimensional structure of bacterial complex I in vitrified ice was determined by electron cryo-microscopy and single particle analysis. The structure of the Escherichia coli enzyme incubated with either NAD+ (as a reference) or NADH was calculated to 35 and 39 Å resolution, respectively. The X-ray structure of the peripheral arm of Thermus thermophilus complex I was docked into the reference EM structure. The model obtained indicates that Fe-S cluster N2 is close to the membrane domain interface, allowing for effective electron transfer to membrane-embedded quinone. At the current resolution, the structures in the presence of NAD+ or NADH are similar. Additionally, side-view class averages were calculated for the negatively stained bovine enzyme. The structures of bovine complex I in the presence of either NAD+ or NADH also appeared to be similar. These observations indicate that conformational changes upon reduction with NADH, suggested to occur by a range of studies, are smaller than had been thought previously. The model of the entire bacterial complex I could be built from the crystal structures of subcomplexes using the EM envelope described here.}, author = {Morgan, David J and Leonid Sazanov}, journal = {Biochimica et Biophysica Acta - Bioenergetics}, number = {7-8}, pages = {711 -- 718}, publisher = {Elsevier}, title = {{Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides}}, doi = {10.1016/j.bbabio.2008.03.023}, volume = {1777}, year = {2008}, } @article{1982, abstract = {In the bacterium Escherichia coli, the Min proteins oscillate between the cell poles to select the cell center as division site. This dynamic pattern has been proposed to arise by self-organization of these proteins, and several models have suggested a reaction-diffusion type mechanism. Here, we found that the Min proteins spontaneously formed planar surface waves on a flat membrane in vitro. The formation and maintenance of these patterns, which extended for hundreds of micrometers, required adenosine 5′-triphosphate (ATP), and they persisted for hours. We present a reaction-diffusion model of the MinD and MinE dynamics that accounts for our experimental observations and also captures the in vivo oscillations.}, author = {Martin Loose and Fischer-Friedrich, Elisabeth and Ries, Jonas and Kruse, Karsten and Schwille, Petra }, journal = {Science}, number = {5877}, pages = {789 -- 792}, publisher = {American Association for the Advancement of Science}, title = {{Spatial regulators for bacterial cell division self-organize into surface waves in vitro}}, doi = {10.1126/science.1154413}, volume = {320}, year = {2008}, } @article{2065, abstract = {Population genetics models show that, under certain conditions, the X chromosome is expected to be under more efficient selection than the autosomes. This could lead to 'faster-X evolution', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in Drosophila. We used a multispecies approach to test this: Muller's element D, an autosomal arm, is fused to the ancestral X chromosome in Drosophila pseudoobscura and its sister species, Drosophila affinis. We tested whether the same set of genes had higher rates of non-synonymous evolution when they were X-linked (in the D. pseudoobscura/D. affinis comparison) than when they were autosomal (in Drosophila melanogaster/Drosophila yakuba). Although not significant, our results suggest this may be the case, but only for genes under particularly strong positive selection/weak purifying selection. They also suggest that genes that have become X-linked have higher levels of codon bias and slower synonymous site evolution, consistent with more effective selection on codon usage at X-linked sites.}, author = {Beatriz Vicoso and Haddrill, Penelope R and Charlesworth, Brian}, journal = {Genetical Research}, number = {5}, pages = {421 -- 431}, publisher = {Cambridge University Press}, title = {{A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila}}, doi = {10.1017/S0016672308009804}, volume = {90}, year = {2008}, } @inproceedings{2078, abstract = {This paper presents a novel method for real-time animation of highly-detailed facial expressions based on a multi-scale decomposition of facial geometry into large-scale motion and fine-scale details, such as expression wrinkles. Our hybrid animation is tailored to the specific characteristics of large- and fine-scale facial deformations: Large-scale deformations are computed with a fast linear shell model, which is intuitively and accurately controlled through a sparse set of motion-capture markers or user-defined handle points. Fine-scale facial details are incorporated using a novel pose-space deformation technique, which learns the correspondence of sparse measurements of skin strain to wrinkle formation from a small set of example poses. Our hybrid method features real-time animation of highly-detailed faces with realistic wrinkle formation, and allows both large-scale deformations and fine-scale wrinkles to be edited intuitively. Furthermore, our pose-space representation enables the transfer of facial details to novel expressions or other facial models.}, author = {Bickel, Bernd and Lang, Manuel and Botsch, Mario and Otaduy, Miguel and Gross, Markus}, pages = {57 -- 66}, publisher = {ACM}, title = {{Pose-space animation and transfer of facial details}}, doi = {10.2312/SCA/SCA08/057-066}, year = {2008}, } @article{2120, abstract = {We consider the linear stochastic Cauchy problem dX (t) =AX (t) dt +B dWH (t), t≥ 0, where A generates a C0-semigroup on a Banach space E, WH is a cylindrical Brownian motion over a Hilbert space H, and B: H → E is a bounded operator. Assuming the existence of a unique minimal invariant measure μ∞, let Lp denote the realization of the Ornstein-Uhlenbeck operator associated with this problem in Lp (E, μ∞). Under suitable assumptions concerning the invariance of the range of B under the semigroup generated by A, we prove the following domain inclusions, valid for 1 < p ≤ 2: Image omitted. Here WHk, p (E, μinfin; denotes the kth order Sobolev space of functions with Fréchet derivatives up to order k in the direction of H. No symmetry assumptions are made on L p.}, author = {Jan Maas and van Neerven, Jan M}, journal = {Infinite Dimensional Analysis, Quantum Probability and Related Topics}, number = {4}, pages = {603 -- 626}, publisher = {World Scientific Publishing}, title = {{On the domain of non-symmetric Ornstein-Uhlenbeck operators in banach spaces}}, doi = {10.1142/S0219025708003245}, volume = {11}, year = {2008}, } @article{2121, abstract = {Let H be a separable real Hubert space and let double struck F sign = (ℱt)t∈[0,T] be the augmented filtration generated by an H-cylindrical Brownian motion (WH(t))t∈[0,T] on a probability space (Ω, ℱ ℙ). We prove that if E is a UMD Banach space, 1 ≤ p < ∞, and F ∈ double struck D sign1,p(Ω E) is ℱT-measurable, then F = double struck E sign(F) + ∫0T Pdouble struck F sign(DF) dW H, where D is the Malliavin derivative of F and P double struck F sign is the projection onto the F-adapted elements in a suitable Banach space of Lp-stochastically integrable ℒ(H, E)-valued processes.}, author = {van Neerven, Jan M and Jan Maas}, journal = {Electronic Communications in Probability}, pages = {151 -- 164}, publisher = {Institute of Mathematical Statistics}, title = {{A Clark-Ocone formula in UMD Banach spaces}}, volume = {13}, year = {2008}, } @article{2148, abstract = {Despite the growing geological evidence that fluid boiling and vapour-liquid separation affect the distribution of metals in magmatic-hydrothermal systems significantly, there are few experimental data on the chemical status and partitioning of metals in the vapour and liquid phases. Here we report on an in situ measurement, using X-ray absorption fine structure (XAFS) spectroscopy, of antimony speciation and partitioning in the system Sb2O3-H2O-NaCl-HCl at 400°C and pressures 270–300 bar corresponding to the vapour-liquid equilibrium. Experiments were performed using a spectroscopic cell which allows simultaneous determination of the total concentration and atomic environment of the absorbing element (Sb) in each phase. Results show that quantitative vapour-brine separation of a supercritical aqueous salt fluid can be achieved by a controlled decompression and monitoring the X-ray absorbance of the fluid phase. Antimony concentrations in equilibrium with Sb2O3 (cubic, senarmontite) in the coexisting vapour and liquid phases and corresponding SbIII vapour-liquid partitioning coefficients are in agreement with recent data obtained using batch-reactor solubility techniques. The XAFS spectra analysis shows that hydroxy-chloride complexes, probably Sb(OH)2Cl0, are dominant both in the vapour and liquid phase in a salt-water system at acidic conditions. This first in situ XAFS study of element fractionation between coexisting volatile and dense phases opens new possibilities for systematic investigations of vapour-brine and fluid-melt immiscibility phenomena, avoiding many experimental artifacts common in less direct techniques.}, author = {Pokrovski, Gleb S and Roux, Jacques L and Hazemann, Jean L and Borisova, Anastassia Y and Gonchar, Anastasia A and Mikhail Lemeshko}, journal = {Mineralogical Magazine}, number = {2}, pages = {667 -- 681}, publisher = {Mineralogical Society}, title = {{In situ X-ray absorption spectroscopy measurement of vapour-brine fractionation of antimony at hydrothermal conditions}}, doi = {10.1180/minmag.2008.072.2.667 }, volume = {72}, year = {2008}, } @article{2146, abstract = {We present an analytic model of thermal state-to-state rotationally inelastic collisions of polar molecules in electric fields. The model is based on the Fraunhofer scattering of matter waves and requires Legendre moments characterizing the “shape” of the target in the body-fixed frame as its input. The electric field orients the target in the space-fixed frame and thereby effects a striking alteration of the dynamical observables: both the phase and amplitude of the oscillations in the partial differential cross sections undergo characteristic field-dependent changes that transgress into the partial integral cross sections. As the cross sections can be evaluated for a field applied parallel or perpendicular to the relative velocity, the model also offers predictions about steric asymmetry. We exemplify the field-dependent quantum collision dynamics with the behavior of the Ne–OCS(Σ1) and Ar–NO(Π2) systems. A comparison with the close-coupling calculations available for the latter system [Chem. Phys. Lett.313, 491 (1999)] demonstrates the model’s ability to qualitatively explain the field dependence of all the scattering features observed.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Journal of Chemical Physics}, number = {2}, publisher = {American Institute of Physics}, title = {{An analytic model of rotationally inelastic collisions of polar molecules in electric fields}}, doi = {10.1063/1.2948392}, volume = {129}, year = {2008}, } @misc{2147, abstract = {We present the physics of the quantum Zeno effect, whose gist is often expressed by invoking the adage "a watched pot never boils". We review aspects of the theoretical and experimental work done on the effect since its inception in 1977, and mention some applications. We dedicate the article - with our very best wishes - to Rudolf Zahradnik at the occasion of his great jubilee. Perhaps Rudolf's lasting youthfulness and freshness are due to that he himself had been frequently observed throughout his life: until the political turn-around in 1989 by those who wished, by their surveillance, to prevent Rudolf from spoiling the youth by his personal culture and his passion for science and things beautiful and useful in general. This attempt had failed. Out of gratitude, the youth has infected Rudolf with its youthfulness. Chronically. Since 1989, Rudolf has been closely watched by the public at large. For the same traits of his as before, but with the opposite goal and for the benefit of all generations. We relish keeping him in sight...}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, booktitle = {Chemicke Listy}, number = {10}, pages = {880 -- 883}, publisher = {Czech Society of Chemical Engineering}, title = {{Kvantový Zenonův jev aneb co nesejde z očí, nezestárne}}, volume = {102}, year = {2008}, } @article{224, abstract = {Let n ≥ 4 and let Q ∈ [X1, ..., Xn] be a non-singular quadratic form. When Q is indefinite we provide new upper bounds for the least non-trivial integral solution to the equation Q = 0, and when Q is positive definite we provide improved upper bounds for the greatest positive integer k for which the equation Q = k is insoluble in integers, despite being soluble modulo every prime power.