TY - JOUR
AB - In July, 2011, a 32-year-old man presented with thoracic pain radiating to the left arm and upper dorsum, shortness of breath, and palpitations. He had had upper back tension for 6 months. Medical history was unremarkable apart from moderate nicotine use (two pack-years). Echocardiography, electrocardiography, and laboratory tests were unremarkable, excluding a cardiac event. CT of the chest after chest radiography showed a large bulla of 16 cm diameter in the right hemithorax (figure A). We did not detect radiological evidence of underlying pulmonary disease. The bulla wall was unremarkable and no structures were seen within the bulla.
AU - Erne, Barbara
AU - Graff, Mareike
AU - Klemm, Wolfram
AU - Danzl, Johann G
AU - Leschber, Gunda
ID - 1055
IS - 9849
JF - The Lancet
TI - Bulla in the lung
VL - 380
ER -
TY - JOUR
AB - We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation.
AU - Mark, Manfred
AU - Haller, Elmar
AU - Lauber, Katharina
AU - Danzl, Johann G
AU - Janisch, Alexander
AU - Büchler, Hans
AU - Daley, Andrew
AU - Nägerl, Hanns
ID - 1056
IS - 21
JF - Physical Review Letters
TI - Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions
VL - 108
ER -
TY - JOUR
AB - We report on an investigation of the solidification of a cornstarch and water suspension during normal impact on its surface. We find that a finite time after impact, the suspension displays characteristics reminiscent of a solid, including localized stress transmission, the development of a yield stress, and some elastic energy storage. The time dependence of these characteristics depends on the thickness of the cornstarch layer, showing that the solidification is a dynamic process driven by the impacting object. These findings confirm previous speculations that rapidly applied normal stress transforms the normally fluid-like suspension into a temporarily jammed solid and draw a clear distinction between the effects of normal stress and shear stress in dense suspensions.
AU - Waitukaitis, Scott R
AU - Jaeger, Heinrich
ID - 114
IS - 1E
JF - Revista Cubana de Fisica
TI - Solidification of a cornstarch and water suspension
VL - 29
ER -
TY - JOUR
AB - Although liquids typically flow around intruding objects, a counterintuitive phenomenon occurs in dense suspensions of micrometre-sized particles: they become liquid-like when perturbed lightly, but harden when driven strongly. Rheological experiments have investigated how such thickening arises under shear, and linked it to hydrodynamic interactions or granular dilation. However, neither of these mechanisms alone can explain the ability of suspensions to generate very large, positive normal stresses under impact. To illustrate the phenomenon, such stresses can be large enough to allow a person to run across a suspension without sinking, and far exceed the upper limit observed under shear or extension. Here we show that these stresses originate from an impact-generated solidification front that transforms an initially compressible particle matrix into a rapidly growing jammed region, ultimately leading to extraordinary amounts of momentum absorption. Using high-speed videography, embedded force sensing and X-ray imaging, we capture the detailed dynamics of this process as it decelerates a metal rod hitting a suspension of cornflour (cornstarch) in water. We develop a model for the dynamic solidification and its effect on the surrounding suspension that reproduces the observed behaviour quantitatively. Our findings suggest that prior interpretations of the impact resistance as dominated by shear thickening need to be revisited.
AU - Waitukaitis, Scott R
AU - Jaeger, Heinrich
ID - 113
IS - 7406
JF - Nature
TI - Impact-activated solidification of dense suspensions via dynamic jamming fronts
VL - 487
ER -
TY - CONF
AB - Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.
AU - Beyer, Dirk
AU - Henzinger, Thomas A
AU - Keremoglu, Mehmet
AU - Wendler, Philipp
ID - 1384
T2 - Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering
TI - Conditional model checking: A technique to pass information between verifiers
ER -
TY - JOUR
AB - Given a possibly reducible and non-reduced spectral cover π: X → C over a smooth projective complex curve C we determine the group of connected components of the Prym variety Prym(X/C). As an immediate application we show that the finite group of n-torsion points of the Jacobian of C acts trivially on the cohomology of the twisted SL n-Higgs moduli space up to the degree which is predicted by topological mirror symmetry. In particular this yields a new proof of a result of Harder-Narasimhan, showing that this finite group acts trivially on the cohomology of the twisted SL n stable bundle moduli space.
AU - Tamas Hausel
AU - Pauly, Christian
ID - 1471
IS - 3
JF - Geometry and Topology
TI - Prym varieties of spectral covers
VL - 16
ER -
TY - JOUR
AB - For G = GL 2, PGL 2, SL 2 we prove that the perverse filtration associated with the Hitchin map on the rational cohomology of the moduli space of twisted G-Higgs bundles on a compact Riemann surface C agrees with the weight filtration on the rational cohomology of the twisted G character variety of C when the cohomologies are identified via non-Abelian Hodge theory. The proof is accomplished by means of a study of the topology of the Hitchin map over the locus of integral spectral curves.
AU - De Cataldo, Mark A
AU - Tamas Hausel
AU - Migliorini, Luca
ID - 1472
IS - 3
JF - Annals of Mathematics
TI - Topology of hitchin systems and Hodge theory of character varieties: The case A 1
VL - 175
ER -
TY - JOUR
AB - The spatial organization of cell fates during development involves the interpretation of morphogen gradients by cellular signaling cascades and transcriptional networks. Recent studies use biophysical models, genetics, and quantitative imaging to unravel how tissue-level morphogen behavior arises from subcellular events. Moreover, data from several systems show that morphogen gradients, downstream signaling, and the activity of cell-intrinsic transcriptional networks change dynamically during pattern formation. Studies from Drosophila and now also vertebrates suggest that transcriptional network dynamics are central to the generation of gene expression patterns. Together, this leads to the view that pattern formation is an emergent behavior that results from the coordination of events occurring across molecular, cellular, and tissue scales. The development of novel approaches to study this complex process remains a challenge.
AU - Anna Kicheva
AU - Cohen, Michael H
AU - Briscoe, James
ID - 1725
IS - 6104
JF - Science
TI - Developmental pattern formation: Insights from physics and biology
VL - 338
ER -
TY - JOUR
AB - For given non-zero integers a, b, q we investigate the density of solutions (x, y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ.
AU - Timothy Browning
AU - Baier, Stephan
ID - 171
IS - 680
JF - Journal fur die Reine und Angewandte Mathematik
TI - Inhomogeneous cubic congruences and rational points on del Pezzo surfaces
VL - 2013
ER -
TY - JOUR
AB - We report on the electronic transport properties of multiple-gate devices fabricated from undoped silicon nanowires. Understanding and control of the relevant transport mechanisms was achieved by means of local electrostatic gating and temperature-dependent measurements. The roles of the source/drain contacts and of the silicon channel could be independently evaluated and tuned. Wrap gates surrounding the silicide-silicon contact interfaces were proved to be effective in inducing a full suppression of the contact Schottky barriers, thereby enabling carrier injection down to liquid helium temperature. By independently tuning the effective Schottky barrier heights, a variety of reconfigurable device functionalities could be obtained. In particular, the same nanowire device could be configured to work as a Schottky barrier transistor, a Schottky diode, or a p-n diode with tunable polarities. This versatility was eventually exploited to realize a NAND logic gate with gain well above one.
AU - Mongillo, Massimo
AU - Spathis, Panayotis N
AU - Georgios Katsaros
AU - Gentile, Pascal
AU - De Franceschi, Silvano
ID - 1756
IS - 6
JF - Nano Letters
TI - Multifunctional devices and logic gates with undoped silicon nanowires
VL - 12
ER -
TY - JOUR
AB - Self-assembled Ge wires with a height of only 3 unit cells and a length of up to 2 micrometers were grown on Si(001) by means of a catalyst-free method based on molecular beam epitaxy. The wires grow horizontally along either the [100] or the [010] direction. On atomically flat surfaces, they exhibit a highly uniform, triangular cross section. A simple thermodynamic model accounts for the existence of a preferential base width for longitudinal expansion, in quantitative agreement with the experimental findings. Despite the absence of intentional doping, the first transistor-type devices made from single wires show low-resistive electrical contacts and single-hole transport at sub-Kelvin temperatures. In view of their exceptionally small and self-defined cross section, these Ge wires hold promise for the realization of hole systems with exotic properties and provide a new development route for silicon-based nanoelectronics.
AU - Zhang, Jianjun
AU - Georgios Katsaros
AU - Montalenti, Francesco
AU - Scopece, Daniele
AU - Rezaev, Roman O
AU - Mickel, Christine H
AU - Rellinghaus, Bernd
AU - Miglio, Leo P
AU - De Franceschi, Silvano
AU - Rastelli, Armando
AU - Schmidt, Oliver G
ID - 1757
IS - 8
JF - Physical Review Letters
TI - Monolithic growth of ultrathin Ge nanowires on Si(001)
VL - 109
ER -
TY - JOUR
AB - We studied the low-energy states of spin-1/2 quantum dots defined in InAs/InP nanowires and coupled to aluminum superconducting leads. By varying the superconducting gap Δ with a magnetic field B we investigated the transition from strong coupling Δ≪T K to weak-coupling Δ≫T K, where T K is the Kondo temperature. Below the critical field, we observe a persisting zero-bias Kondo resonance that vanishes only for low B or higher temperatures, leaving the room to more robust subgap structures at bias voltages between Δ and 2Δ. For strong and approximately symmetric tunnel couplings, a Josephson supercurrent is observed in addition to the Kondo peak. We ascribe the coexistence of a Kondo resonance and a superconducting gap to a significant density of intragap quasiparticle states, and the finite-bias subgap structures to tunneling through Shiba states. Our results, supported by numerical calculations, own relevance also in relation to tunnel-spectroscopy experiments aiming at the observation of Majorana fermions in hybrid nanostructures.
