@article{1720, abstract = {How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis.}, author = {Wartlick, Ortrud and Anna Kicheva and González-Gaitán, Marcos A}, journal = {Cold Spring Harbor perspectives in biology}, number = {3}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Morphogen gradient formation }}, doi = {10.1101/cshperspect.a001255}, volume = {1}, year = {2009}, } @article{1769, abstract = {We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers.}, author = {Johannes Fink and Bianchetti, R and Baur, Matthias P and Göppl, M and Steffen, L. Kraig and Filipp, Stefan and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Dressed collective qubit states and the Tavis-Cummings model in circuit QED}}, doi = {10.1103/PhysRevLett.103.083601}, volume = {103}, year = {2009}, } @article{1767, abstract = {We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives.}, author = {Baur, Matthias P and Filipp, Stefan and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Leek, Peter J and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {24}, publisher = {American Physical Society}, title = {{Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit}}, doi = {10.1103/PhysRevLett.102.243602}, volume = {102}, year = {2009}, } @article{1766, abstract = {We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation.}, author = {Leek, Peter J and Filipp, Stefan and Maurer, Patrick and Baur, Matthias P and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Wallraff, Andreas}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {18}, publisher = {American Physical Society}, title = {{Using sideband transitions for two-qubit operations in superconducting circuits}}, doi = {10.1103/PhysRevB.79.180511}, volume = {79}, year = {2009}, } @article{1768, abstract = {Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states.}, author = {Filipp, Stefan and Maurer, Patrick and Leek, Peter J and Baur, Matthias P and Bianchetti, R and Johannes Fink and Göppl, M and Steffen, L. Kraig and Gambetta, Jay M and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Two-qubit state tomography using a joint dispersive readout}}, doi = {10.1103/PhysRevLett.102.200402}, volume = {102}, year = {2009}, } @article{1770, abstract = {The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.}, author = {Bianchetti, R and Filipp, Stefan and Baur, Matthias P and Johannes Fink and Göppl, M and Leek, Peter J and Steffen, L. Kraig and Blais, Alexandre and Wallraff, Andreas}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics}}, doi = {10.1103/PhysRevA.80.043840}, volume = {80}, year = {2009}, } @article{1771, abstract = {The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits.}, author = {Johannes Fink and Baur, Matthias P and Bianchetti, R and Filipp, Stefan and Göppl, M and Leek, Peter J and Steffen, L. Kraig and Blais, Alexandre and Wallraff, Andreas}, journal = {Physica Scripta T}, publisher = {IOP Publishing Ltd.}, title = {{Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics}}, doi = {10.1088/0031-8949/2009/T137/014013}, volume = {T137}, year = {2009}, } @article{1799, abstract = {The detection of approaching objects, such as looming predators, is necessary for survival. Which neurons and circuits mediate this function? We combined genetic labeling of cell types, two-photon microscopy, electrophysiology and theoretical modeling to address this question. We identify an approach-sensitive ganglion cell type in the mouse retina, resolve elements of its afferent neural circuit, and describe how these confer approach sensitivity on the ganglion cell. The circuit's essential building block is a rapid inhibitory pathway: it selectively suppresses responses to non-approaching objects. This rapid inhibitory pathway, which includes AII amacrine cells connected to bipolar cells through electrical synapses, was previously described in the context of night-time vision. In the daytime conditions of our experiments, the same pathway conveys signals in the reverse direction. The dual use of a neural pathway in different physiological conditions illustrates the efficiency with which several functions can be accommodated in a single circuit.}, author = {Münch, Thomas A and Da Silveira, Ravá A and Sandra Siegert and Viney, Tim J and Awatramani, Gautam B and Roska, Botond M}, journal = {Nature Neuroscience}, number = {10}, pages = {1308 -- 1316}, publisher = {Nature Publishing Group}, title = {{Approach sensitivity in the retina processed by a multifunctional neural circuit}}, doi = {10.1038/nn.2389}, volume = {12}, year = {2009}, } @article{1798, abstract = {The mammalian brain is assembled from thousands of neuronal cell types that are organized in distinct circuits to perform behaviorally relevant computations. Transgenic mouse lines with selectively marked cell types would facilitate our ability to dissect functional components of complex circuits. We carried out a screen for cell type-specific green fluorescent protein expression in the retina using BAC transgenic mice from the GENSAT project. Among others, we identified mouse lines in which the inhibitory cell types of the night vision and directional selective circuit were selectively labeled. We quantified the stratification patterns to predict potential synaptic connectivity between marked cells of different lines and found that some of the lines enabled targeted recordings and imaging of cell types from developing or mature retinal circuits. Our results suggest the potential use of a stratification-based screening approach for characterizing neuronal circuitry in other layered brain structures, such as the neocortex.}, author = {Sandra Siegert and Scherf, Brigitte G and Del Punta, Karina and Didkovsky, Nick and Heintz, Nathaniel M and Roska, Botond M}, journal = {Nature Neuroscience}, number = {9}, pages = {1197 -- 1204}, publisher = {Nature Publishing Group}, title = {{Genetic address book for retinal cell types}}, doi = {10.1038/nn.2370}, volume = {12}, year = {2009}, } @article{1825, abstract = {Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model. }, author = {Tamar Friedlander and Brenner, Naama}, journal = {PNAS}, number = {52}, pages = {22558 -- 22563}, publisher = {National Academy of Sciences}, title = {{Adaptive response by state-dependent inactivation}}, doi = {10.1073/pnas.0902146106 }, volume = {106}, year = {2009}, } @article{1971, abstract = {Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several α-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.}, author = {Berrisford, John M and Leonid Sazanov}, journal = {Journal of Biological Chemistry}, number = {43}, pages = {29773 -- 29783}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Structural basis for the mechanism of respiratory complex I}}, doi = {10.1074/jbc.M109.032144}, volume = {284}, year = {2009}, } @article{1984, abstract = {In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14-18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.}, author = {Dinarina, Ana and Pugieux, Céline and Corral, Maria M and Martin Loose and Spatz, Joachim P and Karsenti, Éric and Nédélec, François J}, journal = {Cell}, number = {3}, pages = {502 -- 513}, publisher = {Cell Press}, title = {{Chromatin shapes the mitotic spindle}}, doi = {10.1016/j.cell.2009.05.027}, volume = {138}, year = {2009}, } @article{1983, abstract = {During many cellular processes such as cell division, polarization and motility, the plasma membrane does not only represent a passive physical barrier, but also provides a highly dynamic platform for the interplay between lipids, membrane binding proteins and cytoskeletal elements. Even though many regulators of these interactions are known, their mutual interdependence appears to be highly complex and difficult to study in a living cell. Over the past few years, in vitro studies on membrane-cytoskeleton interactions using biomimetic membranes turned out to be extremely helpful to get better mechanistic insight into the dynamics of these processes. In this review, we discuss some of the recent developments using in vitro assays to dissect the role of the players involved: lipids in the membrane, proteins binding to membranes and proteins binding to membrane proteins. We also summarize advantages and disadvantages of supported lipid bilayers as model membrane.}, author = {Martin Loose and Schwille, Petra }, journal = {Journal of Structural Biology}, number = {1}, pages = {143 -- 151}, publisher = {Academic Press}, title = {{Biomimetic membrane systems to study cellular organization}}, doi = {10.1016/j.jsb.2009.03.016}, volume = {168}, year = {2009}, } @article{2067, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Genetics}, number = {4}, pages = {1699 -- 1701}, publisher = {Genetics Society of America}, title = {{Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster}}, doi = {10.1534/genetics.108.098004}, volume = {181}, year = {2009}, } @article{2068, abstract = {In Drosophila, there is a consistent deficit of male-biased genes on the X chromosome. It has been suggested that male-biased genes may evolve from initially unbiased genes as a result of increased expression levels in males. If transcription rates are limited, a large increase in expression in the testis may be harder to achieve for single-copy X-linked genes than for autosomal genes, because they are already hypertranscribed due to dosage compensation. This hypothesis predicts that the larger the increase in expression required to make a male-biased gene, the lower the chance of this being achievable if it is located on the X chromosome. Consequently, highly expressed male-biased genes should be located on the X chromosome less often than lowly expressed male-biased genes. This pattern is observed in our analysis of publicly available data, where microarray data or EST data are used to detect male-biased genes in D. melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome.}, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Journal of Molecular Evolution}, number = {5}, pages = {576 -- 583}, publisher = {Springer}, title = {{The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation?}}, doi = {10.1007/s00239-009-9235-4}, volume = {68}, year = {2009}, } @article{2069, abstract = {Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (NeX) is equal to three-quarters of the autosomal population size (NeA). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that NeX/NeA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when NeX/N eA > 3/4. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution.}, author = {Beatriz Vicoso and Charlesworth, Brian}, journal = {Evolution}, number = {9}, pages = {2413 -- 2426}, publisher = {Wiley-Blackwell}, title = {{Effective population size and the faster-X effect: An extended model}}, doi = {10.1111/j.1558-5646.2009.00719.x}, volume = {63}, year = {2009}, } @article{2070, abstract = {In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression levels of X-linked genes relative to autosomes accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. This review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and functional genomics that have substantially increased our understanding of the molecular mechanisms of dosage compensation and how it evolved. We review processes involved in sex chromosome evolution, and discuss the dynamic interaction between Y degeneration and the acquisition of dosage compensation. We compare mechanisms of dosage compensation and the origin of dosage compensation genes between different taxa and comment on sex chromosomes that apparently lack compensation mechanisms. Finally, we discuss how dosage compensation systems can also influence the evolution of well-established sex chromosomes.}, author = {Beatriz Vicoso and Bachtrog, Doris}, journal = {Chromosome Research}, number = {5}, pages = {585 -- 602}, publisher = {Springer}, title = {{Progress and prospects toward our understanding of the evolution of dosage compensation}}, doi = {10.1007/s10577-009-9053-y}, volume = {17}, year = {2009}, } @inproceedings{2094, abstract = {This paper introduces a data-driven representation and modeling technique for simulating non-linear heterogeneous soft tissue. It simplifies the construction of convincing deformable models by avoiding complex selection and tuning of physical material parameters, yet retaining the richness of non-linear heterogeneous behavior. We acquire a set of example deformations of a real object, and represent each of them as a spatially varying stress-strain relationship in a finite-element model. We then model the material by non-linear interpolation of these stress-strain relationships in strain-space. Our method relies on a simple-to-build capture system and an efficient run-time simulation algorithm based on incremental loading, making it suitable for interactive computer graphics applications. We present the results of our approach for several non-linear materials and biological soft tissue, with accurate agreement of our model to the measured data. }, author = {Bernd Bickel and Bac̈her, Moritz and Otaduy, Miguel A and Matusik, Wojciech and Pfister, Hanspeter and Groß, Markus S}, number = {3}, publisher = {ACM}, title = {{Capture and modeling of non-linear heterogeneous soft tissue}}, doi = {10.1145/1576246.1531395 }, volume = {28}, year = {2009}, } @article{2119, abstract = {Let (E, H, μ) be an abstract Wiener space and let DV : = V D, where D denotes the Malliavin derivative and V is a closed and densely defined operator from H into another Hilbert space under(H, {combining low line}). Given a bounded operator B on under(H, {combining low line}), coercive on the range over(R (V), -), we consider the operators A : = V* B V in H and under(A, {combining low line}) : = V V* B in under(H, {combining low line}), as well as the realisations of the operators L : = DV* B DV and under(L, {combining low line}) : = DV DV* B in Lp (E, μ) and Lp (E, μ ; under(H, {combining low line})) respectively, where 1 < p < ∞. Our main result asserts that the following four assertions are equivalent: (1)D (sqrt(L)) = D (DV) with {norm of matrix} sqrt(L) f {norm of matrix}p {minus tilde} {norm of matrix} DV f {norm of matrix}p for f ∈ D (sqrt(L));(2)under(L, {combining low line}) admits a bounded H∞-functional calculus on over(R (DV), -);(3)D (sqrt(A)) = D (V) with {norm of matrix} sqrt(A) h {norm of matrix} {minus tilde} {norm of matrix} V h {norm of matrix} for h ∈ D (sqrt(A));(4)under(A, {combining low line}) admits a bounded H∞-functional calculus on over(R (V), -). Moreover, if these conditions are satisfied, then D (L) = D (DV2) ∩ D (DA). The equivalence (1)-(4) is a non-symmetric generalisation of the classical Meyer inequalities of Malliavin calculus (where under(H, {combining low line}) = H, V = I, B = frac(1, 2) I). A one-sided version of (1)-(4), giving Lp-boundedness of the Riesz transform DV / sqrt(L) in terms of a square function estimate, is also obtained. As an application let -A generate an analytic C0-contraction semigroup on a Hilbert space H and let -L be the Lp-realisation of the generator of its second quantisation. Our results imply that two-sided bounds for the Riesz transform of L are equivalent with the Kato square root property for A. The boundedness of the Riesz transform is used to obtain an Lp-domain characterisation for the operator L.