}, author = {Timothy Browning and Dietmann, Rainer}, journal = {Proceedings of the London Mathematical Society}, number = {2}, pages = {389 -- 416}, publisher = {John Wiley and Sons Ltd}, title = {{On the representation of integers by quadratic forms}}, doi = {10.1112/plms/pdm032}, volume = {96}, year = {2008}, } @article{225, abstract = {We revisit recent work of Heath-Brown on the average order of the quantity r(L1(x))⋯r(L4(x)), for suitable binary linear forms L1,...,L4, as x=(x1,x2) ranges over quite general regions in ℤ2. In addition to improving the error term in Heath-Browns estimate, we generalise his result to cover a wider class of linear forms.}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Compositio Mathematica}, number = {6}, pages = {1375 -- 1402}, publisher = {Cambridge University Press}, title = {{Binary linear forms as sums of two squares}}, doi = {10.1112/S0010437X08003692}, volume = {144}, year = {2008}, } @inproceedings{2332, abstract = {We present a rigorous proof of the appearance of quantized vortices in dilute trapped Bose gases with repulsive two-body interactions subject to rotation, which was obtained recently in joint work with Elliott Lieb.14 Starting from the many-body Schrödinger equation, we show that the ground state of such gases is, in a suitable limit, well described by the nonlinear Gross-Pitaevskii equation. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state.}, author = {Robert Seiringer}, pages = {241 -- 254}, publisher = {World Scientific Publishing}, title = {{Vortices and Spontaneous Symmetry Breaking in Rotating Bose Gases}}, doi = {10.1142/9789812832382_0017}, year = {2008}, } @inproceedings{2331, abstract = {We present a review of recent work on the mathematical aspects of the BCS gap equation, covering our results of Ref. 9 as well our recent joint work with Hamza and Solovej and with Frank and Naboko, respectively. In addition, we mention some related new results.}, author = {Hainzl, Christian and Robert Seiringer}, pages = {117 -- 136}, publisher = {World Scientific Publishing}, title = {{ Spectral properties of the BCS gap equation of superfluidity}}, doi = {10.1142/9789812832382_0009}, year = {2008}, } @article{2376, abstract = {We derive upper and lower bounds on the critical temperature Tc and the energy gap Ξ (at zero temperature) for the BCS gap equation, describing spin- 1 2 fermions interacting via a local two-body interaction potential λV(x). At weak coupling λ 1 and under appropriate assumptions on V(x), our bounds show that Tc ∼A exp(-B/λ) and Ξ∼C exp(-B/λ) for some explicit coefficients A, B, and C depending on the interaction V(x) and the chemical potential μ. The ratio A/C turns out to be a universal constant, independent of both V(x) and μ. Our analysis is valid for any μ; for small μ, or low density, our formulas reduce to well-known expressions involving the scattering length of V(x).}, author = {Hainzl, Christian and Robert Seiringer}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {18}, publisher = {American Physical Society}, title = {{Critical temperature and energy gap for the BCS equation}}, doi = {10.1103/PhysRevB.77.184517}, volume = {77}, year = {2008}, } @article{2374, abstract = {A lower bound is derived on the free energy (per unit volume) of a homogeneous Bose gas at density Q and temperature T. In the dilute regime, i.e., when a3 1, where a denotes the scattering length of the pair-interaction potential, our bound differs to leading order from the expression for non-interacting particles by the term 4πa(2 2}-[ - c]2+). Here, c(T) denotes the critical density for Bose-Einstein condensation (for the non-interacting gas), and [ · ]+ = max{ ·, 0} denotes the positive part. Our bound is uniform in the temperature up to temperatures of the order of the critical temperature, i.e., T ~ 2/3 or smaller. One of the key ingredients in the proof is the use of coherent states to extend the method introduced in [17] for estimating correlations to temperatures below the critical one.}, author = {Robert Seiringer}, journal = {Communications in Mathematical Physics}, number = {3}, pages = {595 -- 636}, publisher = {Springer}, title = {{Free energy of a dilute Bose gas: Lower bound}}, doi = {10.1007/s00220-008-0428-2}, volume = {279}, year = {2008}, } @article{2382, abstract = {We show that the Lieb-Liniger model for one-dimensional bosons with repulsive δ-function interaction can be rigorously derived via a scaling limit from a dilute three-dimensional Bose gas with arbitrary repulsive interaction potential of finite scattering length. For this purpose, we prove bounds on both the eigenvalues and corresponding eigenfunctions of three-dimensional bosons in strongly elongated traps and relate them to the corresponding quantities in the Lieb-Liniger model. In particular, if both the scattering length a and the radius r of the cylindrical trap go to zero, the Lieb-Liniger model with coupling constant g ∼ a/r 2 is derived. Our bounds are uniform in g in the whole parameter range 0 ≤ g ≤ ∞, and apply to the Hamiltonian for three-dimensional bosons in a spectral window of size ∼ r -2 above the ground state energy.}, author = {Robert Seiringer and Yin, Jun}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {459 -- 479}, publisher = {Springer}, title = {{The Lieb-Liniger model as a limit of dilute bosons in three dimensions}}, doi = {10.1007/s00220-008-0521-6}, volume = {284}, year = {2008}, } @article{2380, abstract = {The Bardeen-Cooper-Schrieffer (BCS) functional has recently received renewed attention as a description of fermionic gases interacting with local pairwise interactions. We present here a rigorous analysis of the BCS functional for general pair interaction potentials. For both zero and positive temperature, we show that the existence of a non-trivial solution of the nonlinear BCS gap equation is equivalent to the existence of a negative eigenvalue of a certain linear operator. From this we conclude the existence of a critical temperature below which the BCS pairing wave function does not vanish identically. For attractive potentials, we prove that the critical temperature is non-zero and exponentially small in the strength of the potential.}, author = {Hainzl, Christian and Hamza, Eman and Robert Seiringer and Solovej, Jan P}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {349 -- 367}, publisher = {Springer}, title = {{The BCS functional for general pair interactions}}, doi = {10.1007/s00220-008-0489-2}, volume = {281}, year = {2008}, } @article{2383, abstract = {We study the relativistic electron-positron field at positive temperature in the Hartree-Fock approximation. We consider both the case with and without exchange terms, and investigate the existence and properties of minimizers. Our approach is non-perturbative in the sense that the relevant electron subspace is determined in a self-consistent way. The present work is an extension of previous work by Hainzl, Lewin, Séré and Solovej where the case of zero temperature was considered.}, author = {Hainzl, Christian and Lewin, Mathieu and Robert Seiringer}, journal = {Reviews in Mathematical Physics}, number = {10}, pages = {1283 -- 1307}, publisher = {World Scientific Publishing}, title = {{A nonlinear model for relativistic electrons at positive temperature}}, doi = {10.1142/S0129055X08003547}, volume = {20}, year = {2008}, } @article{2378, abstract = {We derive a lower bound on the ground state energy of the Hubbard model for given value of the total spin. In combination with the upper bound derived previously by Giuliani (J. Math. Phys. 48:023302, [2007]), our result proves that in the low density limit the leading order correction compared to the ground state energy of a non-interacting lattice Fermi gas is given by 8πaσ uσ d , where σ u(d) denotes the density of the spin-up (down) particles, and a is the scattering length of the contact interaction potential. This result extends previous work on the corresponding continuum model to the lattice case.}, author = {Robert Seiringer and Yin, Jun}, journal = {Journal of Statistical Physics}, number = {6}, pages = {1139 -- 1154}, publisher = {Springer}, title = {{Ground state energy of the low density hubbard model}}, doi = {10.1007/s10955-008-9527-x}, volume = {131}, year = {2008}, } @article{2381, abstract = {We determine the sharp constant in the Hardy inequality for fractional Sobolev spaces. To do so, we develop a non-linear and non-local version of the ground state representation, which even yields a remainder term. From the sharp Hardy inequality we deduce the sharp constant in a Sobolev embedding which is optimal in the Lorentz scale. In the appendix, we characterize the cases of equality in the rearrangement inequality in fractional Sobolev spaces.}, author = {Frank, Rupert L and Robert Seiringer}, journal = {Journal of Functional Analysis}, number = {12}, pages = {3407 -- 3430}, publisher = {Academic Press}, title = {{Non-linear ground state representations and sharp Hardy inequalities}}, doi = {10.1016/j.jfa.2008.05.015}, volume = {255}, year = {2008}, } @article{2377, abstract = {We prove that the critical temperature for the BCS gap equation is given by T c = μ ( 8\π e γ-2+ o(1)) e π/(2μa) in the low density limit μ→ 0, with γ denoting Euler's constant. The formula holds for a suitable class of interaction potentials with negative scattering length a in the absence of bound states.}, author = {Hainzl, Christian and Robert Seiringer}, journal = {Letters in Mathematical Physics}, number = {2-3}, pages = {99 -- 107}, publisher = {Springer}, title = {{The BCS critical temperature for potentials with negative scattering length}}, doi = {10.1007/s11005-008-0242-y}, volume = {84}, year = {2008}, } @article{2379, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer}, journal = {Journal of the American Mathematical Society}, number = {4}, pages = {925 -- 950}, publisher = {American Mathematical Society}, title = {{Hardy-Lieb-Thirring inequalities for fractional Schrödinger operators}}, doi = {10.1090/S0894-0347-07-00582-6}, volume = {21}, year = {2008}, } @inbook{2415, author = {Uli Wagner}, booktitle = {Surveys on Discrete and Computational Geometry: Twenty Years Later}, editor = {Goodman, Jacob E and Pach, János and Pollack, Richard}, pages = {443 -- 514}, publisher = {American Mathematical Society}, title = {{k-Sets and k-facets}}, doi = {10.1090/conm/453}, volume = {453}, year = {2008}, } @inproceedings{2432, abstract = {We study the disk containment problem introduced by Neumann-Lara and Urrutia and its generalization to higher dimensions. We relate the problem to centerpoints and lower centerpoints of point sets. Moreover, we show that for any set of n points in ℝd, there is a subset A ⊆ S of size [d+3/2] such that any ball containing A contains at least roughly 4/5ed 3n points of S. This improves previous bounds for which the constant was exponentially small in d. We also consider a generalization of the planar disk containment problem to families of pseudodisks.}, author = {Smorodinsky, Shakhar and Sulovský, Marek and Uli Wagner}, pages = {363 -- 373}, publisher = {Springer}, title = {{On center regions and balls containing many points}}, doi = {10.1007/978-3-540-69733-6_36}, volume = {5092}, year = {2008}, } @article{2497, abstract = {Cyclic nucleotide phosphodiesterase 10A (PDE10A) is a member of phosphodiesterase families that degrade cAMP and/or cGMP in distinct intracellular sites. PDE10A has a dual activity on hydrolysis of both cAMP and cGMP, and is prominently expressed in the striatum and the testis. Previous studies suggested that PDE10A is involved in regulation of locomotor activity and potentially related to psychosis, but concrete physiological roles of PDE10A remains elusive yet. In this study, we genetically inactivated PDE10A2, a prominent isoform of PDE10A in the brain, in mice, and demonstrate that PDE10A2 deficiency results in increased social interaction without any major influence on different other behaviors, along with increased levels of striatal cAMP. We also demonstrate that PDE10A2 is selectively distributed in medium spiny neurons, but not interneurons, of the striatal complex. Thus, our results establish a physiological role for PDE10A2 in regulating cAMP pathway and social interaction, and suggest that cAMP signaling cascade in striatal medium spiny neurons might be involved in regulating social interaction behavior in mice.