@article{2743, abstract = {We consider the supersymmetric quantum mechanical system which is obtained by dimensionally reducing d = 6, N = 1 supersymmetric gauge theory with gauge group U(1) and a single charged hypermultiplet. Using the deformation method and ideas introduced by Porrati and Rozenberg [1], we present a detailed proof of the existence of a normalizable ground state for this system.}, author = {László Erdös and Hasler, David G and Solovej, Jan P}, journal = {Annales Henri Poincare}, number = {2}, pages = {247 -- 267}, publisher = {Birkhäuser}, title = {{Existence of the D0-D4 bound state: A detailed proof}}, doi = {10.1007/s00023-005-0205-0}, volume = {6}, year = {2005}, } @article{2744, abstract = {We study the long time evolution of a quantum particle interacting with a random potential in the Boltzmann-Grad low density limit. We prove that the phase space density of the quantum evolution defined through the Husimi function converges weakly to a linear Boltzmann equation. The Boltzmann collision kernel is given by the full quantum scattering cross-section of the obstacle potential.}, author = {Eng, David and László Erdös}, journal = {Reviews in Mathematical Physics}, number = {6}, pages = {669 -- 743}, publisher = {World Scientific Publishing}, title = {{The linear Boltzmann equation as the low density limit of a random Schrödinger equation}}, doi = {10.1142/S0129055X0500242X}, volume = {17}, year = {2005}, } @article{2788, abstract = {We present the results of an experimental investigation into the nature and structure of turbulent pipe flow at moderate Reynolds numbers. A turbulence regeneration mechanism is identified which sustains a symmetric traveling wave within the flow. The periodicity of the mechanism allows comparison to the wavelength of numerically observed exact traveling wave solutions and close agreement is found. The advection speed of the upstream turbulence laminar interface in the experimental flow is observed to form a lower bound on the phase velocities of the exact traveling wave solutions. Overall our observations suggest that the dynamics of the turbulent flow at moderate Reynolds numbers are governed by unstable nonlinear traveling waves.}, author = {Björn Hof and van Doorne, Casimir W and Westerweel, Jerry and Nieuwstadt, Frans T}, journal = {Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Turbulence regeneration in pipe flow at moderate reynolds numbers}}, doi = {10.1103/PhysRevLett.95.214502}, volume = {95}, year = {2005}, } @article{2789, abstract = {Transitional pipe flow is investigated in two different experimental set-ups. In the first the stability threshold and the initial growth of localized perturbations are studied. Good agreement is found with an earlier investigation of the transition threshold. The measurement technique applied in the last part of this study allows the reconstruction of the streamwise vorticity in a turbulent puff.}, author = {Björn Hof}, journal = {Fluid Mechanics and its Applications}, pages = {221 -- 231}, publisher = {Springer}, title = {{Transition to turbulence in pipe flow}}, doi = {10.1007/1-4020-4049-0_12}, volume = {77}, year = {2005}, } @article{2790, abstract = {We present the results of an experimental investigation of the effect of a magnetic field on the stability of convection in a liquid metal. A rectangular container of gallium is subjected to a horizontal temperature gradient and a uniform magnetic field is applied separately in three directions. The magnetic field suppresses the oscillation most effectively when it is applied in the vertical direction and is least efficient when applied in the direction of the temperature gradient. The critical temperature difference required for the onset of oscillations is found to scale exponentially with the magnitude of the magnetic field for all three orientations. Comparisons are made with available theory and qualitative differences are discussed.