}, author = {Jan Maas and van Neerven, Jan M}, journal = {Journal of Functional Analysis}, number = {8}, pages = {2410 -- 2475}, publisher = {Academic Press}, title = {{Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces}}, doi = {10.1016/j.jfa.2009.07.001}, volume = {257}, year = {2009}, } @inproceedings{2136, abstract = {The local atomic structure of PbTiO3, BaTiO3, and KNbO3 perovskite-type crystals and K x Na1 − x NbO3 solid solutions in different phases is investigated using the angular dependence of the pre-edge structure of the Ti and Nb K X-ray absorption spectra and the EXAFS data. In noncubic phases, a considerable deviation of the local structure from the structure determined from diffraction data is observed only for the tetragonal phase of the BaTiO3 crystal. It is revealed that, in the cubic phase of niobates, the niobium atoms are characterized by significant displacements from the centrosymmetric positions along the threefold axes, so that they are close in the magnitude and the direction to the displacements in the low-temperatures rhombohedral phases.}, author = {Vedrinskiǐ, Rostislav V and Kraǐzman, V. L and Mikhail Lemeshko and Nazarenko, Elena S and Novakovich, Alexander A and Reznichenko, Larisa A and Fokin, Vladimir N and Shuvaeva, Victoria A}, number = {7}, pages = {1394 -- 1398}, publisher = {Springer}, title = {{Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data}}, doi = {10.1134/S106378340907018X}, volume = {51}, year = {2009}, } @article{2137, abstract = {Relying on the quantization rule of Raab and Friedrich [Phys. Rev. A (2009) in press], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecular ion. We also provide analytic estimates of the rotational constants of any such levels up to threshold for dissociation and obtain a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential.}, author = {Mikhail Lemeshko and Frierich, Bretislav}, journal = {Journal of Atomic and Molecular Sciences}, number = {1}, pages = {41 -- 47}, publisher = {Global Science Press}, title = {{Rotational structure of weakly bound molecular ions}}, doi = {10.4208/jams.101009.110209a}, volume = {1}, year = {2009}, } @article{2149, abstract = {We investigate the effects of a magnetic field on the dynamics of rotationally inelastic collisions of open-shell molecules (Σ2, Σ3, and Π2) with closed-shell atoms. Our treatment makes use of the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric [M. Lemeshko and B. Friedrich, J. Chem. Phys. 129, 024301 (2008)] and radiative fields [M. Lemeshko and B. Friedrich, Int. J. Mass. Spec. 280, 19 (2009)]. A magnetic field aligns the molecule in the space-fixed frame and thereby alters the effective shape of the diffraction target. This significantly affects the differential and integral scattering cross sections. We exemplify our treatment by evaluating the magnetic-field-dependent scattering characteristics of the He-CaH (XΣ+2), He-O2 (XΣ–3), and He-OH (XΠΩ2) systems at thermal collision energies. Since the cross sections can be obtained for different orientations of the magnetic field with respect to the relative velocity vector, the model also offers predictions about the frontal-versus-lateral steric asymmetry of the collisions. The steric asymmetry is found to be almost negligible for the He-OH system, weak for the He-CaH collisions, and strong for the He-O2. While odd ΔM transitions dominate the He-OH [J=3/2,f→J′,e/f] integral cross sections in a magnetic field parallel to the relative velocity vector, even ΔM transitions prevail in the case of the He-CaH (X2Σ+) and He-O2 (XΣ−3) collision systems. For the latter system, the magnetic field opens inelastic channels that are closed in the absence of the field. These involve the transitions N=1,J=0→N′, J′ with J′=N′.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {1}, publisher = {American Physical Society}, title = {{Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves}}, doi = {10.1103/PhysRevA.79.012718}, volume = {79}, year = {2009}, } @article{2150, abstract = {We examine the effects of a linearly polarized nonresonant radiative field on the dynamics of rotationally inelastic Na+ + N2 collisions at eV collision energies. Our treatment is based on the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric fields [M. Lemeshko, B. Friedrich, J. Chem. Phys. 129 (2008) 024301]. The nonresonant radiative field changes the effective shape of the target molecule by aligning it in the space-fixed frame. This markedly alters the differential and integral scattering cross-sections. As the cross-sections can be evaluated for a polarization of the radiative field collinear or perpendicular to the relative velocity vector, the model also offers predictions about steric asymmetry of the collisions.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {International Journal of Mass Spectrometry}, number = {1-3}, pages = {19 -- 25}, publisher = {Elsevier}, title = {{The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions}}, doi = {10.1016/j.ijms.2008.06.010 }, volume = {280}, year = {2009}, } @article{2192, abstract = {We develop an analytic model of thermal state-to-state rotationally inelastic collisions of asymmetric-top molecules with closed-shell atoms in electric fields and apply it to the Ar-H2O collision system. The predicted cross sections as well as the steric asymmetry of the collisions show at fields up to 150 kV/cm characteristic field-dependent features which can be experimentally tested. Particularly suitable candidates for such tests are the 000 → 220 and 101→ 221 channels, arising from the relaxation of the field-free selection rules due to the hybridization of J states by the field. Averaging over the M' product channels is found to largely obliterate the orientation effects brought about by the field.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Journal of Physical Chemistry A}, number = {52}, pages = {15055 -- 15063}, publisher = {American Chemical Society}, title = {{Model analysis of rotationally inelastic Ar + H2O scattering in an electric field}}, doi = {10.1021/jp9051598}, volume = {113}, year = {2009}, } @article{2191, abstract = {By making use of the quantization rule of Raab and Friedrich [Phys. Rev. A 78, 022707 (2008)], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecule and the rotational constants of any such levels up to the threshold, and provide a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential and are applicable to halo molecules. }, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {5}, publisher = {American Physical Society}, title = {{Rotational and rotationless states of weakly bound molecules}}, doi = {10.1103/PhysRevA.79.050501}, volume = {79}, year = {2009}, } @article{2193, abstract = {We show that weakly bound molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations applied to the Rb2 and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wave function and, by inversion, also the long-range part of the molecular potential.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Physical Review Letters}, number = {5}, publisher = {American Physical Society}, title = {{Probing weakly bound molecules with nonresonant light}}, doi = {10.1103/PhysRevLett.103.053003}, volume = {103}, year = {2009}, } @article{226, abstract = {The Manin conjecture is established for a split singular del Pezzo surface of degree four, with singularity type A4.}, author = {Timothy Browning and Derenthal, Ulrich}, journal = {Annales de l'Institut Fourier}, number = {3}, pages = {1231 -- 1265}, publisher = {Association des Annales de l'Institut Fourier}, title = {{Manin's conjecture for a quartic del Pezzo surface with A4 singularity}}, doi = {10.5802/aif.2462}, volume = {59}, year = {2009}, } @book{227, abstract = {Winner of the Ferran Sunyer i Balaguer Prize 2009. First attempt to systematically survey the range of available tools from analytic number theory that can be applied to study the density of rational points on projective varieties. Designed to rapidly guide the reader to the many areas of ongoing research in the domain. Provides an extensive bibliography.}, author = {Browning, Timothy D}, isbn = {9-783-0346-0128-3}, issn = {2296-505X}, pages = {XIII, 160}, publisher = {Birkhäuser Basel}, title = {{Quantitative Arithmetic of Projective Varieties}}, doi = {10.1007/978-3-0346-0129-0}, volume = {277}, year = {2009}, } @article{228, abstract = {Let X be a projective non-singular quartic hypersurface of dimension 39 or more, which is defined over . We show that X() is non-empty provided that X() is non-empty and X has p-adic points for every prime p.}, author = {Timothy Browning and Heath-Brown, Roger}, journal = {Journal fur die Reine und Angewandte Mathematik}, number = {629}, pages = {37 -- 88}, publisher = {Walter de Gruyter}, title = {{Rational points on quartic hypersurfaces}}, doi = {10.1515/CRELLE.2009.026}, year = {2009}, } @article{229, abstract = {An upper bound of the expected order of magnitude is established for the number of ℚ-rational points of bounded height on Châtelet surfaces defined over ℚ.}, author = {Timothy Browning}, journal = {Mathematische Annalen}, number = {1}, pages = {41 -- 50}, publisher = {Springer Nature}, title = {{Linear growth for Châtelet surfaces}}, doi = {10.1007/s00208-009-0383-z}, volume = {346}, year = {2009}, } @article{230, abstract = {The Manin conjecture is established for a split singular cubic surface in ℙ 3, with singularity type D 5.}, author = {Timothy Browning and Derenthal, Ulrich}, journal = {International Mathematics Research Notices}, number = {14}, pages = {2620 -- 2647}, publisher = {Oxford University Press}, title = {{Manin's conjecture for a cubic surface with D 5 singularity}}, doi = {10.1093/imrn/rnp029}, volume = {2009}, year = {2009}, } @book{2326, abstract = {Research into the stability of matter has been one of the most successful chapters in mathematical physics, and is a prime example of how modern mathematics can be applied to problems in physics. A unique account of the subject, this book provides a complete, self-contained description of research on the stability of matter problem. It introduces the necessary quantum mechanics to mathematicians, and aspects of functional analysis to physicists. The topics covered include electrodynamics of classical and quantized fields, Lieb-Thirring and other inequalities in spectral theory, inequalities in electrostatics, stability of large Coulomb systems, gravitational stability of stars, basics of equilibrium statistical mechanics, and the existence of the thermodynamic limit. The book is an up-to-date account for researchers, and its pedagogical style makes it suitable for advanced undergraduate and graduate courses in mathematical physics.}, author = {Lieb, Élliott and Seiringer, Robert}, isbn = {978-0-521-19118-0 }, pages = {310}, publisher = {Cambridge University Press}, title = {{The Stability of Matter in Quantum Mechanics}}, year = {2009}, } @inproceedings{2330, author = {Hainzl, Christian and Robert Seiringer}, pages = {101 -- 104}, publisher = {American Mathematical Society}, title = {{A linear criterion for solutions of non-linear equations, with application to the BCS gap equation}}, doi = {10.1090/conm/500/09823}, volume = {500}, year = {2009}, } @article{2384, abstract = {We prove the Lee-Huang-Yang formula for the ground state energy of the 3D Bose gas with repulsive interactions described by the exponential function, in a simultaneous limit of weak coupling and high density. In particular, we show that the Bogoliubov approximation is exact in an appropriate parameter regime, as far as the ground state energy is concerned.