AU - Lee, Eduardo J
AU - Jiang, Xiaocheng
AU - Aguado, Ramón
AU - Georgios Katsaros
AU - Lieber, Charles M
AU - De Franceschi, Silvano
ID - 1758
IS - 18
JF - Physical Review Letters
TI - Zero-bias anomaly in a nanowire quantum dot coupled to superconductors
VL - 109
ER -
TY - JOUR
AB - Steering a quantum harmonic oscillator state along cyclic trajectories leads to a path-dependent geometric phase. Here we describe its experimental observation in an electronic harmonic oscillator. We use a superconducting qubit as a nonlinear probe of the phase, which is otherwise unobservable due to the linearity of the oscillator. We show that the geometric phase is, for a variety of cyclic paths, proportional to the area enclosed in the quadrature plane. At the transition to the nonadiabatic regime, we study corrections to the phase and dephasing of the qubit caused by qubit-resonator entanglement. In particular, we identify parameters for which this dephasing mechanism is negligible even in the nonadiabatic regime. The demonstrated controllability makes our system a versatile tool to study geometric phases in open quantum systems and to investigate their potential for quantum information processing.
AU - Pechal, M
AU - Berger, Stefan T
AU - Abdumalikov, Abdufarrukh A
AU - Johannes Fink
AU - Mlynek, Jonas A
AU - Steffen, L. Kraig
AU - Wallraff, Andreas
AU - Filipp, Stefan
ID - 1782
IS - 17
JF - Physical Review Letters
TI - Geometric phase and nonadiabatic effects in an electronic harmonic oscillator
VL - 108
ER -
TY - JOUR
AB - Nonlinearity and entanglement are two important properties by which physical systems can be identified as nonclassical. We study the dynamics of the resonant interaction of up to N=3 two-level systems and a single mode of the electromagnetic field sharing a single excitation dynamically. We observe coherent vacuum Rabi oscillations and their nonlinear √N speedup by tracking the populations of all qubits and the resonator in time. We use quantum state tomography to show explicitly that the dynamics generates maximally entangled states of the W class in a time limited only by the collective interaction rate. We use an entanglement witness and the 3-tangle to characterize the state whose fidelity F=78% is limited in our experiments by crosstalk arising during the simultaneous qubit manipulations which is absent in a sequential approach with F=91%.
AU - Mlynek, Jonas A
AU - Abdumalikov, Abdufarrukh A
AU - Johannes Fink
AU - Steffen, L. Kraig
AU - Baur, Matthias P
AU - Lang, C
AU - Van Loo, Arjan F
AU - Wallraff, Andreas
ID - 1783
IS - 5
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics
VL - 86
ER -
TY - JOUR
AB - A localized qubit entangled with a propagating quantum field is well suited to study nonlocal aspects of quantum mechanics and may also provide a channel to communicate between spatially separated nodes in a quantum network. Here, we report the on-demand generation and characterization of Bell-type entangled states between a superconducting qubit and propagating microwave fields composed of zero-, one-, and two-photon Fock states. Using low noise linear amplification and efficient data acquisition we extract all relevant correlations between the qubit and the photon states and demonstrate entanglement with high fidelity.
AU - Eichler, Christopher
AU - Lang, C
AU - Johannes Fink
AU - Govenius, J
AU - Filipp, Stefan
AU - Wallraff, Andreas
ID - 1784
IS - 24
JF - Physical Review Letters
TI - Observation of entanglement between itinerant microwave photons and a superconducting qubit
VL - 109
ER -
TY - JOUR
AB - Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of an individual adult brain region differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes in one brain region, the mouse retina. We found that each adult cell type expressed a specific set of genes, including a unique set of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes carried enough information to categorize cells into morphological classes and types. Several genes that were specifically expressed in particular retinal circuit elements, such as inhibitory neuron types, are associated with eye diseases. The resource described here allows gene expression to be compared across adult retinal cell types, experimenting with specific transcription factors to differentiate stem or somatic cells to retinal cell types, and predicting cellular targets of newly discovered disease-associated genes.
AU - Sandra Siegert
AU - Cabuy, Erik
AU - Scherf, Brigitte G
AU - Kohler, Hubertus
AU - Panda, Satchidananda
AU - Le, Yunzheng
AU - Fehling, Hans J
AU - Gaidatzis, Dimos
AU - Stadler, Michael B
AU - Roska, Botond M
ID - 1801
IS - 3
JF - Nature Neuroscience
TI - Transcriptional code and disease map for adult retinal cell types
VL - 15
ER -
TY - JOUR
AB - Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a "membrane lyzozyme" The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins.
AU - Efremov, Rouslan G
AU - Leonid Sazanov
ID - 1972
IS - 3
JF - Journal of Structural Biology
TI - Structure of Escherichia coli OmpF porin from lipidic mesophase
VL - 178
ER -
TY - GEN
AB - Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes.
AU - Efremov, Rouslan G
AU - Leonid Sazanov
ID - 1976
IS - 10
T2 - Biochimica et Biophysica Acta - Bioenergetics
TI - The coupling mechanism of respiratory complex i - A structural and evolutionary perspective
VL - 1817
ER -
TY - JOUR
AB - In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction-diffusion system.
AU - Schweizer, Jakob
AU - Martin Loose
AU - Bonny, Mike
AU - Kruse, Karsten
AU - Mönch, Ingolf
AU - Schwille, Petra
ID - 1987
IS - 38
JF - PNAS
TI - Geometry sensing by self-organized protein patterns
VL - 109
ER -
TY - CONF
AB - Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively.
AU - Faust, Sebastian
AU - Pietrzak, Krzysztof Z
AU - Schipper, Joachim
ID - 2048
T2 - Conference proceedings CHES 2012
TI - Practical leakage-resilient symmetric cryptography
VL - 7428
ER -
TY - CONF
AB - We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices.
Performance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES.
AU - Heyse, Stefan
AU - Kiltz, Eike
AU - Lyubashevsky, Vadim
AU - Paar, Christof
AU - Pietrzak, Krzysztof Z
ID - 2049
T2 - Conference proceedings FSE 2012
TI - Lapin: An efficient authentication protocol based on ring-LPN
VL - 7549
ER -
TY - JOUR
AB - Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.
AU - Zhou, Qi
AU - Zhu, Hongmei
AU - Huang, Quanfei
AU - Zhao, Li
AU - Zhang, Guo J
AU - Roy, Scott W
AU - Beatriz Vicoso
AU - Xuan, Zhaolin
AU - Ruan, Jue
AU - Zhang, Yue
AU - Zhao, Ruoping
AU - Ye, Chen
AU - Zhang, Xiuqing
AU - Wang, Jùn
AU - Wang, Wen
AU - Bachtrog, Doris
ID - 2073
IS - 1
JF - BMC Genomics
TI - Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
VL - 13
ER -
TY - JOUR
AB - We introduce an algorithm and representation for fabricating 3D shape abstractions using mutually intersecting planar cut-outs. The planes have prefabricated slits at their intersections and are assembled by sliding them together. Often such abstractions are used as a sculptural art form or in architecture and are colloquially called ‘cardboard sculptures’. Based on an analysis of construction rules, we propose an extended binary space partitioning tree as an efficient representation of such cardboard models which allows us to quickly evaluate the feasibility of newly added planar elements. The complexity of insertion order quickly increases with the number of planar elements and manual analysis becomes intractable. We provide tools for generating cardboard sculptures with guaranteed constructibility. In combination with a simple optimization and sampling strategy for new elements, planar shape abstraction models can be designed by iteratively adding elements. As an output, we obtain a fabrication plan that can be printed or sent to a laser cutter. We demonstrate the complete process by designing and fabricating cardboard models of various well-known 3D shapes.
AU - Hildebrand, Kristian
AU - Bernd Bickel
AU - Alexa, Marc
ID - 2079
IS - 2pt3
JF - Computer Graphics Forum
TI - crdbrd: Shape fabrication by sliding planar slices
VL - 31
ER -
TY - JOUR
AB - Articulated deformable characters are widespread in computer animation. Unfortunately, we lack methods for their automatic fabrication using modern additive manufacturing (AM) technologies. We propose a method that takes a skinned mesh as input, then estimates a fabricatable single-material model that approximates the 3D kinematics of the corresponding virtual articulated character in a piecewise linear manner. We first extract a set of potential joint locations. From this set, together with optional, user-specified range constraints, we then estimate mechanical friction joints that satisfy inter-joint non-penetration and other fabrication constraints. To avoid brittle joint designs, we place joint centers on an approximate medial axis representation of the input geometry, and maximize each joint's minimal cross-sectional area. We provide several demonstrations, manufactured as single, assembled pieces using 3D printers.
AU - Bac̈her, Moritz
AU - Bernd Bickel
AU - James, Doug L
AU - Pfister, Hanspeter
ID - 2101
IS - 4
JF - ACM Transactions on Graphics
TI - Fabricating articulated characters from skinned meshes
VL - 31
ER -
TY - JOUR
AB - We propose a complete process for designing, simulating, and fabricating synthetic skin for an animatronics character that mimics the face of a given subject and its expressions. The process starts with measuring the elastic properties of a material used to manufacture synthetic soft tissue. Given these measurements we use physicsbased simulation to predict the behavior of a face when it is driven by the underlying robotic actuation. Next, we capture 3D facial expressions for a given target subject. As the key component of our process, we present a novel optimization scheme that determines the shape of the synthetic skin as well as the actuation parameters that provide the best match to the target expressions. We demonstrate this computational skin design by physically cloning a real human face onto an animatronics figure.
AU - Bernd Bickel
AU - Kaufmann, Peter
AU - Skouras, Mélina
AU - Thomaszewski, Bernhard
AU - Bradley, Derek J
AU - Beeler, Thabo
AU - Jackson, Philip V
AU - Marschner, Steve
AU - Matusik, Wojciech
AU - Groß, Markus S
ID - 2102
IS - 4
JF - ACM Transactions on Graphics
TI - Physical face cloning
VL - 31
ER -
TY - JOUR
AB - Although facial hair plays an important role in individual expression, facial-hair reconstruction is not addressed by current facecapture systems. Our research addresses this limitation with an algorithm that treats hair and skin surface capture together in a coupled fashion so that a high-quality representation of hair fibers as well as the underlying skin surface can be reconstructed. We propose a passive, camera-based system that is robust against arbitrary motion since all data is acquired within the time period of a single exposure. Our reconstruction algorithm detects and traces hairs in the captured images and reconstructs them in 3D using a multiview stereo approach. Our coupled skin-reconstruction algorithm uses information about the detected hairs to deliver a skin surface that lies underneath all hairs irrespective of occlusions. In dense regions like eyebrows, we employ a hair-synthesis method to create hair fibers that plausibly match the image data. We demonstrate our scanning system on a number of individuals and show that it can successfully reconstruct a variety of facial-hair styles together with the underlying skin surface.