}, author = {Björn Hof and Juel, Anne and Mullin, Tom P}, journal = {Journal of Fluid Mechanics}, pages = {193 -- 201}, publisher = {Cambridge University Press}, title = {{Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection}}, doi = {10.1017/S0022112005006762}, volume = {545}, year = {2005}, } @article{2867, abstract = {The plant hormone auxin elicits many specific context-dependent developmental responses. Auxin promotes degradation of Aux/IAA proteins that prevent transcription factors of the auxin response factor (ARF) family from regulating auxin-responsive target genes. Aux/IAAs and ARFs are represented by large gene families in Arabidopsis. Here we show that stabilization of BDL/IAA12 or its sister protein IAA13 prevents MP/ARF5-dependent embryonic root formation whereas stabilized SHY2/IAA3 interferes with seedling growth. Although both bdl and shy2-2 proteins inhibited MP/ARF5-dependent reporter gene activation, shy2-2 was much less efficient than bdl to interfere with embryonic root initiation when expressed from the BDL promoter. Similarly, MP was much more efficient than ARF16 in this process. When expressed from the SHY2 promoter, both shy2-2 and bdl inhibited cell elongation and auxin-induced gene expression in the seedling hypocotyl. By contrast, gravitropism and auxin-induced gene expression in the root, which were promoted by functionally redundant NPH4/ARF7 and ARF19 proteins, were inhibited by shy2-2, but not by bdl protein. Our results suggest that auxin signals are converted into specific responses by matching pairs of coexpressed ARF and Aux/IAA proteins.}, author = {Weijers, Dolf and Eva Benková and Jäger, Katja E and Schlereth, Alexandra and Hamann, Thorsten and Kientz, Marika and Wilmoth, Jill C and Reed, Jason W and Jürgens, Gerd}, journal = {EMBO Journal}, number = {10}, pages = {1874 -- 1885}, publisher = {Wiley-Blackwell}, title = {{Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators}}, doi = {10.1038/sj.emboj.7600659}, volume = {24}, year = {2005}, } @article{2895, abstract = {One of the fundamental properties of the immune system is its capacity to avoid autoimmune diseases. The mechanism underlying this process, known as self-tolerance, is hitherto unresolved but seems to involve the control of clonal expansion of autoreactive lymphocytes. This article reviews mathematical modeling of self-tolerance, addressing two specific hypotheses. The first hypothesis posits that self-tolerance is mediated by tuning of activation thresholds, which makes autoreactive T lymphocytes reversibly "anergic" and unable to proliferate. The second hypothesis posits that the proliferation of autoreactive T lymphocytes is instead controlled by specific regulatory T lymphocytes. Models representing the population dynamics of autoreactive T lymphocytes according to these two hypotheses were derived. For each model we identified how cell density affects tolerance, and predicted the corresponding phase spaces and bifurcations. We show that the simple induction of proliferative anergy, as modeled here, has a density dependence that is only partially compatible with adoptive transfers of tolerance, and that the models of tolerance mediated by specific regulatory T cells are closer to the observations.}, author = {Carneiro, Jorge and Tiago Paixao and Milutinovic, Dejan and Sousa, João and Leon, Kalet and Gardner, Rui and Faro, Jose}, journal = {Journal of Computational and Applied Mathematics}, number = {1}, pages = {77 -- 100}, publisher = {Elsevier}, title = {{Immunological self tolerance: Lessons from mathematical modeling}}, doi = {10.1016/j.cam.2004.10.025}, volume = {184}, year = {2005}, } @article{3000, abstract = {In plants, cell polarity is an issue more recurring than in other systems, because plants, due to their adaptive and flexible development, often change cell polarity postembryonically according to intrinsic cues and demands of the environment. Recent findings on the directional movement of the plant signalling molecule auxin provide a unique connection between individual cell polarity and the establishment of polarity at the tissue, organ, and whole-plant levels. Decisions about the subcellular polar targeting of PIN auxin transport components determine the direction of auxin flow between cells and consequently mediate multiple developmental events. In addition, mutations or chemical interference with PIN-based auxin transport result in abnormal cell divisions. Thus, the complicated links between cell polarity establishment, auxin transport, cytoskeleton, and oriented cell divisions now begin to emerge. Here we review the available literature on the issues of cell polarity in both plants and animals to extend our understanding on the generation, maintenance, and transmission of cell polarity in plants.