}, author = {Giuliani, Alessandro and Robert Seiringer}, journal = {Journal of Statistical Physics}, number = {5-6}, pages = {915 -- 934}, publisher = {Springer}, title = {{The ground state energy of the weakly interacting Bose gas at high density}}, doi = {10.1007/s10955-009-9718-0}, volume = {135}, year = {2009}, } @article{2385, abstract = {We consider an ultracold rotating Bose gas in a harmonic trap close to the critical angular velocity, so that the system can be considered to be confined to the lowest Landau level. With this assumption we prove that the Gross-Pitaevskii energy functional accurately describes the ground-state energy of the corresponding N -body Hamiltonian with contact interaction provided the total angular momentum L is much less than N2. While the Gross-Pitaevskii energy is always an obvious variational upper bound to the ground-state energy, a more refined analysis is needed to establish it as an exact lower bound. We also discuss the question of Bose-Einstein condensation in the parameter range considered. Coherent states together with inequalities in spaces of analytic functions are the main technical tools.}, author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {6}, publisher = {American Physical Society}, title = {{Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime}}, doi = {10.1103/PhysRevA.79.063626}, volume = {79}, year = {2009}, } @article{2386, abstract = {We prove exponential decay of the off-diagonal correlation function in the two-dimensional homogeneous Bose gas when a2 ρ is small and the temperature T satisfies T> 4πρ ln | ln (a2 ρ) |. Here, a is the scattering length of the repulsive interaction potential and ρ is the density. To the leading order in a2 ρ, this bound agrees with the expected critical temperature for superfluidity. In the three-dimensional Bose gas, exponential decay is proved when T- Tc (0) Tc (0) >5 a ρ1/3, where Tc (0) is the critical temperature of the ideal gas. While this condition is not expected to be sharp, it gives a rigorous upper bound on the critical temperature for Bose-Einstein condensation.}, author = {Robert Seiringer and Ueltschi, Daniel}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {1}, publisher = {American Physical Society}, title = {{Rigorous upper bound on the critical temperature of dilute Bose gases}}, doi = {10.1103/PhysRevB.80.014502}, volume = {80}, year = {2009}, } @article{2387, abstract = {We consider a system of trapped spinless bosons interacting with a repulsive potential and subject to rotation. In the limit of rapid rotation and small scattering length, we rigorously show that the ground state energy converges to that of a simplified model Hamiltonian with contact interaction projected onto the Lowest Landau Level. This effective Hamiltonian models the bosonic analogue of the Fractional Quantum Hall Effect (FQHE). For a fixed number of particles, we also prove convergence of states; in particular, in a certain regime we show convergence towards the bosonic Laughlin wavefunction. This is the first rigorous justification of the effective FQHE Hamiltonian for rapidly rotating Bose gases. We review previous results on this effective Hamiltonian and outline open problems.}, author = {Lewin, Mathieu and Robert Seiringer}, journal = {Journal of Statistical Physics}, number = {5}, pages = {1040 -- 1062}, publisher = {Springer}, title = {{Strongly correlated phases in rapidly rotating Bose gases}}, doi = {10.1007/s10955-009-9833-y}, volume = {137}, year = {2009}, } @article{2388, abstract = {This paper provides self-contained proof of a theorem relating probabilistic coherence of forecasts to their non-domination by rival forecasts with respect to any proper scoring rule. The theorem recapitulates insights achieved by other investigators, and clarifies the connection of coherence and proper scoring rules to Bregman divergence.}, author = {Predd, Joel B and Robert Seiringer and Lieb, Élliott H and Osherson, Daniel N and Poor, Harold V and Kulkarni, Sanjeev R}, journal = {IEEE Transactions on Information Theory}, number = {10}, pages = {4786 -- 4792}, publisher = {IEEE}, title = {{Probabilistic coherence and proper scoring rules}}, doi = {10.1109/TIT.2009.2027573}, volume = {55}, year = {2009}, } @article{2434, abstract = {For a planar point set we consider the graph whose vertices are the crossing-free straight-line spanning trees of the point set, and two such spanning trees are adjacent if their union is crossing-free. An upper bound on the diameter of this graph implies an upper bound on the diameter of the flip graph of pseudo-triangulations of the underlying point set. We prove a lower bound of Ω(logn/loglogn) for the diameter of the transformation graph of spanning trees on a set of n points in the plane. This nearly matches the known upper bound of O(logn). If we measure the diameter in terms of the number of convex layers k of the point set, our lower bound construction is tight, i.e., the diameter is in Ω(logk) which matches the known upper bound of O(logk). So far only constant lower bounds were known.}, author = {Buchin, Kevin and Razen, Andreas and Uno, Takeaki and Uli Wagner}, journal = {Computational Geometry: Theory and Applications}, number = {8}, pages = {724 -- 730}, publisher = {Elsevier}, title = {{Transforming spanning trees: A lower bound}}, doi = {10.1016/j.comgeo.2008.03.005}, volume = {42}, year = {2009}, } @inproceedings{2433, abstract = {Let EMBEDk→d be the following algorithmic problem: Given a finite simplicial complex K of dimension at most k, does there exist a (piecewise linear) embedding of K into ℝd? Known results easily imply polynomiality of EMBEDk→2 (k = 1, 2; the case k = 1, d = 2 is graph planarity) and of EMBEDk→2k for all k ≥ 3 (even if k is not considered fixed). We show that the celebrated result of Novikov on the algorithmic unsolvability of recognizing the 5-sphere implies that EMBED d→d and EMBED(d-1)→d are undecidable for each d ≥ 5. Our main result is NP-hardness of EMBED2→4 and, more generally, of EMBEDk→d for all k, d with d ≥ 4 and d ≥ k ≥ (2d - 2)/3.}, author = {Matoušek, Jiří and Martin Tancer and Uli Wagner}, pages = {855 -- 864}, publisher = {SIAM}, title = {{Hardness of embedding simplicial complexes in ℝd}}, year = {2009}, } @article{2498, abstract = {Activation of G protein-gated inwardly-rectifying K+ (GIRK or Kir3) channels by metabotropic gamma-aminobutyric acid (B) (GABAB) receptors is an essential signalling pathway controlling neuronal excitability and synaptic transmission in the brain. To investigate the relationship between GIRK channel subunits and GABAB receptors in cerebellar Purkinje cells at post- and pre-synaptic sites, we used biochemical, functional and immunohistochemical techniques. Co-immunoprecipitation analysis demonstrated that GIRK subunits are co-assembled with GABAB receptors in the cerebellum. Immunoelectron microscopy showed that the subunit composition of GIRK channels in Purkinje cell spines is compartment-dependent. Thus, at extrasynaptic sites GIRK channels are formed by GIRK1/GIRK2/GIRK3, post-synaptic densities contain GIRK2/GIRK3 and dendritic shafts contain GIRK1/GIRK3. The post-synaptic association of GIRK subunits with GABAB receptors in Purkinje cells is supported by the subcellular regulation of the ion channel and the receptor in mutant mice. At pre-synaptic sites, GIRK channels localized to parallel fibre terminals are formed by GIRK1/GIRK2/GIRK3 and co-localize with GABAB receptors. Consistent with this morphological evidence we demonstrate their functional interaction at axon terminals in the cerebellum by showing that GIRK channels play a role in the inhibition of glutamate release by GABAB receptors. The association of GIRK channels and GABA B receptors with excitatory synapses at both post- and pre-synaptic sites indicates their intimate involvement in the modulation of glutamatergic neurotransmission in the cerebellum.}, author = {Fernández-Alacid, Laura and Aguado, Carolina and Ciruela, Francisco and Martín, Ricardo J and Colón, José and Cabañero, María José and Gassmann, Martin and Watanabe, Masahiko and Ryuichi Shigemoto and Wickman, Kevin D and Bettler, Bernhard and Sánchez-Prieto, José and Luján, Rafael}, journal = {Journal of Neurochemistry}, number = {4}, pages = {1363 -- 1376}, publisher = {Wiley-Blackwell}, title = {{ Subcellular compartment-specific molecular diversity of pre- and post-synaptic GABAB-activated GIRK channels in Purkinje cells}}, doi = {10.1111/j.1471-4159.2009.06229.x}, volume = {110}, year = {2009}, } @article{2500, abstract = {To examine the intrasynaptic arrangement of postsynaptic receptors in relation to the functional role of the synapse,we quantitatively analyzed the two-dimensional distribution of AMPA and NMDA receptors (AMPARs and NMDARs, respectively) using SDS-digested freeze-fracture replica labeling (SDS-FRL) and assessed the implication of distribution differences on the postsynaptic responses by simulation. In the dorsal lateral geniculate nucleus, corticogeniculate (CG) synapses were twice as large as retinogeniculate (RG) synapses but expressed similar numbers of AMPARs. Two-dimensional views of replicas revealed that AMPARs form microclusters in both synapses to a similar extent, resulting in larger AMPAR-lacking areas in the CG synapses. Despite the broad difference in the AMPAR distribution within a synapse, our simulations based on the actual receptor distributions suggested that the AMPAR quantal response at individual RG synapses is only slightly larger in amplitude, less variable, and faster in kinetics than that at CG synapses having a similar number of the receptors. NMDARs at the CG synapses were expressed twice as many as those in the RG synapses. Electrophysiological recordings confirmed a larger contribution of NMDAR relative to AMPAR-mediated responses in CG synapses. We conclude that synapse size and the density and distribution of receptors have minor influences on quantal responses and that the number of receptors acts as a predominant postsynaptic determinant of the synaptic strength mediated by both the AMPARs and NMDARs. }, author = {Tarusawa, Etsuko and Matsui, Ko and Budisantoso, Timotheus and Molnár, Elek and Watanabe, Masahiko and Matsui, Minoru and Fukazawa, Yugo and Ryuichi Shigemoto}, journal = {Journal of Neuroscience}, number = {41}, pages = {12896 -- 12908}, publisher = {Society for Neuroscience}, title = {{Input-specific intrasynaptic arrangements of ionotropic glutamate receptors and their impact on postsynaptic responses}}, doi = {10.1523/JNEUROSCI.6160-08.2009}, volume = {29}, year = {2009}, } @article{2499, abstract = {G protein-coupled receptors (GPCRs) have critical functions in intercellular communication. Although a wide range of different receptors have been identified in the same cells, the mechanism by which signals are integrated remains elusive. The ability of GPCRs to form dimers or larger hetero-oligomers is thought to generate such signal integration. We examined the molecular mechanisms responsible for the GABAB receptor-mediated potentiation of the mGlu receptor signalling reported in Purkinje neurons. We showed that this effect does not require a physical interaction between both receptors. Instead, it is the result of a more general mechanism in which the βγ subunits produced by the Gi-coupled GABAB receptor enhance the mGlu-mediated Gq response. Most importantly, this mechanism could be generally applied to other pairs of Gi- and Gq-coupled receptors and the signal integration varied depending on the time delay between activation of each receptor. Such a mechanism helps explain specific properties of cells expressing two different Gi- and Gq-coupled receptors activated by a single transmitter, or properties of GPCRs naturally coupled to both types of the G protein.}, author = {Rives, Marie L and Vol, Claire and Fukazawa, Yugo and Tinel, Norbert and Trinquet, Eric and Ayoub, Mohammed A and Ryuichi Shigemoto and Pin, Jean-Philippe and Prezèau, Laurent}, journal = {EMBO Journal}, number = {15}, pages = {2195 -- 2208}, publisher = {Wiley-Blackwell}, title = {{Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration}}, doi = {10.1038/emboj.2009.177}, volume = {28}, year = {2009}, } @article{2502, abstract = {In order to acquire phase-contrast images with adequate contrast, conventional TEM requires large amount of defocus. Increasing the defocus improves the low-frequency components but attenuates the high-frequency ones. On the other hand, Zernike phase-contrast TEM (ZPC-TEM) can recover low-frequency components without losing the high-frequency ones under in-focus conditions. ZPC-TEM however, has another problem, especially in imaging of complex biological specimens such as cells and tissues; strong halos appear around specimen structures, and these halos hinder the interpretation of images. Due to this problem, the application of ZPC-TEM has been restricted to imaging of smaller particles. In order to improve the halo appearance, we fabricated a new quarter-wave thin film phase-plate with a smaller central hole and tested it on vitreous biological specimens. ZPC-TEM with the new plate could successfully visualize, in in-focus images, the intracellular fine features of cultured cells and brain tissues. This result indicates that reduction of the central hole diameter makes ZPC-TEM applicable on size scales ranging from protein particles to tissue sections. The application of ZPC-TEM to vitreous biological specimens will be a powerful method to advance the new field of imaging science for ultrastructures in close-to-physiological state.