AU - Beeler, Thabo
AU - Bernd Bickel
AU - Noris, Gioacchino
AU - Beardsley, Paul A
AU - Marschner, Steve
AU - Sumner, Robert W
AU - Groß, Markus S
ID - 2103
IS - 4
JF - ACM Transactions on Graphics
TI - Coupled 3D reconstruction of sparse facial hair and skin
VL - 31
ER -
TY - CONF
AB - In recent years, various methods have been introduced to exploit pre-recorded data to improve the performance and/or realism of dynamic deformations, but their differences and similarities have not been adequately analyzed or discussed. So far, the proposed methods have been explored mainly in the research context. They have not been adopted by the computer graphics industry. This course bridges the gap between research labs and industry to present a unifying theory and understanding of data-driven methods for dynamic deformations that may inspire development of novel solutions. It focuses on application of data-driven methods to three areas of computer animation: dynamic deformation of faces, soft volumetric tissue, and cloth. And it describes how to approach these challenges in a data-driven manner, classifies the various methods, and demonstrates how data-driven methods can work in other settings.
AU - Otaduy, Miguel A
AU - Bernd Bickel
AU - Bradley, Derek J
AU - Wang, Huamin
ID - 2104
TI - Data-driven simulation methods in computer graphics: Cloth, tissue and faces
ER -
TY - CONF
AU - Skouras, Mélina
AU - Thomaszewski, Bernhard
AU - Bernd Bickel
AU - Groß, Markus S
ID - 2105
IS - 2
TI - Computational design of rubber balloons
VL - 31
ER -
TY - CONF
AB - Progress in cloth simulation for computer animation and apparel design has led to a multitude of deformation models, each with its own way of relating geometry, deformation, and forces. As simulators improve, differences between these models become more important, but it is difficult to choose a model and a set of parameters to match a given real material simply by looking at simulation results. This paper provides measurement and fitting methods that allow nonlinear models to be fit to the observed deformation of a particular cloth sample. Unlike standard textile testing, our system measures complex 3D deformations of a sheet of cloth, not just one-dimensional force-displacement curves, so it works under a wider range of deformation conditions. The fitted models are then evaluated by comparison to measured deformations with motions very different from those used for fitting.
AU - Miguel, Eder
AU - Bradley, Derek J
AU - Thomaszewski, Bernhard
AU - Bernd Bickel
AU - Matusik, Wojciech
AU - Otaduy, Miguel A
AU - Marschner, Steve
ID - 2106
IS - 2
TI - Data-driven estimation of cloth simulation models
VL - 31
ER -
TY - JOUR
AB - We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs.
AU - Hairer, Martin M
AU - Jan Maas
ID - 2125
IS - 4
JF - Annals of Probability
TI - A spatial version of the Itô-Stratonovich correction
VL - 40
ER -
TY - JOUR
AB - We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube.
AU - Erbar, Matthias
AU - Jan Maas
ID - 2127
IS - 3
JF - Archive for Rational Mechanics and Analysis
TI - Ricci curvature of finite Markov chains via convexity of the entropy
VL - 206
ER -
TY - JOUR
AB - We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein.
AU - Jan Maas
AU - van Neerven, Jan M
AU - Portal, Pierre
ID - 2128
IS - 2
JF - Arkiv för Matematik
TI - Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure
VL - 50
ER -
TY - JOUR
AU - Mikhail Lemeshko
AU - Krems, Roman V
AU - Weimer, Hendrik A
ID - 2151
IS - 4
JF - Physical Review Letters
TI - Erratum: Nonadiabatic preparation of spin crystals with ultracold polar molecules
VL - 109
ER -
TY - JOUR
AB - We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation.
AU - Mikhail Lemeshko
AU - Krems, Roman V
AU - Weimer, Hendrik
ID - 2201
IS - 3
JF - Physical Review Letters
TI - Nonadiabatic preparation of spin crystals with ultracold polar molecules
VL - 109
ER -
TY - JOUR
AB - We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime.
AU - Alyabyshev, Sergey V
AU - Mikhail Lemeshko
AU - Krems, Roman V
ID - 2202
IS - 1
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Sensitive imaging of electromagnetic fields with paramagnetic polar molecules
VL - 86
ER -
TY - JOUR
AB - We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off-resonant optical field. The combined interaction potential becomes tunable by variation of wavelength, polarisation and intensity of the optical field and its dependence on the intermolecular separation exhibits a crossover from an inverse-power to an oscillating behaviour. The ability thereby offered to control molecular interactions opens up avenues toward the creation and manipulation of novel phases of ultracold polar gases among whose characteristics is a long-range entanglement of the dipoles' mutual orientation. We devised an accurate analytic model of such optical-field-dressed dipole-dipole interaction potentials, which enables a straightforward access to the optical-field parameters required for the design of intermolecular interactions in the laboratory.
AU - Mikhail Lemeshko
AU - Friedrich, Břetislav
ID - 2203
IS - 15-16
JF - Molecular Physics
TI - Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other
VL - 110
ER -
TY - JOUR
AB - Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM.
AU - Tasic, Bosiljka
AU - Miyamichi, Kazunari
AU - Simon Hippenmeyer
AU - Dani, Vardhan S.
AU - Zeng, H.
AU - Joo, William
AU - Zong, Hui
AU - Chen-Tsai, Yanru
AU - Luo, Liqun
ID - 2262
IS - 3
JF - PLoS One
TI - Extensions of MADM (Mosaic Analysis with Double Markers) in Mice
VL - 7
ER -
TY - JOUR
AB - Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.
AU - Liang, Huixuan
AU - Hippenmeyer, Simon
AU - Ghashghaei, H.
ID - 2263
IS - 12
JF - Biology open
TI - A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors
VL - 1
ER -
TY - CONF
AB - Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications.
AU - Preiner, Reinhold
AU - Jeschke, Stefan
AU - Wimmer, Michael
ID - 2267
TI - Auto splats: Dynamic point cloud visualization on the GPU
ER -
TY - CONF
AB - This paper presents an analytic formulation for anti-aliased sampling of 2D polygons and 3D polyhedra. Our framework allows the exact evaluation of the convolution integral with a linear function defined on the polytopes. The filter is a spherically symmetric polynomial of any order, supporting approximations to refined variants such as the Mitchell-Netravali filter family. This enables high-quality rasterization of triangles and tetrahedra with linearly interpolated vertex values to regular and non-regular grids. A closed form solution of the convolution is presented and an efficient implementation on the GPU using DirectX and CUDA C is described.
AU - Thomas Auzinger
AU - Guthe, Michael
AU - Stefan Jeschke
ID - 2268
IS - 121
TI - Analytic anti-aliasing of linear functions on polytopes
VL - 31
ER -
TY - JOUR
AB - We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.
AU - Henzinger, Thomas A
AU - Mateescu, Maria
ID - 2302
IS - 2
JF - IEEE ACM Transactions on Computational Biology and Bioinformatics
TI - The propagation approach for computing biochemical reaction networks
VL - 10
ER -
TY - JOUR
AB - The Manin conjecture is established for Châtelet surfaces over Q aris-ing as minimal proper smooth models of the surface Y 2 + Z 2 = f(X) in A 3 Q, where f ∈ Z[X] is a totally reducible polynomial of degree 3 without repeated roots. These surfaces do not satisfy weak approximation.
AU - de la Bretèche, Régis
AU - Timothy Browning
AU - Peyre, Emmanuel
ID - 237
IS - 1
JF - Annals of Mathematics
TI - On Manin's conjecture for a family of Châtelet surfaces
VL - 175
ER -
TY - JOUR
AB - For given positive integers a, b, q we investigate the density of solutions (x, y) ∈ Z2 to congruences ax + by2 ≡ 0 mod q.
AU - Baier, Stephan
AU - Timothy Browning
ID - 238
IS - 2
JF - Functiones et Approximatio, Commentarii Mathematici
TI - Inhomogeneous quadratic congruences
VL - 47
ER -
TY - JOUR
AB - We study the BCS gap equation for a Fermi gas with unequal population of spin-up and spin-down states. For cosh (δ μ/T) ≤ 2, with T the temperature and δμ the chemical potential difference, the question of existence of non-trivial solutions can be reduced to spectral properties of a linear operator, similar to the unpolarized case studied previously in [Frank, R. L., Hainzl, C., Naboko, S., and Seiringer, R., J., Geom. Anal.17, 559-567 (2007)10.1007/BF02937429; Hainzl, C., Hamza, E., Seiringer, R., and Solovej, J. P., Commun., Math. Phys.281, 349-367 (2008)10.1007/s00220-008-0489-2; and Hainzl, C. and Seiringer, R., Phys. Rev. B77, 184517-110 435 (2008)]10.1103/PhysRevB.77.184517. For cosh (δ μ/T) > 2 the phase diagram is more complicated, however. We derive upper and lower bounds for the critical temperature, and study their behavior in the small coupling limit.
AU - Freiji, Abraham
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2394
IS - 1
JF - Journal of Mathematical Physics
TI - The gap equation for spin-polarized fermions
VL - 53
ER -
TY - JOUR
AB - We give the first rigorous derivation of the celebrated Ginzburg-Landau (GL) theory, starting from the microscopic Bardeen-Cooper-Schrieffer (BCS) model. Close to the critical temperature, GL arises as an effective theory on the macroscopic scale. The relevant scaling limit is semiclassical in nature, and semiclassical analysis, with minimal regularity assumptions, plays an important part in our proof.
AU - Frank, Rupert L
AU - Hainzl, Christian
AU - Robert Seiringer
AU - Solovej, Jan P
ID - 2395
IS - 3
JF - Journal of the American Mathematical Society
TI - Microscopic derivation of Ginzburg-Landau theory
VL - 25
ER -
TY - JOUR
AB - A positive temperature analogue of the scattering length of a potential V can be defined via integrating the difference of the heat kernels of -Δ and, with Δ the Laplacian. An upper bound on this quantity is a crucial input in the derivation of a bound on the critical temperature of a dilute Bose gas (Seiringer and Ueltschi in Phys Rev B 80:014502, 2009). In (Seiringer and Ueltschi in Phys Rev B 80:014502, 2009), a bound was given in the case of finite range potentials and sufficiently low temperature. In this paper, we improve the bound and extend it to potentials of infinite range.