}, author = {Sano, Hiromi and Nagai, Yumiko and Miyakawa, Tsuyoshi and Ryuichi Shigemoto and Yokoi, Mineto}, journal = {Journal of Neurochemistry}, number = {2}, pages = {546 -- 556}, publisher = {Wiley-Blackwell}, title = {{Increased social interaction in mice deficient of the striatal medium spiny neuron-specific phosphodiesterase 10A2}}, doi = {10.1111/j.1471-4159.2007.05152.x}, volume = {105}, year = {2008}, } @article{2675, abstract = {Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels that generate Ih currents are widely distributed in the brain and have been shown to contribute to various neuronal functions. In the present study, we investigated the functions of Ih in the motion-sensitive projection neurons [wide field vertical (WFV) cells] of the superior colliculus, a pivotal visual center for detection of and orientating to salient objects. Combination of whole cell recordings and immunohistochemical investigations suggested that HCN1 channels dominantly contribute to the Ih in WFV cells among HCN isoforms expressed in the superficial superior colliculus and mainly located on their expansive dendritic trees. We found that blocking Ih suppressed the initiation of short- and fixed-latency dendritic spike responses and led instead to long- and fluctuating-latency somatic spike responses to optic fiber stimulations. These results suggest that the dendritic Ih facilitates the dendritic initiation and/or propagation of action potentials and ensures that WFV cells generate spike responses to distal synaptic inputs in a sensitive and robustly time-locked manner, probably by acting as continuous depolarizing drive and fixing dendritic membrane potentials close to the spike threshold. These functions are different from known functions of dendritic Ih revealed in hippocampal and neocortical pyramidal cells, where they spatiotemporally limit the propagations of synaptic inputs along the apical dendrites by reducing dendritic membrane resistance. Thus we have revealed new functional aspects of Ih, and these dendritic properties are likely critical for visual motion processing in these neurons.}, author = {Endo, Toshiaki and Tarusawa, Etsuko and Notomi, Takuya and Kaneda, Katsuyuki and Hirabayashi, Masumi and Ryuichi Shigemoto and Isa, Tadashi}, journal = {Journal of Neurophysiology}, number = {5}, pages = {2066 -- 2076}, publisher = {American Physiological Society}, title = {{Dendritic Ih ensures high-fidelity dendritic spike responses of motion-sensitive neurons in rat superior colliculus}}, doi = {10.1152/jn.00556.2007}, volume = {99}, year = {2008}, } @article{2676, abstract = {Left-right (L-R) asymmetry is a fundamental feature of higher-order neural function. However, the molecular basis of brain asymmetry remains unclear. We recently reported L-R asymmetry of hippocampal circuitry caused by differential allocation of N-methyl-O-aspartate receptor (NMDAR) subunit GluRε2 (NR2B) in hippocambal synapses. Using electrophysiology and immunocytochemistry, here we analyzed the hippocampal circuitry of the inversus viscerum (iv) mouse that has a randomized laterality of internal organs. The iv mouse hippocampus lacks L-R asymmetry, it exhibits right isomerism in the synaptic distribution of the ε2 subunit, irrespective of the laterality of visceral organs. This independent right isomerism of the hippocampus is the first evidence that a distinct mechanism downstream of the iv mutation generates brain asymmetry.}, author = {Kawakami, Ryosuke and Dobi, Alice and Ryuichi Shigemoto and Ito, Isao}, journal = {PLoS One}, number = {4}, publisher = {Public Library of Science}, title = {{Right isomerism of the brain in inversus viscerum mutant mice}}, doi = {10.1371/journal.pone.0001945}, volume = {3}, year = {2008}, } @misc{2674, author = {Fukazawa, Yugo and Tarusawa, Etsuko and Matsui, Ko and Ryuichi Shigemoto}, booktitle = {Tanpakushitsu kakusan koso Protein nucleic acid enzyme}, number = {4 Suppl}, pages = {436 -- 441}, publisher = {Kyoritsu Shuppan}, title = {{ Ultrastructural insights of postsynaptic glutamate receptor organization }}, volume = {53}, year = {2008}, } @article{2678, abstract = {Mammalian retinas contain abundant neuronal gap junctions, particularly in the inner plexiform layer (IPL), where the two principal neuronal connexin proteins are Cx36 and Cx45. Currently undetermined are coupling relationships between these connexins and whether both are expressed together or separately in a neuronal subtype-specific manner. Although Cx45-expressing neurons strongly couple with Cx36-expressing neurons, possibly via heterotypic gap junctions, Cx45 and Cx36 failed to form functional heterotypic channels in vitro. We now show that Cx36 and Cx45 coexpressed in HeLa cells were colocalized in immunofluorescent puncta between contacting cells, demonstrating targeting/scaffolding competence for both connexins in vitro. However, Cx36 and Cx45 expressed separately did not form immunofluorescent puncta containing both connexins, supporting lack of heterotypic coupling competence. In IPL, 87% of Cx45-immunofluorescent puncta were colocalized with Cx36, supporting either widespread heterotypic coupling or bihomotypic coupling. Ultrastructurally, Cx45 was detected in 9% of IPL gap junction hemiplaques, 90-100% of which also contained Cx36, demonstrating connexin coexpression and cotargeting in virtually all IPL neurons that express Cx45. Moreover, double replicas revealed both connexins in separate domains mirrored on both sides of matched hemiplaques. With previous evidence that Cx36 interacts with PDZ1 domain of zonula occludens-1 (ZO-1), we show that Cx45 interacts with PDZ2 domain of ZO-1, and that Cx36, Cx45, and ZO-1 coimmunoprecipitate, suggesting that ZO-1 provides for coscaffolding of Cx45 with Cx36. These data document that in Cx45-expressing neurons of IPL, Cx45 is almost always accompanied by Cx36, forming "bihomotypic" gap junctions, with Cx45 structurally coupling to Cx45 and Cx36 coupling to Cx36.}, author = {Li, Xinbo and Kamasawa, Naomi and Ciolofan, Cristina and Olson, Carl O and Lu, Shijun and Davidson, Kimberly G and Yasumura, Thomas and Ryuichi Shigemoto and Rash, John E and Nagy, James I}, journal = {Journal of Neuroscience}, number = {39}, pages = {9769 -- 9789}, publisher = {Society for Neuroscience}, title = {{Connexin45-containing neuronal gap junctions in rodent retina also contain connexin36 in both apposing hemiplaques, forming bihomotypic gap junctions, with scaffolding contributed by zonula occludens-1}}, doi = {10.1523/JNEUROSCI.2137-08.2008}, volume = {28}, year = {2008}, } @article{2677, abstract = {The medial septum (MS) is an indispensable component of the subcortical network which synchronizes the hippocampus at theta frequency during specific stages of information processing. GABAergic neurons exhibiting highly regular firing coupled to the hippocampal theta rhythm are thought to form the core of the MS rhythm-generating network. In recent studies the hyperpolarization-activated, cyclic nucleotide-gated non-selective cation (HCN) channel was shown to participate in theta synchronization of the medial septum. Here, we tested the hypothesis that HCN channel expression correlates with theta modulated firing behaviour of MS neurons by a combined anatomical and electrophysiological approach. HCN-expressing neurons represented a subpopulation of GABAergic cells in the MS partly overlapping with parvalbumin (PV)-containing neurons. Rhythmic firing in the theta frequency range was characteristic of all HCN-expressing neurons. In contrast, only a minority of HCN-negative cells displayed theta related activity. All HCN cells had tight phase coupling to hippocampal theta waves. As a group, PV-expressing HCN neurons had a marked bimodal phase distribution, whereas PV-immunonegative HCN neurons did not show group-level phase preference despite significant individual phase coupling. Microiontophoretic blockade of HCN channels resulted in the reduction of discharge frequency, but theta rhythmic firing was perturbed only in a few cases. Our data imply that HCN-expressing GABAergic neurons provide rhythmic drive in all phases of the hippocampal theta activity. In most MS theta cells rhythm genesis is apparently determined by interactions at the level of the network rather than by the pacemaking property of HCN channels alone.}, author = {Varga, Viktor and Hangya, Balázs and Kránitz, Kinga and Ludányi, Anikó and Zemankovics, Rita and Katona, István and Ryuichi Shigemoto and Freund, Tamás F and Borhegyi, Zsolt}, journal = {Journal of Physiology}, number = {16}, pages = {3893 -- 3915}, publisher = {Wiley-Blackwell}, title = {{The presence of pacemaker HCN channels identifies theta rhythmic GABAergic neurons in the medial septum}}, doi = {10.1113/jphysiol.2008.155242}, volume = {586}, year = {2008}, } @article{2679, abstract = {Ionotropic glutamate receptors play important roles in spinal processing of nociceptive sensory signals and induction of central sensitization in chronic pain. Here we applied highly sensitive freeze-fracture replica labeling to laminae I-II of the spinal dorsal horn of rats and investigated the numbers, densities, and colocalization of AMPA- and NMDA-type glutamate receptors at individual postsynaptic membrane specializations with a high resolution. All glutamatergic postsynaptic membranes in laminae I-II expressed AMPA receptors, and most of them (96%) were also immunoreactive for the NR1 subunit of NMDA receptors. The numbers of gold particles for AMPA and NMDA receptors at individual postsynaptic membranes showed a linear correlation with the size of postsynaptic membrane specializations and varied in the range of 8-214 and 5-232 with median values of 37 and 28, whereas their densities varied in the range of 325-3365/μm 2 and 102-2263/μm 2 with median values of 1115/μm 2 and 777/μm 2, respectively. Virtually all (99%) glutamatergic postsynaptic membranes expressed GluR2, and most of them (87%) were also immunoreactive for GluR1. The numbers of gold particles for pan-AMPA, NR1, and GluR2 subunits showed a linear correlation with the size of postsynaptic surface areas. Concerning GluR1, there may be two populations of synapses with high and low GluR1 densities. In synapses larger than 0.1 μm 2, GluR1 subunits were recovered in very low numbers. Differential expression of GluR1 and GluR2 subunits suggests regulation of AMPA receptor subunit composition by presynaptic mechanism.}, author = {Antal, Miklós and Fukazawa, Yugo and Eördögh, Mária and Muszil, Dóra and Molnár, Elek and Itakura, Makoto and Takahashi, Masami and Ryuichi Shigemoto}, journal = {Journal of Neuroscience}, number = {39}, pages = {9692 -- 9701}, publisher = {Society for Neuroscience}, title = {{Numbers, densities, and colocalization of AMPA- and NMDA-type glutamate receptors at individual synapses in the superficial spinal dorsal horn of rats}}, doi = {10.1523/JNEUROSCI.1551-08.2008}, volume = {28}, year = {2008}, } @article{2681, abstract = {Left-right asymmetry of the brain has been studied mostly through psychological examination and functional imaging in primates, leaving its molecular and synaptic aspects largely unaddressed. Here, we show that hippocampal CA1 pyramidal cell synapses differ in size, shape, and glutamate receptor expression depending on the laterality of presynaptic origin. CA1 synapses receiving neuronal input from the right CA3 pyramidal cells are larger and have more perforated PSD and a GluR1 expression level twice as high as those receiving input from the left CA3. The synaptic density of GluR1 increases as the size of a synapse increases, whereas that of NR2B decreases because of the relatively constant NR2B expression in CA1 regardless of synapse size. Densities of other major glutamate receptor subunits show no correlation with synapse size, thus resulting in higher net expression in synapses having right input. Our study demonstrates universal left-right asymmetry of hippocampal synapses with a fundamental relationship between synaptic area and the expression of glutamate receptor subunits.