}, author = {Fukuda, Yoshiyuki and Fukazawa, Yugo and Danev, Radostin S and Ryuichi Shigemoto and Nagayama, Kuniaki}, journal = {Journal of Structural Biology}, number = {3}, pages = {476 -- 484}, publisher = {Academic Press}, title = {{Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens}}, doi = {10.1016/j.jsb.2009.08.011}, volume = {168}, year = {2009}, } @article{2501, abstract = {The brain-specific immediate early gene Arc/Arg3.1 is induced in response to a variety of stimuli, including sensory and behavior-linked neural activity. Here we report the generation of transgenic mice, termed TgArc/Arg3.1-d4EGFP, expressing a 4-h half-life form of enhanced green fluorescent protein (d4EGFP) under the control of the Arc/Arg3.1 promoter. We show that d4EGFP-mediated fluorescence faithfully reports Arc/Arg3.1 induction in response to physiological, pathological and pharmacological stimuli, and that this fluorescence permits electrical recording from activated neurons in the live mouse. Moreover, the fluorescent Arc/Arg3.1 indicator revealed activity changes in circumscribed brain areas in distinct modes of stress and in a mouse model of Alzheimer's disease. These findings identify the TgArc/Arg3.1-d4EGFP mouse as a versatile tool to monitor Arc/Arg3.1 induction in neural circuits, both in vitro and in vivo.}, author = {Grinevich, Valery V and Kolleker, Alexander and Eliava, Marina I and Takada, Naoki and Takuma, Hiroshi and Fukazawa, Yugo and Ryuichi Shigemoto and Kuhl, Dietmar and Waters, Jack and Seeburg, Peter H and Osten, Pavel}, journal = {Journal of Neuroscience Methods}, number = {1}, pages = {25 -- 36}, publisher = {Elsevier}, title = {{Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo}}, doi = {10.1016/j.jneumeth.2009.07.015}, volume = {184}, year = {2009}, } @article{2684, abstract = {Calcium-activated potassium channels have been shown to be critically involved in neuronal function, but an elucidation of their detailed roles awaits identification of the microdomains where they are located. This study was undertaken to unravel the precise subcellular distribution of the large-conductance calcium-activated potassium channels (called BK, KCa1.1, or Slo1) in the somatodendritic compartment of cerebellar Purkinje cells by means of postembedding immunogold cytochemistry and SDS-digested freeze-fracture replica labeling (SDS-FRL). We found BK channels to be unevenly distributed over the Purkinje cell plasma membrane. At distal dendritic compartments, BK channels were scattered over the plasma membrane of dendritic shafts and spines but absent from postsynaptic densities. At the soma and proximal dendrites, BK channels formed two distinct pools. One pool was scattered over the plasma membrane, whereas the other pool was clustered in plasma membrane domains overlying subsurface cisterns. The labeling density ratio of clustered to scattered channels was about 60:1, established in SDS-FRL. Subsurface cisterns, also called hypolemmal cisterns, are subcompartments of the endoplasmic reticulum likely representing calciosomes that unload and refill Ca2+ independently. Purkinje cell subsurface cisterns are enriched in inositol 1,4,5-triphosphate receptors that mediate the effects of several neurotransmitters, hormones, and growth factors by releasing Ca2+ into the cytosol, generating local Ca2+ sparks. Such increases in cytosolic [Ca2+] may be sufficient for BK channel activation. Clustered BK channels in the plasma membrane may thus participate in building a functional unit (plasmerosome) with the underlying calciosome that contributes significantly to local signaling in Purkinje cells.}, author = {Walter Kaufmann and Ferraguti, Francesco and Fukazawa, Yugo and Kasugai, Yu and Ryuichi Shigemoto and Laake, Petter and Sexton, Joseph A and Ruth, Peter and Wietzorrek, Georg and Knaus, Hans G and Storm, Johan F and Ottersen, Ole P}, journal = {Journal of Comparative Neurology}, number = {2}, pages = {215 -- 230}, publisher = {Wiley-Blackwell}, title = {{Large-conductance calcium-activated potassium channels in Purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains}}, doi = {10.1002/cne.22066}, volume = {515}, year = {2009}, } @article{2680, abstract = {GABA B receptor subtypes are based on the subunit isoforms GABA B1a and GABA B1b, which associate with GABA B2 subunits to form pharmacologically indistinguishable GABA B(1a,2) and GABA B(1b,2) receptors. Studies with mice selectively expressing GABA B1a or GABA B1b subunits revealed that GABA B(1a,2) receptors are more abundant than GABA B(1b,2) receptors at glutamatergic terminals. Accordingly, it was found that GABA B(1a,2) receptors are more efficient than GABA B(1b,2) receptors in inhibiting glutamate release when maximally activated by exogenous application of the agonist baclofen. Here, we used a combination of genetic, ultrastructural and electrophysiological approaches to analyze to what extent GABA B(1a,2) and GABA B(1b,2) receptors inhibit glutamate release in response to physiological activation. We first show that at hippocampal mossy fiber (MF)-CA3 pyramidal neuron synapses more GABA B1a than GABA B1b protein is present at presynaptic sites, consistent with the findings at other glutamatergic synapses. In the presence of baclofen at concentrations ≥1 μM, both GABA B(1a,2) and GABA B(1b,2) receptors contribute to presynaptic inhibition of glutamate release. However, at lower concentrations of baclofen, selectively GABA B(1a,2) receptors contribute to presynaptic inhibition. Remarkably, exclusively GABA B(1a,2) receptors inhibit glutamate release in response to synaptically released GABA. Specifically, we demonstrate that selectively GABA B(1a,2) receptors mediate heterosynaptic depression of MF transmission, a physiological phenomenon involving transsynaptic inhibition of glutamate release via presynaptic GABA B receptors. Our data demonstrate that the difference in GABA B1a and GABA B1b protein levels at MF terminals is sufficient to produce a strictly GABA B1a-specific effect under physiological conditions. This consolidates that the differential subcellular localization of the GABA B1a and GABA B1b proteins is of regulatory relevance. }, author = {Guetg, Nicole and Seddik, Riad and Vigot, Réjan and Tureček, Rostislav and Gassmann, Martin and Vogt, Kaspar E and Bräuner-Osborne, Hans and Ryuichi Shigemoto and Kretz, Oliver and Frotscher, Michael and Kulik, Ákos and Bettler, Bernhard}, journal = {Journal of Neuroscience}, number = {5}, pages = {1414 -- 1423}, publisher = {Society for Neuroscience}, title = {{The GABA B1a isoform mediates heterosynaptic depression at hippocampal mossy fiber synapses}}, doi = {10.1523/JNEUROSCI.3697-08.2009}, volume = {29}, year = {2009}, } @article{2683, abstract = {GABAb receptor (GABAbR)-mediated suppression of glutamate release is critical for limiting glutamatergic transmission across the central nervous system (CNS). Here we show that, upon tetanic stimulation of afferents to lateral amygdala, presynaptic GABAbR-mediated inhibition only occurs in glutamatergic inputs to principle neurons (PNs), not to interneurons (INs), despite the presence of GABAbR in terminals to both types of neurons. The selectivity is caused by differential local GABA accumulation; it requires GABA reuptake and parallels distinct spatial distributions of presynaptic GABAbR in terminals to PNs and INs. Moreover, GABAbR-mediated suppression of theta-burst-induced long-term potentiation (LTP) occurs only in the inputs to PNs, not to INs. Thus, target-cell-specific control of glutamate release by presynaptic GABAbR orchestrates the inhibitory dominance inside amygdala and might contribute to prevention of nonadaptive defensive behaviors.}, author = {Pan, Bingxing and Dong, Yu-Lin and Ito, Wataru and Yanagawa, Yuchio and Ryuichi Shigemoto and Morozov, Alexei A}, journal = {Neuron}, number = {6}, pages = {917 -- 929}, publisher = {Elsevier}, title = {{Selective gating of glutamatergic inputs to excitatory neurons of amygdala by presynaptic GABAb receptor}}, doi = {10.1016/j.neuron.2009.01.029}, volume = {61}, year = {2009}, } @article{2682, abstract = {The living cell imaging using a two-photon microscope using gold nanoplates and nanoparticle aggregates was demonstrated. The dimensions of the nanoplates were determined through scanning electron microscopy (SEM) and atomic force microscopy. The height of a 100 nm base-length nanotriangle was around 10 nm, while the height of 300 nm base-length nanotriangle was around 12 nm. A spectrophotometer was also used to determine the extinction spectra of gold nanoparticle colloids. Two-photon-induced photoluminescence (TPIPL) under far-field excitation was tested for gold nanoplates on a glass substrate using two-photon laser scanning microscopy (TPLSM). It was observed that living-cell microscopic imaging can be carried out with TPIPL from gold nanoplates and aggregated nanosphere. This method provided a platform for developing tools for biological and biomedical studies.}, author = {Jiang, Yuqiang and Horimoto, Noriko N and Imura, Kohei and Matsui, Ko and Ryuichi Shigemoto}, journal = {Advanced Materials}, number = {22}, pages = {2309 -- 2313}, publisher = {Wiley-Blackwell}, title = {{Bioimaging with two-photon-induced luminescence from triangular nanoplates and nanoparticle aggregates of gold}}, doi = {10.1002/adma.200802312}, volume = {21}, year = {2009}, } @article{2685, abstract = {Conduction velocity (CV) of myelinated axons has been shown to be regulated by oligodendrocytes even after myelination has been completed. However, how myelinating oligodendrocytes regulate CV, and what the significance of this regulation is for normal brain function remain unknown. To address these questions, we analyzed a transgenic mouse line harboring extra copies of the myelin proteolipid protein 1 (plp1) gene (plp1tg/- mice) at 2 months of age. At this stage, the plp1tg/- mice have an unaffected myelin structure with a normally appearing ion channel distribution, but the CV in all axonal tracts tested in the CNS is greatly reduced. We also found decreased axonal diameters and slightly abnormal paranodal structures, both of which can be a cause for the reduced CV. Interestingly the plp1tg/- mice showed altered anxiety-like behaviors, reduced prepulse inhibitions, spatial learning deficits and working memory deficit, all of which are schizophrenia-related behaviors. Our results implicate that abnormalities in the neuron-glia interactions at the paranodal junctions can result in reduced CV in the CNS, which then induces behavioral abnormalities related to schizophrenia.}, author = {Tanaka, Hisataka and Ma, Jianmei and Tanaka, Kenji F and Takao, Keizo and Komada, Munekazu and Tanda, Koichi and Suzuki, Ayaka and Ishibashi, Tomoko and Baba, Hiroko and Isa, Tadashi and Ryuichi Shigemoto and Ono, Katsuhiko and Miyakawa, Tsuyoshi and Ikenaka, Kazuhiro}, journal = {Journal of Neuroscience}, number = {26}, pages = {8363 -- 8371}, publisher = {Society for Neuroscience}, title = {{Mice with altered myelin proteolipid protein gene expression display cognitive deficits accompanied by abnormal neuron-glia interactions and decreased conduction velocities}}, doi = {10.1523/JNEUROSCI.3216-08.2009}, volume = {29}, year = {2009}, } @article{2686, abstract = {Channelrhodopsin-2 (ChR2), one of the archea-type rhodopsins from green algae, is a potentially useful optogenetic tool for restoring vision in patients with photoreceptor degeneration, such as retinitis pigmentosa. If the ChR2 gene is transferred to retinal ganglion cells (RGCs), which send visual information to the brain, the RGCs may be repurposed to act as photoreceptors. In this study, by using a transgenic rat expressing ChR2 specifically in the RGCs under the regulation of a Thy-1.2 promoter, we tested the possibility that direct photoactivation of RGCs could restore effective vision. Although the contrast sensitivities of the optomotor responses of transgenic rats were similar to those observed in the wild-type rats, they were enhanced for visual stimuli of low-spatial frequency after the degeneration of native photoreceptors. This result suggests that the visual signals derived from the ChR2-expressing RGCs were reinterpreted by the brain to form behavior-related vision.}, author = {Tomita, Hiroshi and Sugano, Eriko and Fukazawa, Yugo and Isago, Hitomi and Sugiyama, Yuka and Hiroi, Teru and Ishizuka, Toru and Mushiake, Hajime and Kato, Megumi and Hirabayashi, Masumi and Ryuichi Shigemoto and Yawo, Hiromu and Tamai, Makoto}, journal = {PLoS One}, number = {11}, publisher = {Public Library of Science}, title = {{Visual properties of transgenic rats harboring the channelrhodopsin-2 gene regulated by the thy-1.2 promoter}}, doi = {10.1371/journal.pone.0007679}, volume = {4}, year = {2009}, } @article{2703, abstract = {We consider N×N Hermitian random matrices with i.i.d. entries. The matrix is normalized so that the average spacing between consecutive eigenvalues is of order 1/N. We study the connection between eigenvalue statistics on microscopic energy scales η≪1 and (de)localization properties of the eigenvectors. Under suitable assumptions on the distribution of the single matrix elements, we first give an upper bound on the density of states on short energy scales of order η∼log N/N. We then prove that the density of states concentrates around the Wigner semicircle law on energy scales η≫N−2/3. We show that most eigenvectors are fully delocalized in the sense that their ℓp-norms are comparable with N1/p−1/2 for p≥2, and we obtain the weaker bound N2/3(1/p−1/2) for all eigenvectors whose eigenvalues are separated away from the spectral edges. We also prove that, with a probability very close to one, no eigenvector can be localized. Finally, we give an optimal bound on the second moment of the Green function. }, author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer}, journal = {Annals of Probability}, number = {3}, pages = {815 -- 852}, publisher = {Institute of Mathematical Statistics}, title = {{Semicircle law on short scales and delocalization of eigenvectors for Wigner random matrices}}, doi = {10.1214/08-AOP421}, volume = {37}, year = {2009}, } @article{2759, abstract = {We consider the evolution of N bosons interacting with a repulsive short range pair potential in three dimensions. The potential is scaled according to the Gross-Pitaevskii scaling, i.e. it is given by N 2 V(N(x i - x j )). We monitor the behaviour of the solution to the N-particle Schrödinger equation in a spatial window where two particles are close to each other. We prove that within this window a short-scale interparticle structure emerges dynamically. The local correlation between the particles is given by the two-body zero energy scattering mode. This is the characteristic structure that was expected to form within a very short initial time layer and to persist for all later times, on the basis of the validity of the Gross-Pitaevskii equation for the evolution of the Bose-Einstein condensate. The zero energy scattering mode emerges after an initial time layer where all higher energy modes disperse out of the spatial window. We can prove the persistence of this structure up to sufficiently small times before three-particle correlations could develop.