AU - Landon, Benjamin
AU - Robert Seiringer
ID - 2396
IS - 3
JF - Letters in Mathematical Physics
TI - The scattering length at positive temperature
VL - 100
ER -
TY - JOUR
AB - We consider the low-density limit of a Fermi gas in the BCS approximation. We show that if the interaction potential allows for a two-particle bound state, the system at zero temperature is well approximated by the Gross-Pitaevskii functional, describing a Bose-Einstein condensate of fermion pairs.
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2397
IS - 2
JF - Letters in Mathematical Physics
TI - Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs
VL - 100
ER -
TY - GEN
AB - We extend the mathematical theory of quantum hypothesis testing to the general W*-algebraic setting and explore its relation with recent developments in non-equilibrium quantum statistical mechanics. In particular, we relate the large deviation principle for the full counting statistics of entropy flow to quantum hypothesis testing of the arrow of time.
AU - Jakšić, Vojkan
AU - Ogata, Yoshiko
AU - Pillet, Claude A
AU - Robert Seiringer
ID - 2398
IS - 6
T2 - Reviews in Mathematical Physics
TI - Quantum hypothesis testing and non-equilibrium statistical mechanics
VL - 24
ER -
TY - CHAP
AB - Bose–Einstein condensation (BEC) in cold atomic gases was first achieved experimentally in 1995 [1, 6]. After initial failed attempts with spin-polarized atomic hydrogen, the first successful demonstrations of this phenomenon used gases of rubidium and sodium atoms, respectively. Since then there has been a surge of activity in this field, with ingenious experiments putting forth more and more astonishing results about the behavior of matter at very cold temperatures.
AU - Robert Seiringer
ED - Rivasseau, Vincent
ED - Robert Seiringer
ED - Solovej, Jan P
ED - Spencer, Thomas
ID - 2399
T2 - Quantum Many Body Systems
TI - Cold quantum gases and bose einstein condensation
VL - 2051
ER -
TY - JOUR
AB - We investigate the frequency of positive squareful numbers x, y, z≤B for which x+y=z and present a conjecture concerning its asymptotic behavior.
AU - Timothy Browning
AU - Valckenborgh, K Van
ID - 240
IS - 2
JF - Experimental Mathematics
TI - Sums of three squareful numbers
VL - 21
ER -
TY - JOUR
AB - If the polaron coupling constant α is large enough, bipolarons or multi-polarons will form. When passing through the critical α c from above, does the radius of the system simply get arbitrarily large or does it reach a maximum and then explode? We prove that it is always the latter. We also prove the analogous statement for the Pekar-Tomasevich (PT) approximation to the energy, in which case there is a solution to the PT equation at α c. Similarly, we show that the same phenomenon occurs for atoms, e. g., helium, at the critical value of the nuclear charge. Our proofs rely only on energy estimates, not on a detailed analysis of the Schrödinger equation, and are very general. They use the fact that the Coulomb repulsion decays like 1/r, while 'uncertainty principle' localization energies decay more rapidly, as 1/r 2.
AU - Frank, Rupert L
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2400
IS - 2
JF - Communications in Mathematical Physics
TI - Binding of polarons and atoms at threshold
VL - 313
ER -
TY - JOUR
AB - We find further implications of the BMV conjecture, which states that for hermitian matrices B≥0 and A, the function λ {mapping} Tr exp(A - λB) is the Laplace transform of a positive measure supported on [0,∞].
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2401
IS - 1
JF - Journal of Statistical Physics
TI - Further implications of the Bessis-Moussa-Villani conjecture
VL - 149
ER -
TY - JOUR
AB - We consider a model of quantum-mechanical particles interacting via point interactions of infinite scattering length. In the case of fermions we prove a Lieb-Thirring inequality for the energy, i.e., we show that the energy is bounded from below by a constant times the integral of the particle density to the power.
AU - Frank, Rupert L
AU - Robert Seiringer
ID - 2402
IS - 9
JF - Journal of Mathematical Physics
TI - Lieb-Thirring inequality for a model of particles with point interactions
VL - 53
ER -
TY - JOUR
AB - We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose-Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wavefunction of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers and strong interactions the wavefunction extends over the whole interval. A high density of scatterers and weak interactions, on the other hand, lead to localization of the wavefunction in a fragmented subset of the interval.
AU - Robert Seiringer
AU - Yngvason, Jakob
AU - Zagrebnov, Valentin A
ID - 2403
IS - 11
JF - Journal of Statistical Mechanics Theory and Experiment
TI - Disordered Bose-Einstein condensates with interaction in one dimension
VL - 2012
ER -
TY - JOUR
AB - The representation of integral binary forms as sums of two squares is discussed and applied to establish the Manin conjecture for certain Châtelet surfaces over ℚ.
AU - de la Bretèche, Régis
AU - Timothy Browning
ID - 241
IS - 2
JF - Israel Journal of Mathematics
TI - Binary forms as sums of two squares and Châtelet surfaces
VL - 191
ER -
TY - JOUR
AB - The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.
AU - Ebersberger, Ingo
AU - De Matos Simoes, Ricardo
AU - Kupczok, Anne
AU - Gube, Matthias
AU - Kothe, Erika
AU - Voigt, Kerstin
AU - Von Haeseler, Arndt
ID - 2411
IS - 5
JF - Molecular Biology and Evolution
TI - A consistent phylogenetic backbone for the fungi
VL - 29
ER -
TY - JOUR
AB - The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders.
AU - Dixon-Salazar, Tracy J
AU - Silhavy, Jennifer L
AU - Udpa, Nitin
AU - Schroth, Jana
AU - Bielas, Stephanie L
AU - Schaffer, Ashleigh E
AU - Olvera, Jesus
AU - Bafna, Vineet K
AU - Zaki, Maha S
AU - Abdel-Salam, Ghada M
AU - Mansour, Lobna A
AU - Selim, Laila A
AU - Abdel-Hadi, Sawsan S
AU - Marzouki, Naima
AU - Ben-Omran, Tawfeg I
AU - Al-Saana, Nouriya A
AU - Sönmez, Fatma M
AU - Celep, Figen
AU - Azam, Matloob
AU - Hill, Kiley J
AU - Collazo, Adrienne
AU - Fenstermaker, Ali G
AU - Gaia Novarino
AU - Akizu, Naiara
AU - Garimella, Kiran V
AU - Sougnez, Carrie L
AU - Russ, Carsten
AU - Gabriel, Stacey B
AU - Gleeson, Joseph G
ID - 2313
IS - 138
JF - Science Translational Medicine
TI - Exome sequencing can improve diagnosis and alter patient management
VL - 4
ER -
TY - JOUR
AB - Autism spectrum disorders are a genetically heterogeneous constellation of syndromes characterized by impairments in reciprocal social interaction. Available somatic treatments have limited efficacy. We have identified inactivating mutations in the gene BCKDK (Branched Chain Ketoacid Dehydrogenase Kinase) in consanguineous families with autism, epilepsy, and intellectual disability. The encoded protein is responsible for phosphorylation-mediated inactivation of the E1α subunit of branched-chain ketoacid dehydrogenase (BCKDH). Patients with homozygous BCKDK mutations display reductions in BCKDK messenger RNA and protein, E1α phosphorylation, and plasma branched-chain amino acids. Bckdk knockout mice show abnormal brain amino acid profiles and neurobehavioral deficits that respond to dietary supplementation. Thus, autism presenting with intellectual disability and epilepsy caused by BCKDK mutations represents a potentially treatable syndrome.
AU - Gaia Novarino
AU - El-Fishawy, Paul
AU - Kayserili, Hülya
AU - Meguid, Nagwa A
AU - Scott, Eric M
AU - Schroth, Jana
AU - Silhavy, Jennifer L
AU - Kara, Majdi
AU - Khalil, Rehab O
AU - Ben-Omran, Tawfeg I
AU - Ercan-Sencicek, Adife G
AU - Hashish, Adel F
AU - Sanders, Stephan J
AU - Gupta, Abha R
AU - Hashem, Hebatalla S
AU - Matern, Dietrich
AU - Gabriel, Stacey B
AU - Sweetman, Lawrence
AU - Rahimi, Yasmeen
AU - Harris, Robert A
AU - State, Matthew W
AU - Gleeson, Joseph G
ID - 2314
IS - 6105
JF - Science
TI - Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy
VL - 338
ER -
TY - CONF
AB - We summarize our recent results on the ground state energy of multi-polaron systems. In particular, we discuss stability and existence of the thermodynamic limit, and we discuss the absence of binding in the case of large Coulomb repulsion and the corresponding binding-unbinding transition. We also consider the Pekar-Tomasevich approximation to the ground state energy and we study radial symmetry of the ground state density.
AU - Frank, Rupert L
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Thomas, Lawrence E
ID - 2316
TI - Ground state properties of multi-polaron systems
ER -
TY - CONF
AB - We present a summary of our recent rigorous derivation of the celebrated Ginzburg-Landau (GL) theory, starting from the microscopic Bardeen-Cooper-Schrieffer (BCS) model. Close to the critical temperature, GL arises as an effective theory on the macroscopic scale. The relevant scaling limit is semiclassical in nature, and semiclassical analysis, with minimal regularity assumptions, plays an important part in our proof.
AU - Frank, Rupert L
AU - Hainzl, Christian
AU - Robert Seiringer
AU - Solovej, Jan P
ID - 2317
TI - Microscopic derivation of the Ginzburg-Landau model
ER -
TY - JOUR
AB - We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential.
AU - Seiringer, Robert
ID - 2318
IS - 3
JF - Journal of Spectral Theory
TI - Absence of bound states implies non-negativity of the scattering length
VL - 2
ER -
TY - JOUR
AB - We investigate the first and second moments of shifted convolutions of the generalized divisor function d 3(n).