}, author = {Shinohara, Yoshiaki and Hirase, Hajime and Watanabe, Masahiko and Itakura, Makoto and Takahashi, Masami and Ryuichi Shigemoto}, journal = {PNAS}, number = {49}, pages = {19498 -- 19503}, publisher = {National Academy of Sciences}, title = {{Left-right asymmetry of the hippocampal synapses with differential subunit allocation of glutamate receptors}}, doi = {10.1073/pnas.0807461105}, volume = {105}, year = {2008}, } @inproceedings{2702, abstract = {We review our proof that in a scaling limit, the time evolution of a quantum particle in a static random environment leads to a diffusion equation. In particular, we discuss the role of Feynman graph expansions and of renormalization. }, author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer}, pages = {167 -- 182}, publisher = {World Scientific Publishing}, title = {{Feynman graphs and renormalization in quantum diffusion}}, doi = {10.1142/9789812833556_0011}, year = {2008}, } @article{2753, abstract = {We consider random Schrödinger equations on R d for d ≽ 3 with a homogeneous Anderson–Poisson type random potential. Denote by λ the coupling constant and ψt the solution with initial data ψ0 . The space and time variables scale as x∼λ−2−ϰ/2 and t∼λ−2−ϰ with 0<ϰ<ϰ0(d) . We prove that, in the limit λ → 0, the expectation of the Wigner distribution of ψt converges weakly to the solution of a heat equation in the space variable x for arbitrary L 2 initial data. The proof is based on analyzing the phase cancellations of multiple scatterings on the random potential by expanding the propagator into a sum of Feynman graphs. In this paper we consider the non-recollision graphs and prove that the amplitude of the non-ladder diagrams is smaller than their “naive size” by an extra λ c factor per non-(anti)ladder vertex for some c > 0. This is the first rigorous result showing that the improvement over the naive estimates on the Feynman graphs grows as a power of the small parameter with the exponent depending linearly on the number of vertices. This estimate allows us to prove the convergence of the perturbation series. }, author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer}, journal = {Acta Mathematica}, number = {2}, pages = {211 -- 277}, publisher = {Springer}, title = {{Quantum diffusion of the random Schrödinger evolution in the scaling limit}}, doi = {10.1007/s11511-008-0027-2}, volume = {200}, year = {2008}, } @article{2754, abstract = {We study the dynamics of an electron weakly coupled to a phonon gas. The initial state of the electron is the superposition of two spatially localized distant bumps moving towards each other, and the phonons are in a thermal state. We investigate the dynamics of the system in the kinetic regime and show that the time evolution makes the non-diagonal terms of the density matrix of the electron decay, destroying the interference between the two bumps. We show that such a damping effect is exponential in time, and the related decay rate is proportional to the total scattering cross section of the electron-phonon interaction.}, author = {Adami, Riccardo and László Erdös}, journal = {Journal of Statistical Physics}, number = {2}, pages = {301 -- 328}, publisher = {Springer}, title = {{Rate of decoherence for an electron weakly coupled to a phonon gas}}, doi = {10.1007/s10955-008-9561-8}, volume = {132}, year = {2008}, } @article{2755, abstract = {Consider N bosons in a finite box Λ= [0,L]3⊂ R3 interacting via a two-body non-negative soft potential V=λ V with V fixed and λ>0 small. We will take the limit L,N→∞ by keeping the density =N/L3 fixed and small. We construct a variational state, which gives an upper bound on the ground-state energy per particle ε, ε≤4πa [1+ (128/15π) (a3) 1/2 Sλ] +O (2 ln ), as →0, with a constant satisfying 1≤ Sλ ≤1+Cλ. Here a is the scattering length of V and thus depends on λ. In comparison, the prediction by Lee and Yang [Phys. Rev. 105, 1119 (1957)] and Lee, Huang, and Yang [Phys. Rev. 106, 1135 (1957)] asserts that Sλ =1 independent of λ.}, author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {5}, publisher = {American Physical Society}, title = {{Ground-state energy of a low-density Bose gas: A second-order upper bound}}, doi = {10.1103/PhysRevA.78.053627}, volume = {78}, year = {2008}, } @article{2795, abstract = {The collapse of turbulence, observable in shear flows at low Reynolds numbers, raises the question if turbulence is generically of a transient nature or becomes sustained at some critical point. Recent data have led to conflicting views with the majority of studies supporting the model of turbulence turning into an attracting state. Here we present lifetime measurements of turbulence in pipe flow spanning 8 orders of magnitude in time, drastically extending all previous investigations. We show that no critical point exists in this regime and that in contrast to the prevailing view the turbulent state remains transient. To our knowledge this is the first observation of superexponential transients in turbulence, confirming a conjecture derived from low-dimensional systems.}, author = {Björn Hof and de Lózar, Alberto and Kuik, Dirk J and Westerweel, Jerry}, journal = {Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Repeller or attractor? Selecting the dynamical model for the onset of turbulence in pipe flow}}, doi = {10.1103/PhysRevLett.101.214501}, volume = {101}, year = {2008}, } @article{2892, author = {Azevedo, Ricardo B and Lohaus, Rolf and Tiago Paixao}, journal = {Evolution & Development}, number = {5}, pages = {514 -- 515}, publisher = {Wiley-Blackwell}, title = {{Networking networks}}, doi = {10.1111/j.1525-142X.2008.00265.x}, volume = {10}, year = {2008}, } @article{3031, abstract = {Many aspects of plant development, including patterning and tropisms, are largely dependent on the asymmetric distribution of the plant signaling molecule auxin. Auxin transport inhibitors (ATIs), which interfere with directional auxin transport, have been essential tools in formulating this concept. However, despite the use of ATIs in plant research for many decades, the mechanism of ATI action has remained largely elusive. Using real-time live-cell microscopy, we show here that prominent ATIs such as 2,3,5-triiodobenzoic acid (TIBA) and 2-(1-pyrenoyl) benzoic acid (PBA) inhibit vesicle trafficking in plant, yeast, and mammalian cells. Effects on micropinocytosis, rab5-labeled endosomal motility at the periphery of HeLa cells and on fibroblast mobility indicate that ATIs influence actin cytoskeleton. Visualization of actin cytoskeleton dynamics in plants, yeast, and mammalian cells show that ATIs stabilize actin. Conversely, stabilizing actin by chemical or genetic means interferes with endocytosis, vesicle motility, auxin transport, and plant development, including auxin transport-dependent processes. Our results show that a class of ATIs act as actin stabilizers and advocate that actin-dependent trafficking of auxin transport components participates in the mechanism of auxin transport. These studies also provide an example of how the common eukaryotic process of actin-based vesicle motility can fulfill a plant-specific physiological role.}, author = {Dhonukshe, Pankaj and Grigoriev, Ilya S and Fischer, Rainer and Tominaga, Motoki and Robinson, David G and Hašek, Jiří and Paciorek, Tomasz and Petrášek, Jan and Seifertová, Daniela and Tejos, Ricardo and Meisel, Lee A and Zažímalová, Eva and Gadella, Theodorus W and Stierhof, York-Dieter and Ueda, Takashi and Oiwa, Kazuhiro and Akhmanova, Anna and Brock, Roland and Spang, Anne and Jirí Friml}, journal = {PNAS}, number = {11}, pages = {4489 -- 4494}, publisher = {National Academy of Sciences}, title = {{Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes}}, doi = {10.1073/pnas.0711414105}, volume = {105}, year = {2008}, } @article{3045, abstract = {Dynamically polarized membrane proteins define different cell boundaries and have an important role in intercellular communication - a vital feature of multicellular development. Efflux carriers for the signalling molecule auxin from the PIN family are landmarks of cell polarity in plants and have a crucial involvement in auxin distribution-dependent development including embryo patterning, organogenesis and tropisms. Polar PIN localization determines the direction of intercellular auxin flow, yet the mechanisms generating PIN polarity remain unclear. Here we identify an endocytosis-dependent mechanism of PIN polarity generation and analyse its developmental implications. Real-time PIN tracking showed that after synthesis, PINs are initially delivered to the plasma membrane in a non-polar manner and their polarity is established by subsequent endocytic recycling. Interference with PIN endocytosis either by auxin or by manipulation of the Arabidopsis Rab5 GTPase pathway prevents PIN polarization. Failure of PIN polarization transiently alters asymmetric auxin distribution during embryogenesis and increases the local auxin response in apical embryo regions. This results in ectopic expression of auxin pathway-associated root-forming master regulators in embryonic leaves and promotes homeotic transformation of leaves to roots. Our results indicate a two-step mechanism for the generation of PIN polar localization and the essential role of endocytosis in this process. It also highlights the link between endocytosis-dependent polarity of individual cells and auxin distribution-dependent cell fate establishment for multicellular patterning.}, author = {Dhonukshe, Pankaj and Tanaka, Hirokazu and Goh, Tatsuaki and Ebine, Kazuo and Mähönen, Ari Pekka and Prasad, Kalika and Blilou, Ikram and Geldner, Niko and Xu, Jian and Uemura, Tomohiro and Chory, Joanne and Ueda, Takashi and Nakano, Akihiko and Scheres, Ben and Jirí Friml}, journal = {Nature}, number = {7224}, pages = {962 -- 966}, publisher = {Nature Publishing Group}, title = {{Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions}}, doi = {10.1038/nature07409}, volume = {456}, year = {2008}, } @article{3041, abstract = {The rate, polarity, and symmetry of the flow of the plant hormone auxin are determined by the polar cellular localization of PIN-FORMED (PIN) auxin efflux carriers. Flavonoids, a class of secondary plant metabolites, have been suspected to modulate auxin transport and tropic responses. Nevertheless, the identity of specific flavonoid compounds involved and their molecular function and targets in vivo are essentially unknown. Here we show that the root elongation zone of agravitropic pin2/eir1/wav6/agr1 has an altered pattern and amount of flavonol glycosides. Application of nanomolar concentrations of flavonols to pin2 roots is sufficient to partially restore root gravitropism. By employing a quantitative cell biological approach, we demonstrate that flavonoids partially restore the formation of lateral auxin gradients in the absence of PIN2. Chemical complementation by flavonoids correlates with an asymmetric distribution of the PIN1 protein. pin2 complementation probably does not result from inhibition of auxin efflux, as supply of the auxin transport inhibitor N-1-naphthylphthalamic acid failed to restore pin2 gravitropism. We propose that flavonoids promote asymmetric PIN shifts during gravity stimulation, thus redirecting basipetal auxin streams necessary for root bending. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.}, author = {Santelia, Diana and Henrichs, Sina and Vincenzetti, Vincent and Sauer, Michael and Bigler, Laurent and Klein, Markus B and Bailly, Aurélien and Lee, Yuree and Jirí Friml and Geisler, Markus and Martinoia, Enrico}, journal = {Journal of Biological Chemistry}, number = {45}, pages = {31218 -- 31226}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses}}, doi = { 10.1074/jbc.M710122200}, volume = {283}, year = {2008}, } @article{3043, abstract = {Plant development is characterized by a profound phenotypic plasticity that often involves redefining of the developmental fate and polarity of cells within differentiated tissues. The plant hormone auxin and its directional intercellular transport play a major role in these processes because they provide positional information and link cell polarity with tissue patterning. This plant-specific mechanism of transport-dependent auxin gradients depends on subcellular dynamics of auxin transport components, in particular on endocytic recycling and polar targeting. Recent insights into these cellular processes in plants have revealed important parallels to yeast and animal systems, including clathrin-dependent endocytosis, retromer function, and transcytosis, but have also emphasized unique features of plant cells such as diversity of polar targeting pathways; integration of environmental signals into subcellular trafficking; and the link between endocytosis, cell polarity, and cell fate specification. We review these advances and focus on the translation of the subcellular dynamics to the regulation of whole-plant development.