}, author = {Dhonukshe, Pankaj and Kleine Vehn, Jürgen and Friml, Jirí}, journal = {Protoplasma}, number = {1-2}, pages = {67 -- 73}, publisher = {Springer}, title = {{Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first?}}, doi = {10.1007/s00709-005-0104-8}, volume = {226}, year = {2005}, } @article{3001, abstract = {One of the mechanisms by which signalling molecules regulate cellular behaviour is modulating subcellular protein translocation. This mode of regulation is often based on specialized vesicle trafficking, termed constitutive cycling, which consists of repeated internalization and recycling of proteins to and from the plasma membrane. No such mechanism of hormone action has been shown in plants although several proteins, including the PIN auxin efflux facilitators, exhibit constitutive cycling. Here we show that a major regulator of plant development, auxin, inhibits endocytosis. This effect is specific to biologically active auxins and requires activity of the Calossin-like protein BIG. By inhibiting the internalization step of PIN constitutive cycling, auxin increases levels of PINs at the plasma membrane. Concomitantly, auxin promotes its own efflux from cells by a vesicle-trafficking-dependent mechanism. Furthermore, asymmetric auxin translocation during gravitropism is correlated with decreased PIN internalization. Our data imply a previously undescribed mode of plant hormone action: by modulating PIN protein trafficking, auxin regulates PIN abundance and activity at the cell surface, providing a mechanism for the feedback regulation of auxin transport.}, author = {Paciorek, Tomasz and Zažímalová, Eva and Ruthardt, Nadia and Petrášek, Jan and Stierhof, York-Dieter and Kleine-Vehn, Jürgen and Morris, David A and Emans, Neil and Jürgens, Gerd and Geldner, Niko and Jirí Friml}, journal = {Nature}, number = {7046}, pages = {1251 -- 1256}, publisher = {Nature Publishing Group}, title = {{Auxin inhibits endocytosis and promotes its own efflux from cells}}, doi = {10.1038/nature03633}, volume = {435}, year = {2005}, } @article{3003, abstract = {Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic: expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development.}, author = {Vieten, Anne and Vanneste, Steffen and Wiśniewska, Justyna and Eva Benková and Benjamins, René and Beeckman, Tom and Luschnig, Christian and Jirí Friml}, journal = {Development}, number = {20}, pages = {4521 -- 4531}, publisher = {Company of Biologists}, title = {{Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression}}, doi = {10.1242/dev.02027}, volume = {132}, year = {2005}, } @article{3004, abstract = {Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.}, author = {Weijers, Dolf and Sauer, Michael and Meurette, Olivier and Jirí Friml and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul and Offringa, Remko}, journal = {Plant Cell}, number = {9}, pages = {2517 -- 2526}, publisher = {American Society of Plant Biologists}, title = {{Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis}}, doi = {10.1105/tpc.105.034637}, volume = {17}, year = {2005}, } @article{3141, abstract = {The two actin-related subunits of the Arp2/3 complex, Arp2 and Arp3, are proposed to form a pseudo actin dimer that nucleates actin polymerization. However, in the crystal structure of the inactive complex, they are too far apart to form such a nucleus. Here, we show using EM that yeast and bovine Arp2/3 complexes exist in a distribution among open, intermediate and closed conformations. The crystal structure docks well into the open conformation. The activator WASp binds at the cleft between Arp2 and Arp3, and all WASp-bound complexes are closed. The inhibitor coronin binds near the p35 subunit, and all coronin-bound complexes are open. Activating and loss-of-function mutations in the p35 subunit skew conformational distribution in opposite directions, closed and open, respectively. We conclude that WASp stabilizes p35-dependent closure of the complex, holding Arp2 and Arp3 closer together to nucleate an actin filament.