AU - Baier, Stephan
AU - Timothy Browning
AU - Marasingha, Gihan
AU - Zhao, Liangyi
ID - 242
IS - 3
JF - Proceedings of the Edinburgh Mathematical Society
TI - Averages of shifted convolutions of d3 (n)
VL - 55
ER -
TY - JOUR
AB - Let P(t) ∈ ℚ[t] be an irreducible quadratic polynomial and suppose that K is a quartic extension of ℚ containing the roots of P(t). Let N K/ℚ(X) be a full norm form for the extension K/ℚ. We show that the variety P(t) =N K/ℚ(X)≠ 0 satisfies the Hasse principle and weak approximation. The proof uses analytic methods.
AU - Timothy Browning
AU - Heath-Brown, Roger
ID - 243
IS - 5
JF - Geometric and Functional Analysis
TI - Quadratic polynomials represented by norm forms
VL - 22
ER -
TY - JOUR
AB - The colored Tverberg theorem asserts that for eve;ry d and r there exists t=t(d,r) such that for every set C ⊂ ℝ d of cardinality (d + 1)t, partitioned into t-point subsets C 1, C 2,...,C d+1 (which we think of as color classes; e. g., the points of C 1 are red, the points of C 2 blue, etc.), there exist r disjoint sets R 1, R 2,...,R r⊆C that are rainbow, meaning that {pipe}R i∩C j{pipe}≤1 for every i,j, and whose convex hulls all have a common point. All known proofs of this theorem are topological. We present a geometric version of a recent beautiful proof by Blagojević, Matschke, and Ziegler, avoiding a direct use of topological methods. The purpose of this de-topologization is to make the proof more concrete and intuitive, and accessible to a wider audience.
AU - Matoušek, Jiří
AU - Martin Tancer
AU - Uli Wagner
ID - 2438
IS - 2
JF - Discrete & Computational Geometry
TI - A geometric proof of the colored Tverberg theorem
VL - 47
ER -
TY - JOUR
AB - A Monte Carlo approximation algorithm for the Tukey depth problem in high dimensions is introduced. The algorithm is a generalization of an algorithm presented by Rousseeuw and Struyf (1998) . The performance of this algorithm is studied both analytically and experimentally.
AU - Chen, Dan
AU - Morin, Pat
AU - Uli Wagner
ID - 2439
IS - 5
JF - Computational Geometry: Theory and Applications
TI - Absolute approximation of Tukey depth: Theory and experiments
VL - 46
ER -
TY - JOUR
AB - We investigate the solubility of the congruence xy ≡ 1 (mod p), where p is a prime and x, y are restricted to lie in suitable short intervals. Our work relies on a mean value theorem for incomplete Kloosterman sums.
AU - Timothy Browning
AU - Haynes, Alan K
ID - 244
IS - 2
JF - International Journal of Number Theory
TI - Incomplete kloosterman sums and multiplicative inverses in short intervals
VL - 9
ER -
TY - CONF
AB - We present an algorithm for computing [X, Y], i.e., all homotopy classes of continuous maps X → Y, where X, Y are topological spaces given as finite simplicial complexes, Y is (d - 1)-connected for some d ≥ 2 (for example, Y can be the d-dimensional sphere S d), and dim X ≤ 2d - 2. These conditions on X, Y guarantee that [X, Y] has a natural structure of a finitely generated Abelian group, and the algorithm finds generators and relations for it. We combine several tools and ideas from homotopy theory (such as Postnikov systems, simplicial sets, and obstruction theory) with algorithmic tools from effective algebraic topology (objects with effective homology). We hope that a further extension of the methods developed here will yield an algorithm for computing, in some cases of interest, the ℤ 2-index, which is a quantity playing a prominent role in Borsuk-Ulam style applications of topology in combinatorics and geometry, e.g., in topological lower bounds for the chromatic number of a graph. In a certain range of dimensions, deciding the embeddability of a simplicial complex into ℝ d also amounts to a ℤ 2-index computation. This is the main motivation of our work. We believe that investigating the computational complexity of questions in homotopy theory and similar areas presents a fascinating research area, and we hope that our work may help bridge the cultural gap between algebraic topology and theoretical computer science.
AU - Čadek, Martin
AU - Marek Krcál
AU - Matoušek, Jiří
AU - Sergeraert, Francis
AU - Vokřínek, Lukáš
AU - Uli Wagner
ID - 2440
TI - Computing all maps into a sphere
ER -
TY - CONF
AB - Eigenvalues associated to graphs are a well-studied subject. In particular the spectra of the adjacency matrix and of the Laplacian of random graphs G(n, p) are known quite precisely. We consider generalizations of these matrices to simplicial complexes of higher dimensions and study their eigenvalues for the Linial-Meshulam model X k(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(log n/n), the eigenvalues of both, the higher-dimensional adjacency matrix and the Laplacian, are a.a.s. sharply concentrated around two values. In a second part of the paper, we discuss a possible higherdimensional analogue of the Discrete Cheeger Inequality. This fundamental inequality expresses a close relationship between the eigenvalues of a graph and its combinatorial expansion properties; in particular, spectral expansion (a large eigenvalue gap) implies edge expansion. Recently, a higher-dimensional analogue of edge expansion for simplicial complexes was introduced by Gromov, and independently by Linial, Meshulam and Wallach and by Newman and Rabinovich. It is natural to ask whether there is a higher-dimensional version of Cheeger's inequality. We show that the most straightforward version of a higher-dimensional Cheeger inequality fails: for every k > 1, there is an infinite family of k-dimensional complexes that are spectrally expanding (there is a large eigenvalue gap for the Laplacian) but not combinatorially expanding.
AU - Gundert, Anna
AU - Uli Wagner
ID - 2441
TI - On Laplacians of random complexes
ER -
TY - JOUR
AB - Left-right asymmetry of human brain function has been known for a century, although much of molecular and cellular basis of brain laterality remains to be elusive. Recent studies suggest that hippocampal CA3-CA1 excitatory synapses are asymmetrically arranged, however, the functional implication of the asymmetrical circuitry has not been studied at the behavioral level. In order to address the left-right asymmetry of hippocampal function in behaving mice, we analyzed the performance of "split-brain" mice in the Barnes maze. The "split-brain" mice received ventral hippocampal commissure and corpus callosum transection in addition to deprivation of visual input from one eye. In such mice, the hippocampus in the side of visual deprivation receives sensory-driven input. Better spatial task performance was achieved by the mice which were forced to use the right hippocampus than those which were forced to use the left hippocampus. In two-choice spatial maze, forced usage of left hippocampus resulted in a comparable performance to the right counterpart, suggesting that both hippocampal hemispheres are capable of conducting spatial learning. Therefore, the results obtained from the Barnes maze suggest that the usage of the right hippocampus improves the accuracy of spatial memory. Performance of non-spatial yet hippocampus-dependent tasks (e.g. fear conditioning) was not influenced by the laterality of the hippocampus.
AU - Shinohara, Yoshiaki
AU - Hosoya, Aki
AU - Yamasaki, Nobuyuki
AU - Ahmed, Hassan
AU - Hattori, Satoko
AU - Eguchi, Megumi
AU - Yamaguchi, Shun
AU - Miyakawa, Tsuyoshi
AU - Hirase, Hajime
AU - Ryuichi Shigemoto
ID - 2687
IS - 2
JF - Hippocampus
TI - Right-hemispheric dominance of spatial memory in split-brain mice
VL - 22
ER -
TY - JOUR
AB - To gain insights into structure-function relationship of excitatory synapses, we revisit our quantitative analysis of synaptic AMPAR by highly sensitive freeze-fracture replica labeling in eight different connections. All of these connections showed linear correlation between synapse size and AMPAR number indicating a common intra-synapse-type relationship in CNS synapses. On the contrary, inter-synapse-type relationship is unexpected indicating no correlation between averages of synapse size and AMPAR number. Interestingly, connections with large average synapse size and low AMPAR density showed high variability of AMPAR number and mosaic distribution within the postsynaptic membrane. We propose an idea that these connections may quickly exhibit synaptic plasticity by modifying AMPAR density/number whereas those with high AMPAR density change their efficacy by modifying synapse size.
AU - Fukazawa, Yugo
AU - Ryuichi Shigemoto
ID - 2688
IS - 3
JF - Current Opinion in Neurobiology
TI - Intra-synapse-type and inter-synapse-type relationships between synaptic size and AMPAR expression
VL - 22
ER -
TY - JOUR
AB - R-type calcium channels (RTCCs) are well known for their role in synaptic plasticity, but little is known about their subcellular distribution across various neuronal compartments. Using subtype-specific antibodies, we characterized the regional and subcellular localization of Ca v2.3 in mice and rats at both light and electron microscopic levels. Ca v2.3 immunogold particles were found to be predominantly presynaptic in the interpeduncular nucleus, but postsynaptic in other brain regions. Serial section analysis of electron microscopic images from the hippocampal CA1 revealed a higher density of immunogold particles in the dendritic shaft plasma membrane compared with the pyramidal cell somata. However, the labeling densities were not significantly different among the apical, oblique, or basal dendrites. Immunogold particles were also observed over the plasma membrane of dendritic spines, including both synaptic and extrasynaptic sites. Individual spine heads contained <20 immunogold particles, with an average density of ~260 immunoparticles per μm 3 spine head volume, in accordance with the density of RTCCs estimated using calcium imaging (Sabatini and Svoboda, 2000). The Ca v2.3 density was variable among similar-sized spine heads and did not correlate with the density in the parent dendrite, implying that spines are individual calcium compartments operating autonomously from their parent dendrites.