}, author = {László Erdös and Michelangeli, Alessandro and Schlein, Benjamin}, journal = {Communications in Mathematical Physics}, number = {3}, pages = {1171 -- 1210}, publisher = {Springer}, title = {{Dynamical formation of correlations in a Bose-Einstein condensate}}, doi = {10.1007/s00220-009-0828-y}, volume = {289}, year = {2009}, } @article{2758, abstract = {We consider N × N Hermitian random matrices with independent identical distributed entries. The matrix is normalized so that the average spacing between consecutive eigenvalues is of order 1/N. Under suitable assumptions on the distribution of the single matrix element, we prove that, away from the spectral edges, the density of eigenvalues concentrates around the Wigner semicircle law on energy scales n ≫ N -1 (log N) 8 . Up to the logarithmic factor, this is the smallest energy scale for which the semicircle law may be valid. We also prove that for all eigenvalues away from the spectral edges, the -tempℓ∞-norm of the corresponding eigenvectors is of order O(N -1/2), modulo logarithmic corrections. The upper bound O(N -1/2) implies that every eigenvector is completely delocalized, i.e., the maximum size of the components of the eigenvector is of the same order as their average size. In the Appendix, we include a lemma by J. Bourgain which removes one of our assumptions on the distribution of the matrix elements.}, author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {641 -- 655}, publisher = {Springer}, title = {{Local semicircle law and complete delocalization for Wigner random matrices}}, doi = {10.1007/s00220-008-0636-9}, volume = {287}, year = {2009}, } @article{2757, abstract = {We propose a new approach for the study of the time evolution of a factorized N-particle bosonic wave function with respect to a mean-field dynamics with a bounded interaction potential. The new technique, which is based on the control of the growth of the correlations among the particles, leads to quantitative bounds on the difference between the many-particle Schrödinger dynamics and the one-particle nonlinear Hartree dynamics. In particular the one-particle density matrix associated with the solution to the N-particle Schrödinger equation is shown to converge to the projection onto the one-dimensional sub-space spanned by the solution to the Hartree equation with a speed of convergence of order 1/N for all fixed times.}, author = {László Erdös and Schlein, Benjamin}, journal = {Journal of Statistical Physics}, number = {5-6}, pages = {859 -- 870}, publisher = {Springer}, title = {{Quantum dynamics with mean field interactions: A new approach}}, doi = {10.1007/s10955-008-9570-7}, volume = {134}, year = {2009}, } @article{2760, author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer}, journal = {Journal of the American Mathematical Society}, number = {4}, pages = {1099 -- 1156}, publisher = {American Mathematical Society}, title = {{Rigorous derivation of the gross-pitaevskii equation with a large interaction potential}}, doi = {10.1090/S0894-0347-09-00635-3}, volume = {22}, year = {2009}, } @inproceedings{2797, abstract = {In pipe flow at low Reynolds number, decay of localized disturbances is observed. As the Reynolds number is increased, the question emerges whether the life time of these disturbances diverges at a finite Reynolds number or remains transient. In the current investigation we determine their life time quantitatively from pressure measurements, while in previous investigations the distance over which a structure survives has been determined. The obtained results confirm that the life time of localized disturbances does not diverge in the range of Reynolds numbers covered in the current experiment.}, author = {Kuik, Dirk J and Poelma, Christian and Björn Hof and Westerweel, Jerry}, pages = {145 -- 148}, publisher = {Springer}, title = {{Quantitative measurement of the life time of turbulence in pipe flow}}, doi = {10.1007/978-3-642-03085-7_36}, volume = {132}, year = {2009}, } @article{2796, abstract = {As reported in a number of recent studies, turbulence in pipe flow is transient for Re<2000 and the flow eventually always returns to the laminar state. Generally, the lifetime of turbulence has been observed to increase rapidly with Reynolds number but there is currently no accord on the exact scaling behaviour. In particular, it is not clear whether a critical point exists where turbulence becomes sustained or if it remains transient. We here aim to clarify if these conflicting results may have been caused by the different experimental and numerical protocols used to trigger turbulence in these studies.}, author = {de Lózar, Alberto and Björn Hof}, journal = {Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences}, number = {1888}, pages = {589 -- 599}, publisher = {Royal Society of London}, title = {{An experimental study of the decay of turbulent puffs in pipe flow}}, doi = {10.1098/rsta.2008.0199}, volume = {367}, year = {2009}, } @article{2868, abstract = {Plants exhibit an amazing developmental flexibility. Plant embryogenesis results in the establishment of a simple apical-basal axis represented by apical shoot and basal root meristems. Later, during postembryonic growth, shaping of the plant body continues by the formation and activation of numerous adjacent meristems that give rise to lateral shoot branches, leaves, flowers, or lateral roots. This developmental plasticity reflects an important feature of the plant's life strategy based on the rapid reaction to different environmental stimuli, such as temperature fluctuations, availability of nutrients, light or water and response resulting in modulation of developmental programs. Plant hormones are important endogenous factors for the integration of these environmental inputs and regulation of plant development. After a period of studies focused primarily on single hormonal pathways that enabled us to understand the hormone perception and signal transduction mechanisms, it became obvious that the developmental output mediated by a single hormonal pathway is largely modified through a whole network of interactions with other hormonal pathways. In this review, we will summarize recent knowledge on hormonal networks that regulate the development and growth of root with focus on the hormonal interactions that shape the root apical meristem. }, author = {Eva Benková and Hejátko, Jan}, journal = {Plant Molecular Biology}, number = {4}, pages = {383 -- 396}, publisher = {Springer}, title = {{Hormone interactions at the root apical meristem}}, doi = {10.1007/s11103-008-9393-6}, volume = {69}, year = {2009}, } @article{2869, abstract = {Lateral root formation is a major determinant of root systems architecture. The degree of root branching impacts the efficiency of water uptake, acquisition of nutrients and anchorage by plants. Understanding the regulation of lateral root development is therefore of vital agronomic importance. The molecular and cellular basis of lateral root formation has been most extensively studied in the plant model Arabidopsis thaliana (Arabidopsis). Significant progress has recently been made in identifying many new Arabidopsis genes that regulate lateral root initiation, patterning and emergence processes. We review how these studies have revealed that the plant hormone auxin represents a common signal that integrates these distinct yet interconnected developmental processes.}, author = {Péret, Benjamin and De Rybel, Bert and Casimiro, Ilda and Eva Benková and Swarup, Ranjan and Laplaze, Laurent and Beeckman, Tom and Bennett, Malcolm J}, journal = {Trends in Plant Science}, number = {7}, pages = {399 -- 408}, publisher = {Cell Press}, title = {{Arabidopsis lateral root development: an emerging story}}, doi = {10.1016/j.tplants.2009.05.002}, volume = {14}, year = {2009}, } @article{2932, abstract = {We describe a new implementation of the Edmonds’s algorithm for computing a perfect matching of minimum cost, to which we refer as Blossom V. A key feature of our implementation is a combination of two ideas that were shown to be effective for this problem: the “variable dual updates” approach of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and the use of priority queues. We achieve this by maintaining an auxiliary graph whose nodes correspond to alternating trees in the Edmonds’s algorithm. While our use of priority queues does not improve the worst-case complexity, it appears to lead to an efficient technique. In the majority of our tests Blossom V outperformed previous implementations of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and Mehlhorn and Schäfer (J Algorithmics Exp (JEA) 7:4, 2002), sometimes by an order of magnitude. We also show that for large VLSI instances it is beneficial to update duals by solving a linear program, contrary to a conjecture by Cook and Rohe. }, author = {Vladimir Kolmogorov}, journal = {Mathematical Programming Computation}, number = {1}, pages = {43 -- 67}, publisher = {Springer}, title = {{Blossom V: A new implementation of a minimum cost perfect matching algorithm}}, doi = {10.1007/s12532-009-0002-8}, volume = {1}, year = {2009}, } @article{3046, abstract = {Plant-parasitic nematodes are destructive plant pathogens that cause significant yield losses. They induce highly specialized feeding sites (NFS) in infected plant roots from which they withdraw nutrients. In order to establish these NFS, it is thought that the nematodes manipulate the molecular and physiological pathways of their hosts. Evidence is accumulating that the plant signalling molecule auxin is involved in the initiation and development of the feeding sites of sedentary plant-parasitic nematodes. Intercellular transport of auxin is essential for various aspects of plant growth and development. Here, we analysed the spatial and temporal expression of PIN auxin transporters during the early events of NFS establishment using promoter-GUS/GFP fusion lines. Additionally, single and double pin mutants were used in infection studies to analyse the role of the different PIN proteins during cyst nematode infection. Based on our results, we postulate a model in which PIN1-mediated auxin transport is needed to deliver auxin to the initial syncytial cell, whereas PIN3 and PIN4 distribute the accumulated auxin laterally and are involved in the radial expansion of the NFS. Our data demonstrate that cyst nematodes are able to hijack the auxin distribution network in order to facilitate the infection process. © 2009 Grunewald et al}, author = {Grunewald, Wim and Cannoot, Bernard and Jirí Friml and Gheysen, Godelieve}, journal = {PLoS Pathogens}, number = {1}, publisher = {Public Library of Science}, title = {{Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection}}, doi = { 10.1371/journal.ppat.1000266}, volume = {5}, year = {2009}, } @article{3061, abstract = {The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies.}, author = {Křeček, Pavel and Skůpa, Petr and Libus, Jiří and Naramoto, Satoshi and Tejos, Ricardo and Friml, Jirí and Zažímalová, Eva}, journal = {Genome Biology}, number = {12}, publisher = {BioMed Central}, title = {{The PIN-FORMED (PIN) protein family of auxin transporters}}, doi = {10.1186/gb-2009-10-12-249}, volume = {10}, year = {2009}, } @article{3058, abstract = {The plant signalling molecule auxin provides positional informa-tion in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell2,3. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients2,4,5. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated develop-ment. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably medi-ating auxin flow from the cytosol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants.}, author = {Mravec, Jozef and Skůpa, Petr and Bailly, Aurélien and Hoyerová, Klára and Křeček, Pavel and Bielach, Agnieszka and Petrášek, Jan and Zhang, Jing and Gaykova, Vassilena and Stierhof, York-Dieter and Dobrev, Petre I and Schwarzerová, Kateřina and Rolčík, Jakub and Seifertová, Daniela and Luschnig, Christian and Eva Benková and Zažímalová, Eva and Geisler, Markus and Jirí Friml}, journal = {Nature}, number = {7250}, pages = {1136 -- 1140}, publisher = {Nature Publishing Group}, title = {{Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter}}, doi = {10.1038/nature08066}, volume = {459}, year = {2009}, } @article{3055, abstract = {ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell migration. However, the regulation of ACAP functions by other cellular proteins is poorly understood. We have reported previously that a plant ACAP, VAN3, plays a pivotal role in plant venation continuity. Here, we report on newly identified VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3 mutants, showing severe vascular continuity. The phenotype of double mutants between van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern formation in the same pathway. Localization analysis revealed that both CVP2 and VAB colocalize with VAN3 in the trans- Golgi network (TGN), supporting their functions in the same pathway. The subcellular localization of VAN3 was dependent on its PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These results suggest that CVP2 and VAB cooperatively regulate the subcellular localization of VAN3 through the interaction between its PH domain and phosphoinositides and/or inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially, enhanced the ARF-GAP activity of VAN3, whereas IP3 inhibited it. These results suggest the existence of PtdIns(4)P and/or IP3-dependent subcellular targeting and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.}, author = {Naramoto, Satoshi and Sawa, Shinichiro and Koizumi, Koji and Uemura, Tomohiro and Ueda, Takashi and Jirí Friml and Nakano, Akihiko and Fukuda, Hiroo}, journal = {Development}, number = {9}, pages = {1529 -- 1538}, publisher = {Company of Biologists}, title = {{Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants}}, doi = {10.1242/dev.030098}, volume = {136}, year = {2009}, } @article{3059, abstract = {The phytohormone auxin plays a major role in embryonic and postembryonic plant development. The temporal and spatial distribution of auxin largely depends on the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation and crucially contributes to the regulation of apical-basal PIN polarity. The GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially mediates PIN recycling at the basal side of the cell. Interference with GNOM activity leads to dynamic PIN transcytosis between different sides of the cell. Our genetic, pharmacological, and cell biological approaches illustrate that PID and GNOM influence PIN polarity and plant development in an antagonistic manner and that the PID-dependent PIN phosphorylation results in GNOM-independent polar PIN targeting. The data suggest that PID and the protein phosphatase 2A not only regulate the static PIN polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN transcytosis. We propose a model that includes PID-dependent PIN phosphorylation at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent pathway for polarity alterations during developmental processes, such as lateral root formation and leaf vasculature development.}, author = {Kleine-Vehn, Jürgen and Huang, Fang and Naramoto, Satoshi and Zhang, Jing and Michniewicz, Marta and Offringa, Remko and Jirí Friml}, journal = {Plant Cell}, number = {12}, pages = {3839 -- 3849}, publisher = {American Society of Plant Biologists}, title = {{PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis}}, doi = {10.1105/tpc.109.071639}, volume = {21}, year = {2009}, } @article{3056, abstract = {Local hormone maxima are essential for the development of multicellular structures and organs. For example, steroid hormones accumulate in specific cell types of the animal fetus to induce sexual differentiation and concentration peaks of the plant hormone auxin direct organ initiation and mediate tissue patterning. Here we provide an example of a regulated local hormone minimum required during organogenesis. Our results demonstrate that formation of a local auxin minimum is necessary for specification of the valve margin separation layer where Arabidopsis fruit opening takes place. Consequently, ectopic production of auxin, specifically in valve margin cells, leads to a complete loss of proper cell fate determination. The valve margin identity factor INDEHISCENT (IND) is responsible for forming the auxin minimum by coordinating auxin efflux in separation-layer cells. We propose that the simplicity of formation and maintenance make local hormone minima particularly well suited to specify a small number of cells such as the stripes at the valve margins.}, author = {Sorefan, Karim and Girin, Thomas and Liljegren, Sarah J and Ljung, Karin and Robles, Pedro and Galván-Ampudia, Carlos S and Offringa, Remko and Jirí Friml and Yanofsky, Martin F and Østergaard, Lars}, journal = {Nature}, number = {7246}, pages = {583 -- 586}, publisher = {Nature Publishing Group}, title = {{A regulated auxin minimum is required for seed dispersal in Arabidopsis}}, doi = {10.1038/nature07875}, volume = {459}, year = {2009}, } @article{3057, abstract = {The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli.}, author = {Petrášek, Jan and Friml, Jirí}, journal = {Development}, number = {16}, pages = {2675 -- 2688}, publisher = {Company of Biologists}, title = {{Auxin transport routes in plant development}}, doi = {10.1242/dev.030353}, volume = {136}, year = {2009}, } @article{3060, author = {Schumacher, Karin and Friml, Jirí}, journal = {Current Opinion in Plant Biology}, number = {6}, pages = {651 -- 652}, publisher = {Elsevier}, title = {{Cell biology}}, doi = {10.1016/j.pbi.2009.10.009}, volume = {12}, year = {2009}, } @inproceedings{3203, abstract = {In recent years the Markov Random Field (MRF) has become the de facto probabilistic model for low-level vision applications. However, in a maximum a posteriori (MAP) framework, MRFs inherently encourage delta function marginal statistics. By contrast, many low-level vision problems have heavy tailed marginal statistics, making the MRF model unsuitable. In this paper we introduce a more general Marginal Probability Field (MPF), of which the MRF is a special, linear case, and show that convex energy MPFs can be used to encourage arbitrary marginal statistics. We introduce a flexible, extensible framework for effectively optimizing the resulting NP-hard MAP problem, based around dual-decomposition and a modified mincost flow algorithm, and which achieves global optimality in some instances. We use a range of applications, including image denoising and texture synthesis, to demonstrate the benefits of this class of MPF over MRFs.}, author = {Woodford, Oliver J and Rother, Carsten and Vladimir Kolmogorov}, pages = {2319 -- 2326}, publisher = {IEEE}, title = {{A global perspective on MAP inference for low level vision}}, doi = {10.1109/ICCV.2009.5459434}, year = {2009}, } @inproceedings{3230, abstract = {We present a new approach to the design of IND-CCA2 secure hybrid encryption schemes in the standard model. Our approach provides an efficient generic transformation from 1-universal to 2-universal hash proof systems. The transformation involves a randomness extractor based on a 4-wise independent hash function as the key derivation function. Our methodology can be instantiated with efficient schemes based on standard intractability assumptions such as Decisional Diffie-Hellman, Quadratic Residuosity, and Paillier's Decisional Composite Residuosity. Interestingly, our framework also allows to prove IND-CCA2 security of a hybrid version of 1991's Damgård's ElGamal public-key encryption scheme under the DDH assumption. }, author = {Kiltz, Eike and Krzysztof Pietrzak and Stam, Martijn and Yung, Moti}, pages = {590 -- 609}, publisher = {Springer}, title = {{A new randomness extraction paradigm for hybrid encryption}}, doi = {10.1007/978-3-642-01001-9_34}, volume = {5479}, year = {2009}, } @inproceedings{3231, abstract = {We investigate the security of "padding-based" encryption schemes in the standard model. This class contains all public-key encryption schemes where the encryption algorithm first applies some invertible public transformation to the message (the "padding"), followed by a trapdoor permutation. In particular, this class contains OAEP and its variants. Our main result is a black-box impossibility result showing that one cannot prove any such padding-based scheme chosen-ciphertext secure even assuming the existence of ideal trapdoor permutations. The latter is a strong ideal abstraction of trapdoor permutations which inherits all security properties of uniform random permutations. }, author = {Kiltz, Eike and Krzysztof Pietrzak}, pages = {389 -- 406}, publisher = {Springer}, title = {{On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model}}, doi = {10.1007/978-3-642-01001-9_23}, volume = {5479}, year = {2009}, } @inproceedings{3232, abstract = {A weak pseudorandom function (wPRF) is a cryptographic primitive similar to - but weaker than - a pseudorandom function: for wPRFs one only requires that the output is pseudorandom when queried on random inputs.We show that unlike "normal" PRFs, wPRFs are seedincompressible, in the sense that the output of a wPRF is pseudorandom even if a bounded amount of information about the key is leaked. As an application of this result we construct a simple mode of operation which - when instantiated with any wPRF - gives a leakage-resilient stream-cipher. The implementation of such a cipher is secure against every side-channel attack, as long as the amount of information leaked per round is bounded, but overall can be arbitrary large. The construction is simpler than the previous one (Dziembowski-Pietrzak FOCS'08) as it only uses a single primitive (a wPRF) in a straight forward manner. }, author = {Krzysztof Pietrzak}, pages = {462 -- 482}, publisher = {Springer}, title = {{A leakage resilient mode of operation}}, doi = {10.1007/978-3-642-01001-9_27}, volume = {5479}, year = {2009}, } @article{3304, abstract = {Complex traits often involve interactions between different genetic loci. This can lead to sign epistasis, whereby mutations that are individually deleterious or neutral combine to confer a fitness benefit. In order to acquire the beneficial genotype, an asexual population must cross a fitness valley or plateau by first acquiring the deleterious or neutral intermediates. Here, we present a complete, intuitive theoretical description of the valley-crossing process across the full spectrum of possible parameter regimes. We calculate the rate at which a population crosses a fitness valley or plateau of arbitrary width, as a function of the mutation rates, the population size, and the fitnesses of the intermediates. We find that when intermediates are close to neutral, a large population can cross even wide fitness valleys remarkably quickly, so that valley-crossing dynamics may be common even when mutations that directly increase fitness are also possible. Thus the evolutionary dynamics of large populations can be sensitive to the structure of an extended region of the fitness landscape — the population may not take directly uphill paths in favor of paths across valleys and plateaus that lead eventually to fitter genotypes. In smaller populations, we find that below a threshold size, which depends on the width of the fitness valley and the strength of selection against intermediate genotypes, valley-crossing is much less likely and hence the evolutionary dynamics are less influenced by distant regions of the fitness landscape.}, author = {Daniel Weissman and Desai, Michael M and Fisher, Daniel S and Feldman, Marcus W}, journal = {Theoretical Population Biology}, number = {4}, pages = {286 -- 300}, publisher = {Academic Press}, title = {{The rate at which asexual populations cross fitness valleys}}, doi = {10.1016/j.tpb.2009.02.006}, volume = {75}, year = {2009}, } @article{337, abstract = {The formation of hollow vs solid particles by means of the oxidation reaction of solid metal particles depends on the differential self-diffusivities of the reactants through the composite shell, the reaction probabilities at each interface, and the concentration and diffusivity of the element in solution. By means of a kinetic model of the oxidation process, we determine the phase diagrams for the geometry of the oxidized particles and propose four shell growth regimes. We experimentally illustrate the different growth scenarios by changing the conditions of oxidation of cadmium spherical crystals using different chalcogen precursors. }, author = {Cabot, Andreu and Ibáñez, Maria and Guardia, Pablo and Alivisatos, Paul}, journal = {Journal of the American Chemical Society}, number = {32}, pages = {11326 -- 11328}, publisher = {ACS}, title = {{Reaction regimes on the synthesis of hollow particles by the Kirkendall effect}}, doi = {10.1021/ja903751p}, volume = {131}, year = {2009}, } @article{3408, abstract = {Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.}, author = {Szymczak, Piotr and Harald Janovjak}, journal = {Journal of Molecular Biology}, number = {3}, pages = {443 -- 456}, publisher = {Elsevier}, title = {{Periodic forces trigger a complex mechanical response in ubiquitin}}, doi = {10.1016/j.jmb.2009.04.071}, volume = {390}, year = {2009}, } @article{3428, abstract = {In this issue of Molecular Cell, Davies et al. (2009) work out a sequence of active cellular events that lead to the death of Escherichia coli in the presence of the drug hydroxyurea.