}, author = {Kleine Vehn, Jürgen and Friml, Jirí}, journal = {Annual Review of Cell and Developmental Biology}, pages = {447 -- 473}, publisher = {Annual Reviews}, title = {{Polar targeting and endocytic recycling in auxin-dependent plant development}}, doi = {10.1146/annurev.cellbio.24.110707.175254}, volume = {24}, year = {2008}, } @article{3039, abstract = {During the development of multicellular organisms, organogenesis and pattern formation depend on formative divisions to specify and maintain pools of stem cells. In higher plants, these activities are essential to shape the final root architecture because the functioning of root apical meristems and the de novo formation of lateral roots entirely rely on it. We used transcript profiling on sorted pericycle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of Arabidopsis as a key factor both in promoting formative cell divisions in the pericycle and in constraining the number of these divisions once organogenesis has been started. In the root tip meristem, ACR4 shows a similar action by controlling cell proliferation activity in the columella cell lineage. Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation.}, author = {De Smet, Ive and Vassileva, Valya and De Rybel, Bert and Levesque, Mitchell P and Grunewald, Wim and Van Damme, Daniël and Van Noorden, Giel and Naudts, Mirande and Van Isterdael, Gert and De Clercq, Rebecca and Wang, Jean Y and Meuli, Nicholas and Vanneste, Steffen and Jirí Friml and Hilson, Pierre and Jürgens, Gerd and Ingram, Gwyneth C and Inzé, Dirk and Benfey, Philip N and Beeckman, Tom}, journal = {Science}, number = {5901}, pages = {594 -- 597}, publisher = {American Association for the Advancement of Science}, title = {{Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root}}, doi = {10.1126/science.1160158}, volume = {322}, year = {2008}, } @article{3042, abstract = {All eukaryotic cells present at the cell surface a specific set of plasma membrane proteins that modulate responses to internal and external cues and whose activity is also regulated by protein degradation. We characterized the lytic vacuole-dependent degradation of membrane proteins in Arabidopsis thaliana by means of in vivo visualization of vacuolar targeting combined with quantitative protein analysis. We show that the vacuolar targeting pathway is used by multiple cargos including PIN-FORMED (PIN) efflux carriers for the phytohormone auxin. In vivo visualization of PIN2 vacuolar targeting revealed its differential degradation in response to environmental signals, such as gravity. In contrast to polar PIN delivery to the basal plasma membrane, which depends on the vesicle trafficking regulator ARF-GEF GNOM, PIN sorting to the lytic vacuolar pathway requires additional brefeldin A-sensitive ARF-GEF activity. Furthermore, we identified putative retromer components SORTING NEXIN1 (SNX1) and VACUOLAR PROTEIN SORTING29 (VPS29) as important factors in this pathway and propose that the retromer complex acts to retrieve PIN proteins from a late/pre-vacuolar compartment back to the recycling pathways. Our data suggest that ARF GEF- and retromer-dependent processes regulate PIN sorting to the vacuole in an antagonistic manner and illustrate instrumentalization of this mechanism for fine-tuning the auxin fluxes during gravitropic response.}, author = {Kleine-Vehn, Jürgen and Leitner, Johannes and Zwiewka, Marta and Sauer, Michael and Abas, Lindy and Luschnig, Christian and Jirí Friml}, journal = {PNAS}, number = {46}, pages = {17812 -- 17817}, publisher = {National Academy of Sciences}, title = {{Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting}}, doi = {10.1073/pnas.0808073105}, volume = {105}, year = {2008}, } @article{3040, abstract = {The polar, sub-cellular localization of PIN auxin efflux carriers determines the direction of intercellular auxin flow, thus defining the spatial aspect of auxin signalling. Dynamic, transcytosis-like relocalizations of PIN proteins occur in response to external and internal signals, integrating these signals into changes in auxin distribution. Here, we examine the cellular and molecular mechanisms of polar PIN delivery and transcytosis. The mechanisms of the ARF-GEF-dependent polar targeting and transcytosis are well conserved and show little variations among diverse Arabidopsis ecotypes consistent with their fundamental importance in regulating plant development. At the cellular level, we refine previous findings on the role of the actin cytoskeleton in apical and basal PIN targeting, and identify a previously unknown role for microtubules, specifically in basal targeting. PIN protein delivery to different sides of the cell is mediated by ARF-dependent trafficking with a previously unknown complex level of distinct ARF-GEF vesicle trafficking regulators. Our data suggest that alternative recruitment of PIN proteins by these distinct pathways can account for cell type- and cargo-specific aspects of polar targeting, as well as for polarity changes in response to different signals. The resulting dynamic PIN positioning to different sides of cells defines a three-dimensional pattern of auxin fluxes within plant tissues.}, author = {Kleine-Vehn, Jürgen and Łangowski, Łukasz and Wiśniewska, Justyna and Dhonukshe, Pankaj and Brewer, Philip B and Jirí Friml}, journal = {Molecular Plant}, number = {6}, pages = {1056 -- 1066}, publisher = {Oxford University Press}, title = {{Cellular and molecular requirements for polar PIN targeting and transcytosis in plants}}, doi = {10.1093/mp/ssn062}, volume = {1}, year = {2008}, } @article{3044, abstract = {The signalling molecule auxin controls plant morphogenesis via its activity gradients, which are produced by intercellular auxin transport. Cellular auxin efflux is the rate-limiting step in this process and depends on PIN and phosphoglycoprotein (PGP) auxin transporters. Mutual roles for these proteins in auxin transport are unclear, as is the significance of their interactions for plant development. Here, we have analysed the importance of the functional interaction between PIN- and PGP-dependent auxin transport in development. We show by analysis of inducible overexpression lines that PINs and PGPs define distinct auxin transport mechanisms: both mediate auxin efflux but they play diverse developmental roles. Components of both systems are expressed during embryogenesis, organogenesis and tropisms, and they interact genetically in both synergistic and antagonistic fashions. A concerted action of PIN- and PGP-dependent efflux systems is required for asymmetric auxin distribution during these processes. We propose a model in which PGP-mediated efflux controls auxin levels in auxin channel-forming cells and, thus, auxin availability for PIN-dependent vectorial auxin movement.}, author = {Mravec, Jozef and Kubeš, Martin and Bielach, Agnieszka and Gaykova, Vassilena and Petrášek, Jan and Skůpa, Petr and Chand, Suresh and Eva Benková and Zažímalová, Eva and Jirí Friml}, journal = {Development}, number = {20}, pages = {3345 -- 3354}, publisher = {Company of Biologists}, title = {{Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development}}, doi = {10.1242/dev.021071}, volume = {135}, year = {2008}, } @inproceedings{3194, abstract = {We consider the problem of optimizing multilabel MRFs, which is in general NP-hard and ubiquitous in low-level computer vision. One approach for its solution is to formulate it as an integer linear programming and relax the integrality constraints. The approach we consider in this paper is to first convert the multi-label MRF into an equivalent binary-label MRF and then to relax it. The resulting relaxation can be efficiently solved using a maximum flow algorithm. Its solution provides us with a partially optimal labelling of the binary variables. This partial labelling is then easily transferred to the multi-label problem. We study the theoretical properties of the new relaxation and compare it with the standard one. Specifically, we compare tightness, and characterize a subclass of problems where the two relaxations coincide. We propose several combined algorithms based on the technique and demonstrate their performance on challenging computer vision problems.}, author = {Kohli, Pushmeet and Shekhovtsov, Alexander and Rother, Carsten and Vladimir Kolmogorov and Torr, Philip H}, pages = {480 -- 487}, publisher = {Omnipress}, title = {{On partial optimality in multi label MRFs}}, doi = {10.1145/1390156.1390217}, year = {2008}, } @inproceedings{3226, abstract = {A family of functions is weakly pseudorandom if a random member of the family is indistinguishable from a uniform random function when queried on random inputs. We point out a subtle ambiguity in the definition of weak PRFs: there are natural weak PRFs whose security breaks down if the randomness used to sample the inputs is revealed. To capture this ambiguity we distinguish between public-coin and secret-coin weak PRFs. We show that the existence of a secret-coin weak PRF which is not also a public-coin weak PRF implies the existence of two pass key-agreement (i.e. public-key encryption). So in Minicrypt, i.e. under the assumption that one-way functions exist but public-key cryptography does not, the notion of public- and secret-coin weak PRFs coincide. Previous to this paper all positive cryptographic statements known to hold exclusively in Minicrypt concerned the adaptive security of constructions using non-adaptively secure components. Weak PRFs give rise to a new set of statements having this property. As another example we consider the problem of range extension for weak PRFs. We show that in Minicrypt one can beat the best possible range expansion factor (using a fixed number of distinct keys) for a very general class of constructions (in particular, this class contains all constructions that are known today). }, author = {Krzysztof Pietrzak and Sjödin, Johan}, number = {PART 2}, pages = {423 -- 436}, publisher = {Springer}, title = {{Weak pseudorandom functions in minicrypt}}, doi = {10.1007/978-3-540-70583-3_35}, volume = {5126}, year = {2008}, } @inproceedings{3228, abstract = { A black-box combiner for collision resistant hash functions (CRHF) is a construction which given black-box access to two hash functions is collision resistant if at least one of the components is collision resistant. In this paper we prove a lower bound on the output length of black-box combiners for CRHFs. The bound we prove is basically tight as it is achieved by a recent construction of Canetti et al [Crypto'07]. The best previously known lower bounds only ruled out a very restricted class of combiners having a very strong security reduction: the reduction was required to output collisions for both underlying candidate hash-functions given a single collision for the combiner (Canetti et al [Crypto'07] building on Boneh and Boyen [Crypto'06] and Pietrzak [Eurocrypt'07]). Our proof uses a lemma similar to the elegant "reconstruction lemma" of Gennaro and Trevisan [FOCS'00], which states that any function which is not one-way is compressible (and thus uniformly random function must be one-way). In a similar vein we show that a function which is not collision resistant is compressible. We also borrow ideas from recent work by Haitner et al. [FOCS'07], who show that one can prove the reconstruction lemma even relative to some very powerful oracles (in our case this will be an exponential time collision-finding oracle). © 2008 Springer-Verlag Berlin Heidelberg.