AU - Parajuli, Laxmi K
AU - Nakajima, Chikako
AU - Kulik, Ákos
AU - Matsui, Ko
AU - Schneider, Toni
AU - Ryuichi Shigemoto
AU - Fukazawa, Yugo
ID - 2689
IS - 39
JF - Journal of Neuroscience
TI - Quantitative regional and ultra structural localization of the Ca v2 3 subunit of R type calcium channel in mouse brain
VL - 32
ER -
TY - JOUR
AB - Constitutive endocytic recycling is a crucial mechanism allowing regulation of the activity of proteins at the plasma membrane and for rapid changes in their localization, as demonstrated in plants for PIN-FORMED (PIN) proteins, the auxin transporters. To identify novel molecular components of endocytic recycling, mainly exocytosis, we designed a PIN1-green fluorescent protein fluorescence imaging-based forward genetic screen for Arabidopsis thaliana mutants that showed increased intracellular accumulation of cargos in response to the trafficking inhibitor brefeldin A (BFA). We identified bex5 (for BFA-visualized exocytic trafficking defective), a novel dominant mutant carrying a missense mutation that disrupts a conserved sequence motif of the small GTPase, RAS GENES FROM RAT BRAINA1b. bex5 displays defects such as enhanced protein accumulation in abnormal BFA compartments, aberrant endosomes, and defective exocytosis and transcytosis. BEX5/RabA1b localizes to trans-Golgi network/early endosomes (TGN/EE) and acts on distinct trafficking processes like those regulated by GTP exchange factors on ADP-ribosylation factors GNOM-LIKE1 and HOPM INTERACTOR7/BFA-VISUALIZED ENDOCYTIC TRAFFICKING DEFECTIVE1, which regulate trafficking at the Golgi apparatus and TGN/EE, respectively. All together, this study identifies Arabidopsis BEX5/RabA1b as a novel regulator of protein trafficking from a TGN/EE compartment to the plasma membrane.
AU - Feraru, Elena
AU - Feraru, Mugurel Ioan
AU - Asaoka, Rin
AU - Paciorek, Tomasz
AU - De Rycke, Riet M
AU - Tanaka, Hirokazu
AU - Nakano, Akihiko
AU - Jirí Friml
ID - 2453
IS - 7
JF - Plant Cell
TI - BEX5/RabA1b regulates trans-Golgi network-to-plasma membrane protein trafficking in Arabidopsis
VL - 24
ER -
TY - JOUR
AB - The third EMBO Conference on Plant Molecular Biology, which focused on ‘Plant development and environmental interactions’,was held in May 2012 in Matera, Italy. Here, we review some of the topics and themes that emerged from the various contributions; namely, steering technologies, transcriptional networks and hormonal regulation, small RNAs, cell and tissue polarity, environmental control and natural variation. We intend to provide the reader who might have missed this remarkable event with a glimpse of the recent progress made in this blossoming research field.
AU - Beeckman, Tom
AU - Friml, Jirí
ID - 2456
IS - 20
JF - Development
TI - Plant developmental biologists meet on stairways in Matera
VL - 139
ER -
TY - JOUR
AB - Initiation and successive development of organs induce mechanical stresses at the cellular level. Using the tomato shoot apex, a new study now proposes that mechanical strain regulates the plasma membrane abundance of the PIN1 auxin transporter, thereby reinforcing a positive feed-back loop between growth and auxin accumulation.
AU - Li, Hongjiang
AU - Friml, Jirí
AU - Grunewald, Wim
ID - 2458
IS - 16
JF - Current Biology
TI - Cell polarity: Stretching prevents developmental cramps
VL - 22
ER -
TY - JOUR
AB - Coordinated, subcellular trafficking of proteins is one of the fundamental properties of the multicellular eukaryotic organisms. Trafficking involves a large diversity of compartments, pathways, cargo molecules, and vesicle-sorting events. It is also crucial in regulating the localization and, thus, the activity of various proteins, but the process is still poorly genetically defined in plants. In the past, forward genetics screens had been used to determine the function of genes by searching for a specific morphological phenotype in the organism population in which mutations had been induced chemically or by irradiation. Unfortunately, these straightforward genetic screens turned out to be limited in identifying new regulators of intracellular protein transport, because mutations affecting essential trafficking pathways often lead to lethality. In addition, the use of these approaches has been restricted by functional redundancy among trafficking regulators. Screens for mutants that rely on the observation of changes in the cellular localization or dynamics of fluorescent subcellular markers enable, at least partially, to circumvent these issues. Hence, such image-based screens provide the possibility to identify either alleles with weak effects or components of the subcellular trafficking machinery that have no strong impact on the plant growth.
AU - Zwiewka, Marta
AU - Friml, Jirí
ID - 2459
IS - May
JF - Frontiers in Plant Science
TI - Fluorescence imaging-based forward genetic screens to identify trafficking regulators in plants
VL - 3
ER -
TY - JOUR
AB - Interneurons are critical for neuronal circuit function, but how their dendritic morphologies and membrane properties influence information flow within neuronal circuits is largely unknown. We studied the spatiotemporal profile of synaptic integration and short-term plasticity in dendrites of mature cerebellar stellate cells by combining two-photon guided electrical stimulation, glutamate uncaging, electron microscopy, and modeling. Synaptic activation within thin (0.4 μm) dendrites produced somatic responses that became smaller and slower with increasing distance from the soma, sublinear subthreshold input-output relationships, and a somatodendritic gradient of short-term plasticity. Unlike most studies showing that neurons employ active dendritic mechanisms, we found that passive cable properties of thin dendrites determine the sublinear integration and plasticity gradient, which both result from large dendritic depolarizations that reduce synaptic driving force. These integrative properties allow stellate cells to act as spatiotemporal filters of synaptic input patterns, thereby biasing their output in favor of sparse presynaptic activity. Stellate cells are critical sources of inhibition in the cerebellum, but how their dendrites integrate excitatory synaptic inputs is unknown. Abrahamsson et al. show that thin dendrites and passive membrane properties of SCs promote sublinear synaptic summation and distance-dependent short-term plasticity.
AU - Abrahamsson, Therese
AU - Cathala, Laurence
AU - Matsui, Ko
AU - Ryuichi Shigemoto
AU - DiGregorio, David A
ID - 2474
IS - 6
JF - Neuron
TI - Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity
VL - 73
ER -
TY - JOUR
AB - Background: One of the best-characterized causative factors of Alzheimer's disease (AD) is the generation of amyloid-β peptide (Aβ). AD subjects are at high risk of epileptic seizures accompanied by aberrant neuronal excitability, which in itself enhances Aβ generation. However, the molecular linkage between epileptic seizures and Aβ generation in AD remains unclear. Results: X11 and X11-like (X11L) gene knockout mice suffered from epileptic seizures, along with a malfunction of hyperpolarization-activated cyclic nucleotide gated (HCN) channels. Genetic ablation of HCN1 in mice and HCN1 channel blockage in cultured Neuro2a (N2a) cells enhanced Aβ generation. Interestingly, HCN1 levels dramatically decreased in the temporal lobe of cynomolgus monkeys (Macaca fascicularis) during aging and were significantly diminished in the temporal lobe of sporadic AD patients. Conclusion: Because HCN1 associates with amyloid-β precursor protein (APP) and X11/X11L in the brain, genetic deficiency of X11/X11L may induce aberrant HCN1 distribution along with epilepsy. Moreover, the reduction in HCN1 levels in aged primates may contribute to augmented Aβ generation. Taken together, HCN1 is proposed to play an important role in the molecular linkage between epileptic seizures and Aβ generation, and in the aggravation of sporadic AD.
AU - Saito, Yuhki
AU - Inoue, Tsuyoshi
AU - Zhu, Gang
AU - Kimura, Naoki
AU - Okada, Motohiro
AU - Nishimura, Masaki
AU - Murayama, Shigeo
AU - Kaneko, Sunao
AU - Ryuichi Shigemoto
AU - Imoto, Keiji
AU - Suzuki, Toshiharu
ID - 2475
IS - 1
JF - Molecular Neurodegeneration
TI - Hyperpolarization-activated cyclic nucleotide gated channels: A potential molecular link between epileptic seizures and Aβ generation in Alzheimer's disease
VL - 7
ER -
TY - JOUR
AB - Recently developed pharmacogenetic and optogenetic approaches, with their own advantages and disadvantages, have become indispensable tools in modern neuroscience. Here, we employed a previously described knock-in mouse line (GABA ARγ2 77Ilox) in which the γ2 subunit of the GABA A receptor (GABA AR) was mutated to become zolpidem insensitive (γ2 77I) and used viral vectors to swap γ2 77I with wild-type, zolpidem-sensitive γ2 subunits (γ2 77F). The verification of unaltered density and subcellular distribution of the virally introduced γ2 subunits requires their selective labelling. For this we generated six N- and six C-terminal-tagged γ2 subunits, with which cortical cultures of GABA ARγ2 -/- mice were transduced using lentiviruses. We found that the N-terminal AU1 tag resulted in excellent immunodetection and unimpaired synaptic localization. Unaltered kinetic properties of the AU1-tagged γ2 ( AU1γ2 77F) channels were demonstrated with whole-cell patch-clamp recordings of spontaneous IPSCs from cultured cells. Next, we carried out stereotaxic injections of lenti- and adeno-associated viruses containing Cre-recombinase and the AU1γ2 77F subunit (Cre-2A- AU1γ2 77F) into the neocortex of GABA ARγ2 77Ilox mice. Light microscopic immunofluorescence and electron microscopic freeze-fracture replica immunogold labelling demonstrated the efficient immunodetection of the AU1 tag and the normal enrichment of the AU1γ2 77F subunits in perisomatic GABAergic synapses. In line with this, miniature and action potential-evoked IPSCs whole-cell recorded from transduced cells had unaltered amplitudes, kinetics and restored zolpidem sensitivity. Our results obtained with a wide range of structural and functional verification methods reveal unaltered subcellular distributions and functional properties of γ2 77I and AU1γ2 77F GABA ARs in cortical pyramidal cells. This transgenic-viral pharmacogenetic approach has the advantage that it does not require any extrinsic protein that might endow some unforeseen alterations of the genetically modified cells. In addition, this virus-based approach opens up the possibility of modifying multiple cell types in distinct brain regions and performing alternative recombination-based intersectional genetic manipulations.