}, author = {Bollenbach, Mark Tobias and Kishony, Roy}, journal = {Molecular Cell}, number = {5}, pages = {728 -- 729}, publisher = {Cell Press}, title = {{Hydroxyurea triggers cellular responses that actively cause bacterial cell death}}, doi = {10.1016/j.molcel.2009.11.027}, volume = {36}, year = {2009}, } @inproceedings{3503, abstract = {We give polynomial-time algorithms for computing the values of Markov decision processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned to each state, and the value of an infinite path in the MDP is the limsup (resp. liminf) of all rewards along the path. The value of an MDP is the maximal expected value of an infinite path that can be achieved by resolving the decisions of the MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup and liminf objectives can be solved in NP ∩ coNP. }, author = {Krishnendu Chatterjee and Thomas Henzinger}, pages = {32 -- 45}, publisher = {Springer}, title = {{Probabilistic systems with limsup and liminf objectives}}, doi = {10.1007/978-3-642-03092-5_4}, volume = {5489}, year = {2009}, } @misc{3699, abstract = {Kernel Canonical Correlation Analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, CCA learns representations tied more closely to underlying process generating the the data and can ignore high-variance noise directions. However, for data where acquisition in a given modality is expensive or otherwise limited, CCA may suffer from small sample effects. We propose to use semisupervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of CCA on human fMRI data, with regression to single and multivariate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of CCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.}, author = {Blaschko,Matthew B and Christoph Lampert and Bartels, Andreas}, booktitle = {BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology}, publisher = {Berlin Institute of Technology}, title = {{Semi-supervised analysis of human fMRI data}}, year = {2009}, } @inproceedings{3703, abstract = {Recent research has shown that the use of contextual cues significantly improves performance in sliding window type localization systems. In this work, we propose a method that incorporates both global and local context information through appropriately defined kernel functions. In particular, we make use of a weighted combination of kernels defined over local spatial regions, as well as a global context kernel. The relative importance of the context contributions is learned automatically, and the resulting discriminant function is of a form such that localization at test time can be solved efficiently using a branch and bound optimization scheme. By specifying context directly with a kernel learning approach, we achieve high localization accuracy with a simple and efficient representation. This is in contrast to other systems that incorporate context for which expensive inference needs to be done at test time. We show experimentally on the PASCAL VOC datasets that the inclusion of context can significantly improve localization performance, provided the relative contributions of context cues are learned appropriately.}, author = {Blaschko,Matthew B and Christoph Lampert}, pages = {1 -- 11}, publisher = {BMVA Press}, title = {{Object localization with global and local context kernels}}, doi = {10.5244/C.23.63}, year = {2009}, } @inproceedings{3704, abstract = {We study the problem of object classification when training and test classes are disjoint, i.e. no training examples of the target classes are available. This setup has hardly been studied in computer vision research, but it is the rule rather than the exception, because the world contains tens of thousands of different object classes and for only a very few of them image, collections have been formed and annotated with suitable class labels. In this paper, we tackle the problem by introducing attribute-based classification. It performs object detection based on a human-specified high-level description of the target objects instead of training images. The description consists of arbitrary semantic attributes, like shape, color or even geographic information. Because such properties transcend the specific learning task at hand, they can be pre-learned, e.g. from image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In order to evaluate our method and to facilitate research in this area, we have assembled a new large-scale dataset, ldquoAnimals with Attributesrdquo, of over 30,000 animal images that match the 50 classes in Osherson‘s classic table of how strongly humans associate 85 semantic attributes with animal classes. Our experiments show that by using an attribute layer it is indeed possible to build a learning object detection system that does not require any training images of the target classes.}, author = {Christoph Lampert and Nickisch,Hannes and Harmeling,Stefan}, pages = {951 -- 958}, publisher = {IEEE}, title = {{Learning to detect unseen object classes by between-class attribute transfer}}, doi = {10.1109/CVPR.2009.5206594}, year = {2009}, } @inproceedings{3715, abstract = {High-speed smooth and accurate visual tracking of objects in arbitrary, unstructured environments is essential for robotics and human motion analysis. However, building a system that can adapt to arbitrary objects and a wide range of lighting conditions is a challenging problem, especially if hard real-time constraints apply like in robotics scenarios. In this work, we introduce a method for learning a discriminative object tracking system based on the recent structured regression framework for object localization. Using a kernel function that allows fast evaluation on the GPU, the resulting system can process video streams at speed of 100 frames per second or more. Consecutive frames in high speed video sequences are typically very redundant, and for training an object detection system, it is sufficient to have training labels from only a subset of all images. We propose an active learning method that select training examples in a data-driven way, thereby minimizing the required number of training labeling. Experiments on realistic data show that the active learning is superior to previously used methods for dataset subsampling for this task.}, author = {Christoph Lampert and Peters, Jan}, pages = {221 -- 231}, publisher = {Springer}, title = {{Active structured learning for high-speed object detection}}, doi = {10.1007/978-3-642-03798-6_23}, volume = {5748}, year = {2009}, } @misc{3717, abstract = {We introduce RTblob, an open-source real-time vision system for 3D object detection that achieves over 200 Hz tracking speed with only off-the-shelf hardware component. It allows fast and accurate tracking of colored objects in 3D without expensive and often custom-built hardware, instead making use of the PC graphics cards for the necessary image processing operations.}, author = {Christoph Lampert and Peters, Jan}, booktitle = {ICCV: International Conference on Computer Vision}, publisher = {IEEE}, title = {{A high-speed object tracker from off-the-shelf components}}, year = {2009}, } @article{3737, abstract = {In order to survive, reproduce, and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable randomness of individual molecular events. Here we explore how cells can maximize their control power in the presence of these physical limits; formally, we solve the theoretical problem of maximizing the information transferred from inputs to outputs when the number of available molecules is held fixed. We start with the simplest version of the problem, in which a single transcription factor protein controls the readout of one or more genes by binding to DNA. We further simplify by assuming that this regulatory network operates in steady state, that the noise is small relative to the available dynamic range, and that the target genes do not interact. Even in this simple limit, we find a surprisingly rich set of optimal solutions. Importantly, for each locally optimal regulatory network, all parameters are determined once the physical constraints on the number of available molecules are specified. Although we are solving an oversimplified version of the problem facing real cells, we see parallels between the structure of these optimal solutions and the behavior of actual genetic regulatory networks. Subsequent papers will discuss more complete versions of the problem.}, author = {Gasper Tkacik and Walczak, Aleksandra M and Bialek, William S}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {3 }, publisher = {American Institute of Physics}, title = {{Optimizing information flow in small genetic networks}}, doi = {10.1103/PhysRevE.80.031920}, volume = {80}, year = {2009}, } @article{3733, abstract = {Evolutionary theory predicts that a population in a new environment will accumulate adaptive substitutions, but precisely how they accumulate is poorly understood. The dynamics of adaptation depend on the underlying fitness landscape. Virtually nothing is known about fitness landscapes in nature, and few methods allow us to infer the landscape from empirical data. With a view toward this inference problem, we have developed a theory that, in the weak-mutation limit, predicts how a population's mean fitness and the number of accumulated substitutions are expected to increase over time, depending on the underlying fitness landscape. We find that fitness and substitution trajectories depend not on the full distribution of fitness effects of available mutations but rather on the expected fixation probability and the expected fitness increment of mutations. We introduce a scheme that classifies landscapes in terms of the qualitative evolutionary dynamics they produce. We show that linear substitution trajectories, long considered the hallmark of neutral evolution, can arise even when mutations are strongly selected. Our results provide a basis for understanding the dynamics of adaptation and for inferring properties of an organism's fitness landscape from temporal data. Applying these methods to data from a long-term experiment, we infer the sign and strength of epistasis among beneficial mutations in the Escherichia coli genome.}, author = {Kryazhimskiy,Sergey and Gasper Tkacik and Plotkin,Joshua B}, journal = {PNAS}, number = {44}, pages = {18638 -- 18643}, publisher = {National Academy of Sciences}, title = {{The dynamics of adaptation on correlated fitness landscapes}}, doi = {10.1073/pnas.0905497106}, volume = {106}, year = {2009}, } @unpublished{3732, abstract = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the salamander retina responding to natural movies. We show that pairwise interactions between neurons account for observed higher-order correlations, and that for groups of 10 or more neurons pairwise interactions can no longer be regarded as small perturbations in an independent system. We then construct network ensembles that generalize the network instances observed in the experiment, and study their thermodynamic behavior and coding capacity. Based on this construction, we can also create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. We examine closely two such behaviors that could be relevant for neural code: tuning of the network to the critical point to maximize the ability to encode diverse stimuli, and using the metastable states of the Ising Hamiltonian as neural code words.}, author = {Gasper Tkacik and Schneidman, Elad and Berry, Michael J and Bialek, William S}, booktitle = {ArXiv}, publisher = {ArXiv}, title = {{Spin glass models for a network of real neurons}}, volume = {q-bio.NC}, year = {2009}, } @inbook{3747, author = {Gasper Tkacik and Bialek, William S}, booktitle = {Encyclopedia of Complexity and Systems Science}, editor = {Meyers,R. A.}, pages = {719 -- 741}, publisher = {Springer}, title = {{Cell Biology: Networks, regulation, pathways}}, doi = {10.1007/978-0-387-30440-3_48}, year = {2009}, } @article{3764, abstract = {We present a method for accurately tracking the moving surface of deformable materials in a manner that gracefully handles topological changes. We employ a Lagrangian surface tracking method, and we use a triangle mesh for our surface representation so that fine features can be retained. We make topological changes to the mesh by first identifying merging or splitting events at a particular grid resolution, and then locally creating new pieces of the mesh in the affected cells using a standard isosurface creation method. We stitch the new, topologically simplified portion of the mesh to the rest of the mesh at the cell boundaries. Our method detects and treats topological events with an emphasis on the preservation of detailed features, while simultaneously simplifying those portions of the material that are not visible. Our surface tracker is not tied to a particular method for simulating deformable materials. In particular, we show results from two significantly different simulators: a Lagrangian FEM simulator with tetrahedral elements, and an Eulerian grid-based fluid simulator. Although our surface tracking method is generic, it is particularly well-suited for simulations that exhibit fine surface details and numerous topological events. Highlights of our results include merging of viscoplastic materials with complex geometry, a taffy-pulling animation with many fold and merge events, and stretching and slicing of stiff plastic material.}, author = {Wojtan, Christopher J and Thürey, Nils and Gross, Markus and Turk, Greg}, journal = {ACM Transactions on Graphics}, number = {3}, publisher = {ACM}, title = {{Deforming meshes that split and merge}}, doi = {10.1145/1531326.1531382}, volume = {28}, year = {2009}, } @article{3768, author = {Anne Kupczok and von Haeseler,Arndt}, journal = {Bioinformatics}, number = {1}, pages = {147 -- 149}, publisher = {Oxford University Press}, title = {{Comment on '{A} congruence index for testing topological similarity between trees'.}}, doi = {4199}, volume = {25}, year = {2009}, } @article{3780, abstract = {Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.