}, author = {Krzysztof Pietrzak}, pages = {413 -- 432}, publisher = {Springer}, title = {{Compression from collisions or why CRHF combiners have a long output}}, doi = {10.1007/978-3-540-85174-5_23}, volume = {5157}, year = {2008}, } @inproceedings{3229, abstract = {We construct a stream-cipher S whose implementation is secure even if a bounded amount of arbitrary (adversarially chosen) information on the internal state ofS is leaked during computation. This captures all possible side-channel attacks on S where the amount of information leaked in a given period is bounded, but overall can be arbitrary large. The only other assumption we make on the implementation of S is that only data that is accessed during computation leaks information. The stream-cipher S generates its output in chunks K1, K2, . . . and arbitrary but bounded information leakage is modeled by allowing the adversary to adaptively chose a function fl : {0,1}* rarr {0, 1}lambda before Kl is computed, she then gets fl(taul) where taul is the internal state ofS that is accessed during the computation of Kg. One notion of security we prove for S is that Kg is indistinguishable from random when given K1,..., K1-1,f1(tau1 ),..., fl-1(taul-1) and also the complete internal state of S after Kg has been computed (i.e. S is forward-secure). The construction is based on alternating extraction (used in the intrusion-resilient secret-sharing scheme from FOCS'07). We move this concept to the computational setting by proving a lemma that states that the output of any PRG has high HILLpseudoentropy (i.e. is indistinguishable from some distribution with high min-entropy) even if arbitrary information about the seed is leaked. The amount of leakage lambda that we can tolerate in each step depends on the strength of the underlying PRG, it is at least logarithmic, but can be as large as a constant fraction of the internal state of S if the PRG is exponentially hard.}, author = {Dziembowski, Stefan and Krzysztof Pietrzak}, pages = {293 -- 302}, publisher = {IEEE}, title = {{Leakage resilient cryptography}}, doi = {10.1109/FOCS.2008.56}, year = {2008}, } @article{3227, abstract = {Large amount of data management can cause a lot of troubles which can be solved by dedicated computer system. To facilitate management of measurement data which are gathered in Institute of Power Engineering - Insulation Department a special system called Elektrowiz® was developed. It allows storing measurement results which concern partial discharges in insulation of turbo- and hydrogenerators in power stations. Multilayer architecture of the system allows reaching gathered data independently on user localization. There are possible different access methods to the system and dependency on current requirements data exploration can be realized with read-only or edit rights.}, author = {Zubielik, Piotr and Nadaczny, Jerzy and Krzysztof Pietrzak and Lawenda, Marcin}, journal = {Przeglad Elektrotechniczny}, number = {10}, pages = {239 -- 242}, publisher = {SIGMA-NOT}, title = {{Elektrowiz – system of measurement data management}}, volume = {84}, year = {2008}, } @misc{3410, abstract = {Membrane proteins are involved in essential biological processes such as energy conversion, signal transduction, solute transport and secretion. All biological processes, also those involving membrane proteins, are steered by molecular interactions. Molecular interactions guide the folding and stability of membrane proteins, determine their assembly, switch their functional states or mediate signal transduction. The sequential steps of molecular interactions driving these processes can be described by dynamic energy landscapes. The conceptual energy landscape allows to follow the complex reaction pathways of membrane proteins while its modifications describe why and how pathways are changed. Single-molecule force spectroscopy (SMFS) detects, quantifies and locates interactions within and between membrane proteins. SMFS helps to determine how these interactions change with temperature, point mutations, oligomerization and the functional states of membrane proteins. Applied in different modes, SMFS explores the co-existence and population of reaction pathways in the energy landscape of the protein and thus reveals detailed insights into local mechanisms, determining its structural and functional relationships. Here we review how SMFS extracts the defining parameters of an energy landscape such as the barrier position, reaction kinetics and roughness with high precision.}, author = {Harald Janovjak and Sapra, Tanuj K and Kedrov, Alexej and Mueller, Daniel J}, booktitle = {ChemPhysChem}, number = {7}, pages = {954 -- 966}, publisher = {Wiley-Blackwell}, title = {{From valleys to ridges: Exploring the energy landscape of single membrane proteins}}, doi = {10.1002/cphc.200700662}, volume = {9}, year = {2008}, } @article{3409, abstract = {With the introduction of single-molecule force spectroscopy (SMFS) it has become possible to directly access the interactions of various molecular systems. A bottleneck in conventional SMFS is collecting the large amount of data required for statistically meaningful analysis. Currently, atomic force microscopy (AFM)-based SMFS requires the user to tediously 'fish' for single molecules. In addition, most experimental and environmental conditions must be manually adjusted. Here, we developed a fully automated single-molecule force spectroscope. The instrument is able to perform SMFS while monitoring and regulating experimental conditions such as buffer composition and temperature. Cantilever alignment and calibration can also be automatically performed during experiments. This, combined with in-line data analysis, enables the instrument, once set up, to perform complete SMFS experiments autonomously.}, author = {Struckmeier, Jens and Wahl, Reiner and Leuschner, Mirko and Nunes, Joao and Harald Janovjak and Geisler, Ulrich and Hofmann, Gerd and Jähnke, Torsten and Mueller, Daniel J}, journal = {Nanotechnology}, number = {38}, publisher = {IOP Publishing Ltd.}, title = {{Fully automated single-molecule force spectroscopy for screening applications}}, doi = {10.1088/0957-4484/19/38/384020}, volume = {19}, year = {2008}, } @inproceedings{3501, abstract = {The Wikipedia is a collaborative encyclopedia: anyone can contribute to its articles simply by clicking on an "edit" button. The open nature of the Wikipedia has been key to its success, but has also created a challenge: how can readers develop an informed opinion on its reliability? We propose a system that computes quantitative values of trust for the text in Wikipedia articles; these trust values provide an indication of text reliability. The system uses as input the revision history of each article, as well as information about the reputation of the contributing authors, as provided by a reputation system. The trust of a word in an article is computed on the basis of the reputation of the original author of the word, as well as the reputation of all authors who edited text near the word. The algorithm computes word trust values that vary smoothly across the text; the trust values can be visualized using varying text-background colors. The algorithm ensures that all changes to an article's text are reflected in the trust values, preventing surreptitious content changes. We have implemented the proposed system, and we have used it to compute and display the trust of the text of thousands of articles of the English Wikipedia. To validate our trust-computation algorithms, we show that text labeled as low-trust has a significantly higher probability of being edited in the future than text labeled as high-trust.}, author = {Adler, B Thomas and Krishnendu Chatterjee and de Alfaro, Luca and Faella, Marco and Pye, Ian and Raman, Vishwanath}, publisher = {ACM}, title = {{Assigning trust to Wikipedia content}}, doi = {10.1145/1822258.1822293}, year = {2008}, } @inproceedings{3502, abstract = {In content-driven reputation systems for collaborative content, users gain or lose reputation according to how their contributions fare: authors of long-lived contributions gain reputation, while authors of reverted contributions lose reputation. Existing content-driven systems are prone to Sybil attacks, in which multiple identities, controlled by the same person, perform coordinated actions to increase their reputation. We show that content-driven reputation systems can be made resistant to such attacks by taking advantage of thefact that the reputation increments and decrements depend on content modifications, which are visible to all. We present an algorithm for content-driven reputation that prevents a set of identities from increasing their maximum reputation without doing any useful work. Here, work is considered useful if it causes content to evolve in a direction that is consistent with the actions of high-reputation users. We argue that the content modifications that require no effort, such as the insertion or deletion of arbitrary text, are invariably non-useful. We prove a truthfullness result for the resulting system, stating that users who wish to perform a contribution do not gain by employing complex contribution schemes, compared to simply performing the contribution at once. In particular, splitting the contribution in multiple portions, or employing the coordinated actions of multiple identities, do not yield additional reputation. Taken together, these results indicate that content-driven systems can be made robust with respect to Sybil attacks. Copyright 2008 ACM.}, author = {Krishnendu Chatterjee and de Alfaro, Luca and Pye, Ian}, pages = {33 -- 42}, publisher = {ACM}, title = {{Robust content-driven reputation}}, doi = {10.1145/1456377.1456387 }, year = {2008}, } @article{3520, abstract = {The hippocampus is thought to be involved in episodic memory formation by reactivating traces of waking experience during sleep. Indeed, the joint firing of spatially tuned pyramidal cells encoding nearby places recur during sleep. We found that the sleep cofiring of rat CA1 pyramidal cells encoding similar places increased relative to the sleep session before exploration. This cofiring increase depended on the number of times that cells fired together with short latencies ( < 50 ms) during exploration, and was strongest between cells representing the most visited places. This is indicative of a Hebbian learning rule in which changes in firing associations between cells are determined by the number of waking coincident firing events. In contrast, cells encoding different locations reduced their cofiring in proportion to the number of times that they fired independently. Together these data indicate that reactivated patterns are shaped by both positive and negative changes in cofiring, which are determined by recent behavior.}, author = {Joseph O'Neill and Senior,Timothy J and Allen, Kevin and Huxter,John R and Jozsef Csicsvari}, journal = {Nature Neuroscience}, number = {2}, pages = {209 -- 215}, publisher = {Nature Publishing Group}, title = {{Reactivation of experience-dependent cell assembly patterns in the hippocampus}}, doi = {10.1038/nn2037}, volume = {11}, year = {2008}, } @article{3537, abstract = {Hippocampal place cells that fire together within the same cycle of theta oscillations represent the sequence of positions (movement trajectory) that a rat traverses on a linear track. Furthermore, it has been suggested that the encoding of these and other types of temporal memory sequences is organized by gamma oscillations nested within theta oscillations. Here, we examined whether gamma-related firing of place cells permits such discrete temporal coding. We found that gamma-modulated CA1 pyramidal cells separated into two classes on the basis of gamma firing phases during waking theta periods. These groups also differed in terms of their spike waveforms, firing rates, and burst firing tendency. During gamma oscillations one group's firing became restricted to theta phases associated with the highest gamma power. Consequently, on the linear track, cells in this group often failed to fire early in theta-phase precession (as the rat entered the place field) if gamma oscillations were present. The second group fired throughout the theta cycle during gamma oscillations, and maintained gamma-modulated firing at different stages of theta-phase precession. Our results suggest that the two different pyramidal cell classes may support different types of population codes within a theta cycle: one in which spike sequences representing movement trajectories occur across subsequent gamma cycles nested within each theta cycle, and another in which firing in synchronized gamma discharges without temporal sequences encode a representation of location. We propose that gamma oscillations during theta-phase precession organize the mnemonic recall of population patterns representing places and movement paths.