}, author = {Rodal, Avital A and Sokolova, Olga and Robins, Deborah B and Daugherty, Karen M and Simon Hippenmeyer and Riezman, Howard and Grigorieff, Nikolaus and Goode, Bruce L}, journal = {Nature Structural and Molecular Biology}, number = {1}, pages = {26 -- 31}, publisher = {Nature Publishing Group}, title = {{Conformational changes in the Arp2 3 complex leading to actin nucleation}}, doi = {10.1038/nsmb870}, volume = {12}, year = {2005}, } @article{3143, abstract = {Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived factors. Their expression controls late aspects of neuronal differentiation such as target invasion and branching. Here, we show that the late onset of ETS gene expression is an essential requirement for normal sensory neuron differentiation. We provide genetic evidence in the mouse that precocious ETS expression in DRG sensory neurons perturbs axonal projections, the acquisition of terminal differentiation markers, and their dependence on neurotrophic support. Together, our findings indicate that DRG sensory neurons exhibit a temporal developmental switch that can be revealed by distinct responses to ETS transcription factor signaling at sequential steps of neuronal maturation.}, author = {Simon Hippenmeyer and Vrieseling, Eline and Sigrist, Markus and Portmann, Thomas and Laengle, Celia and Ladle, David R and Arber, Silvia}, journal = {PLoS Biology}, number = {5}, pages = {0878 -- 0890}, publisher = {Public Library of Science}, title = {{A developmental switch in the response of DRG neurons to ETS transcription factor signaling}}, doi = {10.1371/journal.pbio.0030159}, volume = {3}, year = {2005}, } @inproceedings{3175, abstract = {This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov Random Field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with "almost" metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented.}, author = {Rother, Carsten and Kumar, Sanjiv and Vladimir Kolmogorov and Blake, Andrew}, pages = {589 -- 596}, publisher = {IEEE}, title = {{Digital tapestry}}, doi = {10.1109/CVPR.2005.130}, volume = {1}, year = {2005}, } @inproceedings{3176, abstract = {This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. }, author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten}, pages = {1186 -- 1186}, publisher = {IEEE}, title = {{Bi-layer segmentation of binocular stereo video}}, doi = {10.1109/CVPR.2005.90}, year = {2005}, } @inproceedings{3181, abstract = {Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method.}, author = {Vladimir Kolmogorov and Wainwright, Martin J}, pages = {316 -- 323}, publisher = {AUAI Press}, title = {{On the optimality of tree reweighted max product message passing}}, year = {2005}, } @inproceedings{3182, abstract = {In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such "submodular" metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the "shrinking" problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints.}, author = {Vladimir Kolmogorov and Boykov, Yuri}, pages = {564 -- 571}, publisher = {IEEE}, title = {{What metrics can be approximated by geo cuts or global optimization of length area and flux}}, doi = {10.1109/ICCV.2005.252}, volume = {1}, year = {2005}, } @inproceedings{3183, abstract = {This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.}, author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten}, pages = {407 -- 414}, publisher = {IEEE}, title = {{Bi-layer segmentation of binocular stereo video}}, doi = {10.1109/CVPR.2005.91}, volume = {2}, year = {2005}, } @inproceedings{3211, abstract = {We present an improved bound on the advantage of any q-query adversary at distinguishing between the CBC MAC over a random n-bit permutation and a random function outputting n bits. The result assumes that no message queried is a prefix of any other, as is the case when all messages to be MACed have the same length. We go on to give an improved analysis of the encrypted CBC MAC, where there is no restriction on queried messages. Letting m be the block length of the longest query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate into improved guarantees on the probability of forging these MACs.}, author = {Bellare, Mihir and Krzysztof Pietrzak and Rogaway, Phillip}, pages = {527 -- 545}, publisher = {Springer}, title = {{Improved security analyses for CBC MACs}}, doi = {10.1007/11535218_32}, volume = {3621}, year = {2005}, } @inproceedings{3212, abstract = {The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use. In this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model.}, author = {Dodis, Yevgeniy and Oliveira, Roberto and Krzysztof Pietrzak}, pages = {449 -- 466}, publisher = {Springer}, title = {{On the generic insecurity of the full domain hash}}, doi = {10.1007/11535218_27}, volume = {3621}, year = {2005}, }