}, author = {Davison, Angus and Barton, Nicholas H and Clarke, Bryan}, journal = {Journal of Evolutionary Biology}, number = {8}, pages = {1624 -- 1635}, publisher = {Wiley}, title = {{The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails}}, doi = {10.1111/j.1420-9101.2009.01770.x}, volume = {22}, year = {2009}, } @article{3828, abstract = {Glutamate receptors of the AMPA-subtype (AMPARs), together with the transmembrane AMPAR regulatory proteins (TARPs), mediate fast excitatory synaptic transmission in the mammalian brain. Here, we show by proteomic analysis that the majority of AMPARs in the rat brain are coassembled with two members of the cornichon family of transmembrane proteins, rather than with the TARPs. Coassembly with cornichon homologs 2 and 3 affects AMPARs in two ways: Cornichons increase surface expression of AMPARs, and they alter channel gating by markedly slowing deactivation and desensitization kinetics. These results demonstrate that cornichons are intrinsic auxiliary subunits of native AMPARs and provide previously unknown molecular determinants for glutamatergic neurotransmission in the central nervous system.}, author = {Schwenk, Jochen and Harmel, Nadine and Zolles, Gerd and Bildl, Wolfgang and Kulik, Ákos and Heimrich, Bernd and Chisaka, Osamu and Peter Jonas and Schulte, Uwe and Fakler, Bernd and Klocker, Nikolaj}, journal = {Science}, number = {5919}, pages = {1313 -- 9}, publisher = {American Association for the Advancement of Science}, title = {{Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors}}, doi = {10.1126/science.1167852}, volume = {323}, year = {2009}, } @inproceedings{3843, abstract = {Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous- time Markov chain (CTMC). Standard Uniformization (SU) is an efficient method for the transient analysis of CTMCs. For systems with very different time scales, such as biochemical reaction networks, SU is computationally expensive. In these cases, a variant of SU, called adaptive uniformization (AU), is known to reduce the large number of iterations needed by SU. The additional difficulty of AU is that it requires the solution of a birth process. In this paper we present an on-the-fly variant of AU, where we improve the original algorithm for AU at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.}, author = {Didier, Frédéric and Henzinger, Thomas A and Mateescu, Maria and Wolf, Verena}, location = {Trento, Italy}, number = {6}, pages = {118 -- 127}, publisher = {IEEE}, title = {{Fast adaptive uniformization of the chemical master equation}}, doi = {10.1109/HiBi.2009.23}, volume = {4}, year = {2009}, } @inproceedings{3841, abstract = {We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. }, author = {Henzinger, Thomas A and Jobstmann, Barbara and Wolf, Verena}, location = {Palaiseau, France}, pages = {3 -- 23}, publisher = {Springer}, title = {{Formalisms for specifying Markovian population models}}, doi = {10.1007/978-3-642-04420-5_2}, volume = {5797}, year = {2009}, } @inproceedings{3844, abstract = {The Hierarchical Timing Language (HTL) is a real-time coordination language for distributed control systems. HTL programs must be checked for well-formedness, race freedom, transmission safety (schedulability of inter-host communication), and time safety (schedulability of host computation). We present a modular abstract syntax and semantics for HTL, modular checks of well-formedness, race freedom, and transmission safety, and modular code distribution. Our contributions here complement previous results on HTL time safety and modular code generation. Modularity in HTL can be utilized in easy program composition as well as fast program analysis and code generation, but also in so-called runtime patching, where program components may be modified at runtime.}, author = {Henzinger, Thomas A and Kirsch, Christoph and Marques, Eduardo and Sokolova, Ana}, location = {Washington, DC, United States}, pages = {171 -- 180}, publisher = {IEEE}, title = {{Distributed, modular HTL}}, doi = {10.1109/RTSS.2009.9}, year = {2009}, } @inproceedings{3871, abstract = {Nondeterministic weighted automata are finite automata with numerical weights oil transitions. They define quantitative languages 1, that assign to each word v; a real number L(w). The value of ail infinite word w is computed as the maximal value of all runs over w, and the value of a run as the supremum, limsup liminf, limit average, or discounted sum of the transition weights. We introduce probabilistic weighted antomata, in which the transitions are chosen in a randomized (rather than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics), the value of a word v) is the largest real v such that the runs over w have value at least v with probability I (resp. positive probability). We study the classical questions of automata theory for probabilistic weighted automata: emptiness and universality, expressiveness, and closure under various operations oil languages. For quantitative languages, emptiness university axe defined as whether the value of some (resp. every) word exceeds a given threshold. We prove some, of these questions to he decidable, and others undecidable. Regarding expressive power, we show that probabilities allow its to define a wide variety of new classes of quantitative languages except for discounted-sum automata, where probabilistic choice is no more expressive than nondeterminism. Finally we live ail almost complete picture of the closure of various classes of probabilistic weighted automata for the following, provide, is operations oil quantitative languages: maximum, sum. and numerical complement.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, location = {Bologna, Italy}, pages = {244 -- 258}, publisher = {Springer}, title = {{Probabilistic weighted automata}}, doi = {10.1007/978-3-642-04081-8_17}, volume = {5710}, year = {2009}, } @article{3870, abstract = {Games on graphs with omega-regular objectives provide a model for the control and synthesis of reactive systems. Every omega-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Buchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. We show that finitary parity games can be solved in polynomial time, which is not known for infinitary parity games. For finitary Streett games, we give an EXPTIME algorithm and show that the problem is NP-hard. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {1}, publisher = {ACM}, title = {{Finitary winning in omega-regular games}}, doi = {10.1145/1614431.1614432}, volume = {11}, year = {2009}, } @article{3869, abstract = {We investigate logics and equivalence relations that capture the qualitative behavior of Markov Decision Processes (MDPs). We present Qualitative Randomized CTL (QRCTL): formulas of this logic can express the fact that certain temporal properties hold over all paths, or with probability 0 or 1, but they do not distinguish among intermediate probability values. We present a symbolic, polynomial time model-checking algorithm for QRCTL on MDPs. The logic QRCTL induces an equivalence relation over states of an MDP that we call qualitative equivalence: informally, two states are qualitatively equivalent if the sets of formulas that hold with probability 0 or 1 at the two states are the same. We show that for finite alternating MDPs, where nondeterministic and probabilistic choices occur in different states, qualitative equivalence coincides with alternating bisimulation, and can thus be computed via efficient partition-refinement algorithms. On the other hand, in non-alternating MDPs the equivalence relations cannot be computed via partition-refinement algorithms, but rather, they require non-local computation. Finally, we consider QRCTL*, that extends QRCTL with nested temporal operators in the same manner in which CTL* extends CTL. We show that QRCTL and QRCTL* induce the same qualitative equivalence on alternating MDPs, while on non-alternating MDPs, the equivalence arising from QRCTL* can be strictly finer. We also provide a full characterization of the relation between qualitative equivalence, bisimulation, and alternating bisimulation, according to whether the MDPs are finite, and to whether their transition relations are finitely-branching.}, author = {Krishnendu Chatterjee and de Alfaro, Luca and Faella, Marco and Legay, Axel}, journal = {Logical Methods in Computer Science}, number = {2}, publisher = {International Federation of Computational Logic}, title = {{Qualitative logics and equivalences for probabilistic systems}}, doi = {10.2168/LMCS-5(2:7)2009}, volume = {5}, year = {2009}, } @article{3946, abstract = {We compare anti-parasite defences at the level of multicellular organisms and insect societies, and find that selection by parasites at these two organisational levels is often very similar and has created a number of parallel evolutionary solutions in the host's immune response. The defence mechanisms of both individuals and insect colonies start with border defences to prevent parasite intake and are followed by soma defences that prevent the establishment and spread of the parasite between the body's cells or the social insect workers. Lastly, germ line defences are employed to inhibit infection of the reproductive tissue of organisms or the reproductive individuals in colonies. We further find sophisticated self/non-self-recognition systems operating at both levels, which appear to be vital in maintaining the integrity of the body or colony as a reproductive entity. We then expand on the regulation of immune responses and end with a contemplation of how evolution may shape the different immune components, both within and between levels. The aim of this review is to highlight common evolutionary principles acting in disease defence at the level of both individual organisms and societies, thereby linking the fields of physiological and ecological immunology.}, author = {Cremer, Sylvia and Sixt, Michael K}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1513}, pages = {129 -- 142}, publisher = {Royal Society, The}, title = {{Analogies in the evolution of individual and social immunity}}, doi = {10.1098/rstb.2008.0166}, volume = {364}, year = {2009}, } @article{3947, abstract = {Mature dendritic cells (DCs) moving from the skin to the lymph node are a prototypic example of rapidly migrating amoeboid leukocytes. Interstitial DC migration is directionally guided by chemokines, but independent of specific adhesive interactions with the tissue as well as pericellular proteolysis. Instead, the protrusive flow of the actin cytoskeleton directly drives a basal mode of locomotion that is occasionally supported by actomyosin contractions at the trailing edge to propel the cell's rigid nucleus. We here delete the small GTPase Cdc42 in DCs and find that actin flow and actomyosin contraction are still initiated in response to chemotactic cues. Accordingly, the cells are able to polarize and form protrusions. However, in the absence of Cdc42 the protrusions are temporally and spatially dysregulated, which leads to impaired leading edge coordination. Although this defect still allows the cells to move on 2-dimensional surfaces, their in vivo motility is completely abrogated. We show that this difference is entirely caused by the geometric complexity of the environment, as multiple competing protrusions lead to instantaneous entanglement within 3-dimensional extracellular matrix scaffolds. This demonstrates that the decisive factor for migrating DCs is not specific interaction with the extracellular environment, but adequate coordination of cytoskeletal flow.}, author = {Lämmermann, Tim and Jörg Renkawitz and Wu, Xunwei and Hirsch, Karin and Brakebusch, Cord and Michael Sixt}, journal = {Blood}, number = {23}, pages = {5703 -- 5710}, publisher = {American Society of Hematology}, title = {{Cdc42-dependent leading edge coordination is essential for interstitial dendritic cell migration (Plenary Paper)}}, doi = {10.1182/blood-2008-11-191882}, volume = {113}, year = {2009}, } @article{3948, abstract = {Inhibiting the alpha(4) subunit of the integrin heterodimers alpha(4)beta(1) and alpha(4)beta(7) with the monoclonal antibody natalizumab is an effective treatment for multiple sclerosis (MS). However, the pharmacological action of natalizumab is not understood conclusively. Previous studies suggested that natalizumab inhibits activation, proliferation, or extravasation of inflammatory cells. To specify which mechanisms, cell types, and alpha(4) heterodimers are affected by the antibody treatment, we studied MS-like experimental autoimmune encephalomyelitis (EAE) in mice lacking the beta(1)-integrin gene either in all hematopoietic cells or selectively in T lymphocytes. Our results show that T cells critically rely on beta(1) integrins to accumulate in the central nervous system (CNS) during EAE, whereas CNS infiltration of beta(1)-deficient myeloid cells remains unaffected, suggesting that T cells are the main target of anti-alpha(4)-antibody blockade. We demonstrate that beta(1)-integrin expression on encephalitogenic T cells is critical for EAE development, and we therefore exclude alpha(4)beta(7) as a target integrin of the antibody treatment. T cells lacking beta(1) integrin are unable to firmly adhere to CNS endothelium in vivo, whereas their priming and expansion remain unaffected. Collectively, these results suggest that the primary action of natalizumab is interference with T cell extravasation via inhibition of alpha(4)beta(1) integrins.}, author = {Bauer, Martina and Brakebusch, Cord and Coisne, Caroline and Michael Sixt and Wekerle, Hartmut and Engelhardt, Britta and Fässler, Reinhard}, journal = {PNAS}, number = {6}, pages = {1920 -- 1925}, publisher = {National Academy of Sciences}, title = {{β1 integrins differentially control extravasation of inflammatory cell subsets into the CNS during autoimmunity}}, doi = {10.1073/pnas.0808909106}, volume = {106}, year = {2009}, }