AU - Sümegi, Máté
AU - Fukazawa, Yugo
AU - Matsui, Ko
AU - Lörincz, Andrea
AU - Eyre, Mark D
AU - Nusser, Zoltán
AU - Ryuichi Shigemoto
ID - 2476
IS - 7
JF - Journal of Physiology
TI - Virus-mediated swapping of zolpidem-insensitive with zolpidem-sensitive GABA A receptors in cortical pyramidal cells
VL - 590
ER -
TY - JOUR
AB - Dynamic activity of glia has repeatedly been demonstrated, but if such activity is independent from neuronal activity, glia would not have any role in the information processing in the brain or in the generation of animal behavior. Evidence for neurons communicating with glia is solid, but the signaling pathway leading back from glial-to-neuronal activity was often difficult to study. Here, we introduced a transgenic mouse line in which channelrhodopsin-2, a light-gated cation channel, was expressed in astrocytes. Selective photostimulation of these astrocytes in vivo triggered neuronal activation. Using slice preparations, we show that glial photostimulation leads to release of glutamate, which was sufficient to activate AMPA receptors on Purkinje cells and to induce long-term depression of parallel fiber-to-Purkinje cell synapses through activation of metabotropic glutamate receptors. In contrast to neuronal synaptic vesicular release, glial activation likely causes preferential activation of extrasynaptic receptors that appose glial membrane. Finally, we show that neuronal activation by glial stimulation can lead to perturbation of cerebellar modulated motor behavior. These findings demonstrate that glia can modulate the tone of neuronal activity and behavior. This animal model is expected to be a potentially powerful approach to study the role of glia in brain function.
AU - Sasaki, Takuya
AU - Beppu, Kaoru
AU - Tanaka, Kenji F
AU - Fukazawa, Yugo
AU - Ryuichi Shigemoto
AU - Matsui, Ko
ID - 2477
IS - 50
JF - PNAS
TI - Application of an optogenetic byway for perturbing neuronal activity via glial photostimulation
VL - 109
ER -
TY - JOUR
AB - Visual information must be relayed through the lateral geniculate nucleus before it reaches the visual cortex. However, not all spikes created in the retina lead to postsynaptic spikes and properties of the retinogeniculate synapse contribute to this filtering. To understand the mechanisms underlying this filtering process, we conducted electrophysiology to assess the properties of signal transmission in the Long-Evans rat. We also performed SDS-digested freeze-fracture replica labeling to quantify the receptor and transporter distribution, as well as EM reconstruction to describe the 3D structure. To analyze the impact of transmitter diffusion on the activity of the receptors, simulations were integrated. We identified that a large contributor to the filtering is the marked paired-pulse depression at this synapse, which was intensified by the morphological characteristics of the contacts. The broad presynaptic and postsynaptic contact area restricts transmitter diffusion two dimensionally. Additionally, the presence of multiple closely arranged release sites invites intersynaptic spillover, which causes desensitization of AMPA receptors. The presence of AMPA receptors that slowly recover from desensitization along with the high presynaptic release probability and multivesicular release at each synapse also contribute to the depression. These features contrast with many other synapses where spatiotemporal spread of transmitter is limited by rapid transmitter clearance allowing synapses to operate more independently. We propose that the micrometer-order structure can ultimately affect the visual information processing.
AU - Budisantoso, Timotheus
AU - Matsui, Ko
AU - Kamasawa, Naomi
AU - Fukazawa, Yugo
AU - Ryuichi Shigemoto
ID - 2514
IS - 7
JF - Journal of Neuroscience
TI - Mechanisms underlying signal filtering at a multisynapse contact
VL - 32
ER -
TY - JOUR
AB - We investigated the temporal and spatial expression of SK2 in the developing mouse hippocampus using molecular and biochemical techniques, quantitative immunogold electron microscopy, and electrophysiology. The mRNA encoding SK2 was expressed in the developing and adult hippocampus. Western blotting and immunohistochemistry showed that SK2 protein increased with age. This was accompanied by a shift in subcellular localization. Early in development (P5), SK2 was predominantly localized to the endoplasmic reticulum in the pyramidal cell layer. But by P30 SK2 was almost exclusively expressed in the dendrites and spines. The level of SK2 at the postsynaptic density (PSD) also increased during development. In the adult, SK2 expression on the spine plasma membrane showed a proximal-to-distal gradient. Consistent with this redistribution and gradient of SK2, the selective SK channel blocker apamin increased evoked excitatory postsynaptic potentials (EPSPs) only in CA1 pyramidal neurons from mice older than P15. However, the effect of apamin on EPSPs was not different between synapses in proximal or distal stratum radiatum or stratum lacunosum-moleculare in adult. These results show a developmental increase and gradient in SK2-containing channel surface expression that underlie their influence on neurotransmission, and that may contribute to increased memory acquisition during early development.
AU - Ballesteros-Merino, Carmen
AU - Lin, Michael
AU - Wu, Wendy W
AU - Ferrándiz-Huertas, Clotilde
AU - Cabañero, María José
AU - Watanabe, Masahiko
AU - Fukazawa, Yugo
AU - Ryuichi Shigemoto
AU - Maylie, James G
AU - Adelman, John P
AU - Luján, Rafael
ID - 2515
IS - 6
JF - Hippocampus
TI - Developmental profile of SK2 channel expression and function in CA1 neurons
VL - 22
ER -
TY - CONF
AB - We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning vertices from where the objective can be ensured with probability 1. We study for the first time the average case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average case running time is linear (as compared to the worst case linear number of iterations and quadratic time complexity). Second, for the average case analysis over all MDPs we show that the expected number of iterations is constant and the average case running time is linear (again as compared to the worst case linear number of iterations and quadratic time complexity). Finally we also show that given that all MDPs are equally likely, the probability that the classical algorithm requires more than constant number of iterations is exponentially small.
AU - Chatterjee, Krishnendu
AU - Joglekar, Manas
AU - Shah, Nisarg
ID - 2715
TI - Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives
VL - 18
ER -
TY - JOUR
AB - Consider N × N Hermitian or symmetric random matrices H where the distribution of the (i, j) matrix element is given by a probability measure ν ij with a subexponential decay. Let σ ij 2 be the variance for the probability measure ν ij with the normalization property that Σ iσ i,j 2 = 1 for all j. Under essentially the only condition that c ≤ N σ ij 2 ≤ c -1 for some constant c > 0, we prove that, in the limit N → ∞, the eigenvalue spacing statistics of H in the bulk of the spectrum coincide with those of the Gaussian unitary or orthogonal ensemble (GUE or GOE). We also show that for band matrices with bandwidth M the local semicircle law holds to the energy scale M -1.
AU - László Erdös
AU - Yau, Horng-Tzer
AU - Yin, Jun
ID - 2767
IS - 1-2
JF - Probability Theory and Related Fields
TI - Bulk universality for generalized Wigner matrices
VL - 154
ER -
TY - JOUR
AB - We consider a two dimensional magnetic Schrödinger operator with a spatially stationary random magnetic field. We assume that the magnetic field has a positive lower bound and that it has Fourier modes on arbitrarily short scales. We prove the Wegner estimate at arbitrary energy, i. e. we show that the averaged density of states is finite throughout the whole spectrum. We also prove Anderson localization at the bottom of the spectrum.
AU - László Erdös
AU - Hasler, David G
ID - 2768
IS - 2
JF - Communications in Mathematical Physics
TI - Wegner estimate and Anderson localization for random magnetic fields
VL - 309
ER -
TY - JOUR
AB - We present a generalization of the method of the local relaxation flow to establish the universality of local spectral statistics of a broad class of large random matrices. We show that the local distribution of the eigenvalues coincides with the local statistics of the corresponding Gaussian ensemble provided the distribution of the individual matrix element is smooth and the eigenvalues {X J} N j=1 are close to their classical location {y j} N j=1 determined by the limiting density of eigenvalues. Under the scaling where the typical distance between neighboring eigenvalues is of order 1/N, the necessary apriori estimate on the location of eigenvalues requires only to know that E|x j - γ j| 2 ≤ N-1-ε on average. This information can be obtained by well established methods for various matrix ensembles. We demonstrate the method by proving local spectral universality for sample covariance matrices.
AU - László Erdös
AU - Schlein, Benjamin
AU - Yau, Horng-Tzer
AU - Yin, Jun
ID - 2769
IS - 1
JF - Annales de l'institut Henri Poincare (B) Probability and Statistics
TI - The local relaxation flow approach to universality of the local statistics for random matrices
VL - 48
ER -
TY - JOUR
AB - Consider N×N Hermitian or symmetric random matrices H with independent entries, where the distribution of the (i,j) matrix element is given by the probability measure vij with zero expectation and with variance σ ιj 2. We assume that the variances satisfy the normalization condition Σiσij2=1 for all j and that there is a positive constant c such that c≤Nσ ιj 2 ιc -1. We further assume that the probability distributions νij have a uniform subexponential decay. We prove that the Stieltjes transform of the empirical eigenvalue distribution of H is given by the Wigner semicircle law uniformly up to the edges of the spectrum with an error of order (Nη) -1 where η is the imaginary part of the spectral parameter in the Stieltjes transform. There are three corollaries to this strong local semicircle law: (1) Rigidity of eigenvalues: If γj=γj,N denotes the classical location of the j-th eigenvalue under the semicircle law ordered in increasing order, then the j-th eigenvalue λj is close to γj in the sense that for some positive constants C, c P{double-struck}(∃j:|λ j-γ j|≥(logN) CloglogN[min(j,N-j+1)] -1/3N -2/3)≤ C exp[-(logN) cloglogN] for N large enough. (2) The proof of Dyson's conjecture (Dyson, 1962 [15]) which states that the time scale of the Dyson Brownian motion to reach local equilibrium is of order N -1 up to logarithmic corrections. (3) The edge universality holds in the sense that the probability distributions of the largest (and the smallest) eigenvalues of two generalized Wigner ensembles are the same in the large N limit provided that the second moments of the two ensembles are identical.
AU - László Erdös
AU - Yau, Horng-Tzer
AU - Yin, Jun
ID - 2770
IS - 3
JF - Advances in Mathematics
TI - Rigidity of eigenvalues of generalized Wigner matrices
VL - 229
ER -
TY - JOUR
AB - We consider a magnetic Schrödinger operator in two dimensions. The magnetic field is given as the sum of a large and constant magnetic field and a random magnetic field. Moreover, we allow for an additional deterministic potential as well as a magnetic field which are both periodic. We show that the spectrum of this operator is contained in broadened bands around the Landau levels and that the edges of these bands consist of pure point spectrum with exponentially decaying eigenfunctions. The proof is based on a recent Wegner estimate obtained in Erdos and Hasler (Commun. Math. Phys., preprint, arXiv:1012.5185) and a multiscale analysis.