}, author = {Senior,Timothy J and Huxter,John R and Allen, Kevin and Joseph O'Neill and Jozsef Csicsvari}, journal = {Journal of Neuroscience}, number = {9}, pages = {2274 -- 2286}, publisher = {Society for Neuroscience}, title = {{Gamma oscillatory firing reveals distinct populations of pyramidal cells in the CA1 region of the hippocampus}}, doi = {10.1523/JNEUROSCI.4669-07.2008}, volume = {28}, year = {2008}, } @article{3534, author = {Dupret, David and Pleydell-Bouverie, Barty and Jozsef Csicsvari}, journal = {PNAS}, number = {47}, pages = {18079 -- 18080}, publisher = {National Academy of Sciences}, title = {{Inhibitory interneurons and network oscillations}}, doi = {10.1073/pnas.0810064105}, volume = {105}, year = {2008}, } @inproceedings{3600, abstract = {Scalability is one of the most important issues for optimization algorithms used in wireless sensor networks (WSNs) since there are often many parameters to be optimized at the same time. In this case it is very hard to ensure that an optimization algorithm can be smoothly scaled up from a low-dimensional optimization problem to the one with a high dimensionality. This paper addresses the scalability issue of a novel optimization algorithm inspired by the Shifting Balance Theory (SBT) of evolution in population genetics. Toward this end, a cluster-based WSN is employed in this paper as a benchmark to perform a comparative study. The total energy consumption is minimized under the required quality of service by jointly optimizing the transmission power and rate for each sensor node. The results obtained by the SBT-based algorithm are compared with the Metropolis algorithm (MA) and currently popular particle swarm optimizer (PSO) to assess the scaling performance of the three algorithms against the same WSN optimization problem.}, author = {Yang, Erfu and Nicholas Barton and Arslan, Tughrul and Erdogan, Ahmet T}, pages = {249 -- 260}, publisher = {Springer}, title = {{ Scalability of a novel shifting balance theory-based optimization algorithm: A comparative study on a cluster-based wireless sensor network}}, doi = {10.1007/978-3-540-85857-7_22}, volume = {5216}, year = {2008}, } @article{3606, abstract = {Explicit formulae are given for the effects of a barrier to gene flow on random fluctuations in allele frequency; these formulae can also be seen as generating functions for the distribution of coalescence times. The formulae are derived using a continuous diffusion approximation, which is accurate over all but very small spatial scales. The continuous approximation is confirmed by comparison with the exact solution to the stepping stone model. In both one and two spatial dimensions, the variance of fluctuations in allele frequencies increases near the barrier; when the barrier is very strong, the variance doubles. However, the effect on fluctuations close to the barrier is much greater when the population is spread over two spatial dimensions than when it occupies a linear, one-dimensional habitat: barriers of strength comparable with the dispersal range (B≈σ) can have an appreciable effect in two dimensions, whereas only barriers with strength comparable with the characteristic scale (B\! \approx\! L \equals \sigma \sol \sqrt {2 \mu}\hskip2) are significant in one dimension (μ is the rate of mutation or long-range dispersal). Thus, in a two-dimensional population, barriers to gene flow can be detected through their effect on the spatial pattern of genetic marker alleles.}, author = {Nicholas Barton}, journal = {Genetical Research}, number = {1}, pages = {139 -- 149}, publisher = {Cambridge University Press}, title = {{The effect of a barrier to gene flow on patterns of geographic variation}}, doi = {10.1017/S0016672307009081}, volume = {90}, year = {2008}, } @article{3605, abstract = {Many animals and plants show a correlation between the traits of the individuals in the mating pair, implying assortative mating. Given the ubiquity of assortative mating in nature, why and how it has evolved remain open questions. Here we attempt to answer these questions in those cases where the trait under assortment is the same in males and females. We consider the most favorable scenario for assortment to evolve, where the same trait is under assortment and viability selection. We find conditions for assortment to evolve using a multilocus formalism in a haploid population. Our results show how epistasis in fitness between the loci that control the focal trait is crucial for assortment to evolve. We then assume specific forms of assortment in haploids and diploids and study the limiting cases of selective and nonselective mating. We find that selection for increased assortment is weak and that where increased assortment is costly, it does not invade.}, author = {De Cara, Maria A and Nicholas Barton and Kirkpatrick, Mark}, journal = {American Naturalist}, number = {5}, pages = {580 -- 596}, publisher = {University of Chicago Press}, title = {{A model for the evolution of assortative mating}}, doi = {10.1086/587062}, volume = {171}, year = {2008}, } @inproceedings{3705, abstract = {Sliding window classifiers are among the most successful and widely applied techniques for object localization. However, training is typically done in a way that is not specific to the localization task. First a binary classifier is trained using a sample of positive and negative examples, and this classifier is subsequently applied to multiple regions within test images. We propose instead to treat object localization in a principled way by posing it as a problem of predicting structured data: we model the problem not as binary classification, but as the prediction of the bounding box of objects located in images. The use of a joint-kernel framework allows us to formulate the training procedure as a generalization of an SVM, which can be solved efficiently. We further improve computational efficiency by using a branch-and-bound strategy for localization during both training and testing. Experimental evaluation on the PASCAL VOC and TU Darmstadt datasets show that the structured training procedure improves pe rformance over binary training as well as the best previously published scores.}, author = {Blaschko,Matthew B and Christoph Lampert}, pages = {2 -- 15}, publisher = {Springer}, title = {{Learning to localize objects with structured output regression}}, doi = {10.1007/978-3-540-88682-2_2}, volume = {5302}, year = {2008}, } @inproceedings{3700, abstract = {We propose a new method to partition an unlabeled dataset, called Discriminative Context Partitioning (DCP). It is motivated by the idea of splitting the dataset based only on how well the resulting parts can be separated from a context class of disjoint data points. This is in contrast to typical clustering techniques like K-means that are based on a generative model by implicitly or explicitly searching for modes in the distribution of samples. The discriminative criterion in DCP avoids the problems that density based methods have when the a priori assumption of multimodality is violated, when the number of samples becomes small in relation to the dimensionality of the feature space, or if the cluster sizes are strongly unbalanced. We formulate DCP&amp;amp;amp;amp;amp;amp;amp;amp;lsquo;s separation property as a large-margin criterion, and show how the resulting optimization problem can be solved efficiently. Experiments on the MNIST and USPS datasets of handwritten digits and on a subset of the Caltech256 dataset show that, given a suitable context, DCP can achieve good results even in situation where density-based clustering techniques fail.}, author = {Christoph Lampert}, pages = {1 -- 8}, publisher = {IEEE}, title = {{Partitioning of image datasets using discriminative context information}}, doi = {10.1109/CVPR.2008.4587448}, year = {2008}, } @inproceedings{3716, abstract = {Most current methods for multi-class object classification and localization work as independent 1-vs-rest classifiers. They decide whether and where an object is visible in an image purely on a per-class basis. Joint learning of more than one object class would generally be preferable, since this would allow the use of contextual information such as co-occurrence between classes. However, this approach is usually not employed because of its computational cost. In this paper we propose a method to combine the efficiency of single class localization with a subsequent decision process that works jointly for all given object classes. By following a multiple kernel learning (MKL) approach, we automatically obtain a sparse dependency graph of relevant object classes on which to base the decision. Experiments on the PASCAL VOC 2006 and 2007 datasets show that the subsequent joint decision step clearly improves the accuracy compared to single class detection. }, author = {Christoph Lampert and Blaschko,Matthew B}, pages = {31 -- 40}, publisher = {Springer}, title = {{A multiple kernel learning approach to joint multi-class object detection}}, doi = {10.1007/978-3-540-69321-5_4}, volume = {5096}, year = {2008}, } @inproceedings{3714, abstract = {Most successful object recognition systems rely on binary classification, deciding only if an object is present or not, but not providing information on the actual object location. To perform localization, one can take a sliding window approach, but this strongly increases the computational cost, because the classifier function has to be evaluated over a large set of candidate subwindows. In this paper, we propose a simple yet powerful branchand- bound scheme that allows efficient maximization of a large class of classifier functions over all possible subimages. It converges to a globally optimal solution typically in sublinear time. We show how our method is applicable to different object detection and retrieval scenarios. The achieved speedup allows the use of classifiers for localization that formerly were considered too slow for this task, such as SVMs with a spatial pyramid kernel or nearest neighbor classifiers based on the 2-distance. We demonstrate state-of-the-art performance of the resulting systems on the UIUC Cars dataset, the PASCAL VOC 2006 dataset and in the PASCAL VOC 2007 competition.}, author = {Christoph Lampert and Blaschko,Matthew B and Hofmann,Thomas}, pages = {1 -- 8}, publisher = {IEEE}, title = {{Beyond sliding windows: Object localization by efficient subwindow search}}, doi = {10.1109/CVPR.2008.4587586}, year = {2008}, } @article{3734, abstract = {Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally.}, author = {Gasper Tkacik and Gregor, Thomas and Bialek, William S}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{The role of input noise in transcriptional regulation}}, doi = {10.1371/journal.pone.0002774}, volume = {3}, year = {2008}, } @article{3751, abstract = {Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator sequences binding activators and repressors-of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling.}, author = {Kinkhabwala, Ali and Guet, Calin C}, journal = {PLoS One}, number = {4}, publisher = {Public Library of Science}, title = {{Uncovering cis regulatory codes using synthetic promoter shuffling}}, doi = {10.1371/journal.pone.0002030}, volume = {3}, year = {2008}, } @article{3754, abstract = {Fluorescence correlation spectroscopy (FCS) has permitted the characterization of high concentrations of noncoding RNAs in a single living bacterium. Here, we extend the use of FCS to low concentrations of coding RNAs in single living cells. We genetically fuse a red fluorescent protein (RFP) gene and two binding sites for an RNA-binding protein, whose translated product is the RFP protein alone. Using this construct, we determine in single cells both the absolute [mRNA] concentration and the associated [RFP] expressed from an inducible plasmid. We find that the FCS method allows us to reliably monitor in real-time [mRNA] down to similar to 40 nM (i.e. approximately two transcripts per volume of detection). To validate these measurements, we show that [mRNA] is proportional to the associated expression of the RFP protein. This FCS-based technique establishes a framework for minimally invasive measurements of mRNA concentration in individual living bacteria.