AU - László Erdös
AU - Hasler, David G
ID - 2771
IS - 5
JF - Journal of Statistical Physics
TI - Anderson localization at band edges for random magnetic fields
VL - 146
ER -
TY - JOUR
AB - We consider the semiclassical asymptotics of the sum of negative eigenvalues of the three-dimensional Pauli operator with an external potential and a self-generated magnetic field B. We also add the field energy β ∫ B 2 and we minimize over all magnetic fields. The parameter β effectively determines the strength of the field. We consider the weak field regime with βh 2 ≥ const > 0, where h is the semiclassical parameter. For smooth potentials we prove that the semiclassical asymptotics of the total energy is given by the non-magnetic Weyl term to leading order with an error bound that is smaller by a factor h 1+e{open}, i. e. the subleading term vanishes. However for potentials with a Coulomb singularity, the subleading term does not vanish due to the non-semiclassical effect of the singularity. Combined with a multiscale technique, this refined estimate is used in the companion paper (Erdo{double acute}s et al. in Scott correction for large molecules with a self-generated magnetic field, Preprint, 2011) to prove the second order Scott correction to the ground state energy of large atoms and molecules.
AU - László Erdös
AU - Fournais, Søren
AU - Solovej, Jan P
ID - 2772
IS - 4
JF - Annales Henri Poincare
TI - Second order semiclassics with self generated magnetic fields
VL - 13
ER -
TY - JOUR
AB - Recently we proved [3, 4, 6, 7, 9, 10, 11] that the eigenvalue correlation functions of a general class of random matrices converge, weakly with respect to the energy, to the corresponding ones of Gaussian matrices. Tao and Vu [15] gave a proof that for the special case of Hermitian Wigner matrices the convergence can be strengthened to vague convergence at any fixed energy in the bulk. In this article we show that this theorem is an immediate corollary of our earlier results. Indeed, a more general form of this theorem also follows directly from our work [2].
AU - László Erdös
AU - Yau, Horng-Tzer
ID - 2773
JF - Electronic Journal of Probability
TI - A comment on the Wigner-Dyson-Mehta bulk universality conjecture for Wigner matrices
VL - 17
ER -
TY - JOUR
AB - We consider a large neutral molecule with total nuclear charge Z in non-relativistic quantum mechanics with a self-generated classical electromagnetic field. To ensure stability, we assume that Zα 2 ≤ κ 0 for a sufficiently small κ 0, where α denotes the fine structure constant. We show that, in the simultaneous limit Z → ∞, α → 0 such that κ = Zα 2 is fixed, the ground state energy of the system is given by a two term expansion c 1Z 7/3 + c 2(κ) Z 2 + o(Z 2). The leading term is given by the non-magnetic Thomas-Fermi theory. Our result shows that the magnetic field affects only the second (so-called Scott) term in the expansion.
AU - László Erdös
AU - Fournais, Søren
AU - Solovej, Jan P
ID - 2774
IS - 3
JF - Communications in Mathematical Physics
TI - Scott correction for large atoms and molecules in a self-generated magnetic field
VL - 312
ER -
TY - JOUR
AB - The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large random matrices exhibit universal behavior depending only on the symmetry class of the matrix ensemble. For invariant matrix models, the eigenvalue distributions are given by a log-gas with potential V and inverse temperature β = 1, 2, 4, corresponding to the orthogonal, unitary and symplectic ensembles. For β ∉ {1, 2, 4}, there is no natural random matrix ensemble behind this model, but the statistical physics interpretation of the log-gas is still valid for all β > 0. The universality conjecture for invariant ensembles asserts that the local eigenvalue statistics are independent of V. In this article, we review our recent solution to the universality conjecture for both invariant and non-invariant ensembles. We will also demonstrate that the local ergodicity of the Dyson Brownian motion is the intrinsic mechanism behind the universality. Furthermore, we review the solution of Dyson's conjecture on the local relaxation time of the Dyson Brownian motion. Related questions such as delocalization of eigenvectors and local version of Wigner's semicircle law will also be discussed.
AU - László Erdös
AU - Yau, Horng-Tzer
ID - 2775
IS - 3
JF - Bulletin of the American Mathematical Society
TI - Universality of local spectral statistics of random matrices
VL - 49
ER -
TY - JOUR
AB - We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, i.e. graphs on N vertices where every edge is chosen independently and with probability p ≡ p(N). We rescale the matrix so that its bulk eigenvalues are of order one. Under the assumption pN≫N2/3 , we prove the universality of eigenvalue distributions both in the bulk and at the edge of the spectrum. More precisely, we prove (1) that the eigenvalue spacing of the Erdős-Rényi graph in the bulk of the spectrum has the same distribution as that of the Gaussian orthogonal ensemble; and (2) that the second largest eigenvalue of the Erdős-Rényi graph has the same distribution as the largest eigenvalue of the Gaussian orthogonal ensemble. As an application of our method, we prove the bulk universality of generalized Wigner matrices under the assumption that the matrix entries have at least 4 + ε moments.
AU - László Erdös
AU - Knowles, Antti
AU - Yau, Horng-Tzer
AU - Yin, Jun
ID - 2776
IS - 3
JF - Communications in Mathematical Physics
TI - Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues
VL - 314
ER -
TY - JOUR
AB - We consider a large neutral molecule with total nuclear charge Z in a model with self-generated classical magnetic field and where the kinetic energy of the electrons is treated relativistically. To ensure stability, we assume that Zα < 2/π, where α denotes the fine structure constant. We are interested in the ground state energy in the simultaneous limit Z → ∞, α → 0 such that κ = Zα is fixed. The leading term in the energy asymptotics is independent of κ, it is given by the Thomas-Fermi energy of order Z7/3 and it is unchanged by including the self-generated magnetic field. We prove the first correction term to this energy, the so-called Scott correction of the form S(αZ)Z2. The current paper extends the result of Solovej et al. [Commun. Pure Appl. Math.LXIII, 39-118 (2010)] on the Scott correction for relativistic molecules to include a self-generated magnetic field. Furthermore, we show that the corresponding Scott correction function S, first identified by Solovej et al. [Commun. Pure Appl. Math.LXIII, 39-118 (2010)], is unchanged by including a magnetic field. We also prove new Lieb-Thirring inequalities for the relativistic kinetic energy with magnetic fields.
AU - László Erdös
AU - Fournais, Søren
AU - Solovej, Jan P
ID - 2777
IS - 9
JF - Journal of Mathematical Physics
TI - Relativistic Scott correction in self-generated magnetic fields
VL - 53
ER -
TY - JOUR
AB - We prove the bulk universality of the β-ensembles with non-convex regular analytic potentials for any β > 0. This removes the convexity assumption appeared in the earlier work [P. Bourgade, L. Erdös, and H.-T. Yau, Universality of general β-ensembles, preprint arXiv:0907.5605 (2011)]. The convexity condition enabled us to use the logarithmic Sobolev inequality to estimate events with small probability. The new idea is to introduce a "convexified measure" so that the local statistics are preserved under this convexification.
AU - Bourgade, Paul
AU - László Erdös
AU - Yau, Horng-Tzer
ID - 2778
IS - 9
JF - Journal of Mathematical Physics
TI - Bulk universality of general β-ensembles with non-convex potential
VL - 53
ER -
TY - JOUR
AB - We consider a two-dimensional magnetic Schrödinger operator on a square lattice with a spatially stationary random magnetic field. We prove Anderson localization near the spectral edges. We use a new approach to establish a Wegner estimate that does not rely on the monotonicity of the energy on the random parameters.
AU - László Erdös
AU - Hasler, David G
ID - 2779
IS - 8
JF - Annales Henri Poincare
TI - Wegner estimate for random magnetic Laplacian on ℤ 2
VL - 13
ER -
TY - GEN
AU - László Erdös
ID - 2696
T2 - ArXiv
TI - Universality for random matrices and log-gases
ER -
TY - CONF
AU - László Erdös
ID - 2700
TI - Lecture notes on quantum Brownian motion
VL - 95
ER -
TY - JOUR
AB - When a binary fluid demixes under a slow temperature ramp, nucleation, coarsening and sedimentation of droplets lead to an oscillatory evolution of the phase-separating system. The advection of the sedimenting droplets is found to be chaotic. The flow is driven by density differences between two phases. Here, we show how image processing can be combined with particle tracking to resolve droplet size and velocity simultaneously. Droplets are used as tracer particles, and the sedimentation velocity is determined. Taking these effects into account, droplets with radii in the range of 4-40 μm are detected and tracked. Based on these data, we resolve the oscillations in the droplet size distribution that are coupled to the convective flow.
AU - Lapp, Tobias
AU - Rohloff, Martin
AU - Vollmer, Jürgen T
AU - Björn Hof
ID - 2802
IS - 5
JF - Experiments in Fluids
TI - Particle tracking for polydisperse sedimenting droplets in phase separation
VL - 52
ER -
TY - JOUR
AB - Recent numerical studies suggest that in pipe and related shear flows, the region of phase space separating laminar from turbulent motion is organized by a chaotic attractor, called an edge state, which mediates the transition process. We here confirm the existence of the edge state in laboratory experiments. We observe that it governs the dynamics during the decay of turbulence underlining its potential relevance for turbulence control. In addition we unveil two unstable traveling wave solutions underlying the experimental flow fields. This observation corroborates earlier suggestions that unstable solutions organize turbulence and its stability border.
AU - de Lózar, Alberto
AU - Mellibovsky, Fernando
AU - Avila, Marc
AU - Björn Hof
ID - 2803
IS - 21
JF - Physical Review Letters
TI - Edge state in pipe flow experiments
VL - 108
ER -
TY - JOUR
AB - The analysis of the size distribution of droplets condensing on a substrate (breath figures) is a test ground for scaling theories. Here, we show that a faithful description of these distributions must explicitly deal with the growth mechanisms of the droplets. This finding establishes a gateway connecting nucleation and growth of the smallest droplets on surfaces to gross features of the evolution of the droplet size distribution
AU - Blaschke, Johannes
AU - Lapp, Tobias
AU - Björn Hof
AU - Vollmer, Jürgen T
ID - 2804
IS - 6
JF - Physical Review Letters
TI - Breath figures: Nucleation, growth, coalescence, and the size distribution of droplets
VL - 109
ER -