}, author = {Calin Guet and Bruneaux,Luke and Min,Taejin L and Siegal-Gaskins,Dan and Figueroa,Israel and Emonet,Thierry and Cluzel,Philippe}, journal = {Nucleic Acids Research}, number = {12}, publisher = {Oxford University Press}, title = {{Minimally invasive determination of mRNA concentration in single living bacteria}}, doi = {10.1093/nar/gkn329}, volume = {36}, year = {2008}, } @article{3769, abstract = {The geometrical representation of the space of phylogenetic trees implies a metric on the space of weighted trees. This metric, the geodesic distance, is the length of the shortest path through that space. We present an exact algorithm to compute this metric. For biologically reasonable trees, the implementation allows fast computations of the geodesic distance, although the running time of the algorithm is worst-case exponential. The algorithm was applied to pairs of 118 gene trees of the metazoa. The results show that a special path in tree space, the cone path, which can be computed in linear time, is a good approximation of the geodesic distance. The program GeoMeTree is a python implementation of the geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree.}, author = {Anne Kupczok and von Haeseler,Arndt and Klaere,Steffen}, journal = {Journal of Computational Biology}, number = {6}, pages = {577 -- 591}, publisher = {Mary Ann Liebert}, title = {{An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.}}, doi = {4200}, volume = {15}, year = {2008}, } @article{3826, abstract = {Gamma frequency (30-100 Hz) oscillations in the mature cortex underlie higher cognitive functions. Fast signaling in GABAergic interneuron networks plays a key role in the generation of these oscillations. During development of the rodent brain, gamma activity appears at the end of the first postnatal week, but frequency and synchrony reach adult levels only by the fourth week. However, the mechanisms underlying the maturation of gamma activity are unclear. Here we demonstrate that hippocampal basket cells (BCs), the proposed cellular substrate of gamma oscillations, undergo marked changes in their morphological, intrinsic, and synaptic properties between postnatal day 6 (P6) and P25. During maturation, action potential duration, propagation time, duration of the release period, and decay time constant of IPSCs decreases by approximately 30-60%. Thus, postnatal development converts BCs from slow into fast signaling devices. Computational analysis reveals that BC networks with young intrinsic and synaptic properties as well as reduced connectivity generate oscillations with moderate coherence in the lower gamma frequency range. In contrast, BC networks with mature properties and increased connectivity generate highly coherent activity in the upper gamma frequency band. Thus, late postnatal maturation of BCs enhances coherence in neuronal networks and will thereby contribute to the development of cognitive brain functions.}, author = {Doischer, Daniel and Hosp, Jonas Aurel and Yanagawa, Yuchio and Obata, Kunihiko and Peter Jonas and Vida, Imre and Bartos, Marlene}, journal = {Journal of Neuroscience}, number = {48}, pages = {12956 -- 68}, publisher = {Society for Neuroscience}, title = {{Postnatal differentiation of basket cells from slow to fast signaling devices}}, doi = {10.1523/JNEUROSCI.2890-08.2008}, volume = {28}, year = {2008}, } @article{3827, abstract = {Previous studies revealed that synaptotagmin 1 is the major Ca(2+) sensor for fast synchronous transmitter release at excitatory synapses. However, the molecular identity of the Ca(2+) sensor at hippocampal inhibitory synapses has not been determined. To address the functional role of synaptotagmin 1 at identified inhibitory terminals, we made paired recordings from synaptically connected basket cells (BCs) and granule cells (GCs) in the dentate gyrus in organotypic slice cultures from wild-type and synaptotagmin 1-deficient mice. As expected, genetic elimination of synaptotagmin 1 abolished synchronous transmitter release at excitatory GC-BC synapses. However, synchronous release at inhibitory BC-GC synapses was maintained. Quantitative analysis revealed that elimination of synaptotagmin 1 reduced release probability and depression but maintained the synchrony of transmitter release at BC-GC synapses. Elimination of synaptotagmin 1 also increased the frequency of both miniature excitatory postsynaptic currents (measured in BCs) and miniature inhibitory postsynaptic currents (recorded in GCs), consistent with a clamping function of synaptotagmin 1 at both excitatory and inhibitory terminals. Single-cell reverse-transcription quantitative PCR analysis revealed that single BCs coexpressed multiple synaptotagmin isoforms, including synaptotagmin 1-5, 7, and 11-13. Our results indicate that, in contrast to excitatory synapses, synaptotagmin 1 is not absolutely required for synchronous release at inhibitory BC-GC synapses. Thus, alternative fast Ca(2+) sensors contribute to synchronous release of the inhibitory transmitter GABA in cortical circuits.}, author = {Kerr, Angharad M and Reisinger, Ellen and Peter Jonas}, journal = {PNAS}, number = {40}, pages = {15581 -- 6}, publisher = {National Academy of Sciences}, title = {{Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses}}, doi = {10.1073/pnas.0800621105}, volume = {105}, year = {2008}, } @inproceedings{3504, abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics. We present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated to approximate the metrics using binary search.}, author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath}, pages = {107 -- 118}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Algorithms for game metrics}}, doi = {10.4230/LIPIcs.FSTTCS.2008.1745}, volume = {2}, year = {2008}, } @inproceedings{3875, abstract = {We study the problem of model checking Interval-valued Discrete-time Markov Chains (IDTMC). IDTMCs are discrete-time finite Markov Chains for which the exact transition probabilities are riot known. Instead in IDTMCs, each transition is associated with an interval in which the actual transition probability must lie. We consider two semantic interpretations for the uncertainty in the transition probabilities of an IDTMC. In the first interpretation, we think of an IDTMC as representing a (possibly uncountable) family of (classical) discrete-time Markov Chains, where each member of the family is a Markov Chain whose transition probabilities lie within the interval range given in the IDTMC. We call this semantic interpretation Uncertain Markov Chains (UMC). In the second semantics for an IDTMC, which we call Interval Markov Decision Process (IMDP), we view the uncertainty as being resolved through non-determinism. In other words, each time a state is visited, we adversarially pick a transition distribution that respects the interval constraints, and take a probabilistic step according to the chosen distribution. We introduce a logic omega-PCTL that can express liveness, strong fairness, and omega-regular properties (such properties cannot be expressed in PCTL). We show that the omega-PCTL model checking problem for Uncertain Markov Chain semantics is decidable in PSPACE (same as the best known upper bound for PCTL) and for Interval Markov Decision Process semantics is decidable in coNP (improving the previous known PSPACE bound for PCTL). We also show that the qualitative fragment of the logic can lie solved in coNP for the UMC interpretation, and can be solved in polynomial time for a sub-class of UMCs. We also prove lower bounds for these model checking problems. We show that the model checking problem of IDTMCs with LTL formulas can be solved for both UMC and IMDP semantics by reduction to the model checking problem of IDTMC with omega-PcTL formulas.}, author = {Krishnendu Chatterjee and Thomas Henzinger and Sen, Koushik}, pages = {302 -- 317}, publisher = {Springer}, title = {{Model-checking omega-regular properties of interval Markov chains}}, doi = {10.1007/978-3-540-78499-9_22}, volume = {4962}, year = {2008}, } @inproceedings{3873, abstract = {We study the controller synthesis problem under budget constraints. In this problem, there is a cost associated with making an observation, and a controller can make only a limited number of observations in each round so that the total cost of the observations does not exceed a given fixed budget. The controller must ensure some omega-regular requirement subject to the budget constraint. Budget constraints arise in designing and implementing controllers for resource-constrained embedded systems, where a controller may not have enough power, time, or bandwidth to obtain data from all sensors in each round. They lead to games of imperfect information, where the unknown information is not fixed a priori, but can vary from round to round, based on the choices made by the controller how to allocate its budget. We show that the budget-constrained synthesis problem for W-regular objectives is complete for exponential time. In addition to studying synthesis under a fixed budget constraint, we study the budget optimization problem, where given a plant, an objective, and observation costs, we have to find a controller that achieves the objective with minimal average accumulated cost (or minimal peak cost). We show that this problem is reducible to a game of imperfect information where the winning objective is a conjunction of an omega-regular condition and a long-run average condition (or a least max-cost condition), and this again leads to an exponential-time algorithm. Finally, we extend our results to games over infinite state spaces, and show that the budget-constrained synthesis problem is decidable for infinite state games with stable quotients of finite index. Consequently, the discrete time budget-constrained synthesis problem is decidable for rectangular hybrid automata.}, author = {Krishnendu Chatterjee and Majumdar, Ritankar S and Thomas Henzinger}, pages = {72 -- 86}, publisher = {Springer}, title = {{Controller synthesis with budget constraints}}, doi = {DOI: 10.1007/978-3-540-78929-1_6}, volume = {4981}, year = {2008}, } @inproceedings{3876, abstract = {We consider two-player games played in real time on game structures with clocks and parity objectives. The games are concurrent in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to turn-based (i.e., nonconcurrent) finite-state (i.e., untimed) parity games. The states of the resulting game are pairs of clock regions of the original game. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust strategies. Using a limit-robust strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers.}, author = {Krishnendu Chatterjee and Thomas Henzinger and Prabhu, Vinayak S}, pages = {124 -- 140}, publisher = {Springer}, title = {{Timed parity games: complexity and robustness}}, doi = {10.1007/978-3-540-85778-5_10}, volume = {5215}, year = {2008}, } @inproceedings{3877, abstract = {The synthesis problem asks to construct a reactive finite-state system from an omega-regular specification. Initial specifications are often unrealizable, which means that there is no system that implements the specification. A common reason for unrealizability is that assumptions on the environment of the system are incomplete. We study the problem of correcting an unrealizable specification phi by computing an environment assumption psi such that the new specification psi -> phi is realizable. Our aim is to construct an assumption psi that constrains only the environment and is as weak as possible. We present a two-step algorithm for computing assumptions. The algorithm operates on the game graph that is used to answer the realizability question. First, we compute a safety assumption that removes a minimal set of environment edges from the graph. Second, we compute a liveness assumption that puts fairness conditions on some of the remaining environment edges. We show that the problem of finding a minimal set of fair edges is computationally hard, and we use probabilistic games to compute a locally minimal fairness assumption.}, author = {Krishnendu Chatterjee and Thomas Henzinger and Jobstmann, Barbara}, pages = {147 -- 161}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Environment assumptions for synthesis}}, doi = {10.1007/978-3-540-85361-9_14}, volume = {5201}, year = {2008}, } @inproceedings{3878, abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing “reset” action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies.}, author = {Krishnendu Chatterjee and de Alfaro, Luca and Majumdar, Ritankar S}, pages = {91 -- 106}, publisher = {Springer}, title = {{The complexity of coverage}}, doi = {10.1007/978-3-540-89330-1_7}, volume = {5356}, year = {2008}, }