@article{2990, abstract = {Plant growth is marked by its adaptability to continuous changes in environment. A regulated, differential distribution of auxin underlies many adaptation processes including organogenesis, meristem patterning and tropisms. In executing its multiple roles, auxin displays some characteristics of both a hormone and a morphogen. Studies on auxin transport, as well as tracing the intracellular movement of its molecular components, have suggested a possible scenario to explain how growth plasticity is conferred at the cellular and molecular level. The plant perceives stimuli and changes the subcellular position of auxin-transport components accordingly. These changes modulate auxin fluxes, and the newly established auxin distribution triggers the corresponding developmental response.}, author = {Friml, Jirí}, journal = {Current Opinion in Plant Biology}, number = {1}, pages = {7 -- 12}, publisher = {Elsevier}, title = {{Auxin transport - Shaping the plant}}, doi = {10.1016/S1369526602000031}, volume = {6}, year = {2003}, } @article{2992, abstract = {Plants have many polarized cell types, but relatively little is known about the mechanisms that establish polarity. The orc mutant was identified originally by defects in root patterning, and positional cloning revealed that the affected gene encodes STEROL METHYLTRANSFERASE1, which is required for the appropriate synthesis and composition of major membrane sterols. smt1orc mutants displayed several conspicuous cell polarity defects. Columella root cap cells revealed perturbed polar positioning of different organelles, and in the smt1orc root epidermis, polar initiation of root hairs was more randomized. Polar auxin transport and expression of the auxin reporter DR5-β-glucuronidase were aberrant in smt1orc. Patterning defects in smt1orc resembled those observed in mutants of the PIN gene family of putative auxin efflux transporters. Consistently, the membrane localization of the PIN1 and PIN3 proteins was disturbed in smt1orc, whereas polar positioning of the influx carrier AUX1 appeared normal. Our results suggest that balanced sterol composition is a major requirement for cell polarity and auxin efflux in Arabidopsis.}, author = {Willemsen, Viola and Jirí Friml and Grebe, Markus and Van Den Toorn, Albert and Palme, Klaus and Scheres, Ben}, journal = {Plant Cell}, number = {3}, pages = {612 -- 625}, publisher = {American Society of Plant Biologists}, title = {{Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function}}, doi = {10.1105/tpc.008433}, volume = {15}, year = {2003}, } @article{2993, abstract = {Plant biology is currently experiencing a growing demand for easy and reliable mRNA and protein localisation techniques. Here, we present novel whole mount in situ hybridisation and immunolocalisation protocols, suitable to localise mRNAs and proteins in Arabidopsis seedlings. We demonstrate that these methods can be used in different organs of Arabidopsis seedlings as well as in other plant species. In order to achieve better reproducibility and higher throughput, we modified these protocols for automation to be performed by a liquid handling robot. In addition, we show that other procedures such as reporter enzyme assays and tissue clearing can be similarly automated. We present examples of application of our protocols including mRNA localisation and proteins and epitope tag (co)localisations which demonstrate that these methods provide reliable and versatile tools for expression, localisation and anatomical studies in plants.}, author = {Jirí Friml and Eva Benková and Mayer, Ulrike and Palme, Klaus and Muster, Gerhard}, journal = {Plant Journal}, number = {1}, pages = {115 -- 124}, publisher = {Wiley-Blackwell}, title = {{Automated whole mount localisation techniques for plant seedlings}}, doi = {10.1046/j.1365-313X.2003.01705.x}, volume = {34}, year = {2003}, } @article{2994, abstract = {The regular arrangement of leaves around a plant's stem, called phyllotaxis, has for centuries attracted the attention of philosophers, mathematicians and natural scientists; however, to date, studies of phyllotaxis have been largely theoretical. Leaves and flowers are formed from the shoot apical meristem, triggered by the plant hormone auxin. Auxin is transported through plant tissues by specific cellular influx and efflux carrier proteins. Here we show that proteins involved in auxin transport regulate phyllotaxis. Our data indicate that auxin is transported upwards into the meristem through the epidermis and the outermost meristem cell layer. Existing leaf primordia act as sinks, redistributing auxin and creating its heterogeneous distribution in the meristem. Auxin accumulation occurs only at certain minimal distances from existing primordia, defining the position of future primordia. This model for phyllotaxis accounts for its reiterative nature, as well as its regularity and stability.}, author = {Reinhardt, Didier and Pesce, Eva-Rachele and Stieger, Pia and Mandel, Therese and Baltensperger, Kurt and Bennett, Malcolm and Traas, Jan and Jirí Friml and Kuhlemeier, Cris}, journal = {Nature}, number = {6964}, pages = {255 -- 260}, publisher = {Nature Publishing Group}, title = {{Regulation of phyllotaxis by polar auxin transport}}, doi = {10.1038/nature02081}, volume = {426}, year = {2003}, } @article{2995, abstract = {Axis formation occurs in plants, as in animals, during early embryogenesis. However, the underlying mechanism is not known. Here we show that the first manifestation of the apical-basal axis in plants, the asymmetric division of the zygote, produces a basal cell that transports and an apical cell that responds to the signalling molecule auxin. This apical-basal auxin activity gradient triggers the specification of apical embryo structures and is actively maintained by a novel component of auxin efflux, PIN7, which is located apically in the basal cell. Later, the developmentally regulated reversal of PIN7 and onset of PIN1 polar localization reorganize the auxin gradient for specification of the basal root pole. An analysis of pin quadruple mutants identifies PIN-dependent transport as an essential part of the mechanism for embryo axis formation. Our results indicate how the establishment of cell polarity, polar auxin efflux and local auxin response result in apical-basal axis formation of the embryo, and thus determine the axiality of the adult plant. }, author = {Jirí Friml and Vieten, Anne and Sauer, Michael and Weijers, Dolf and Schwarz, Heinz and Hamann, Thorsten and Offringa, Remko and Jürgens, Gerd}, journal = {Nature}, number = {6963}, pages = {147 -- 153}, publisher = {Nature Publishing Group}, title = {{Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis}}, doi = {10.1038/nature02085}, volume = {426}, year = {2003}, } @article{2996, abstract = {Plants, compared to animals, exhibit an amazing adaptability and plasticity in their development. This is largely dependent on the ability of plants to form new organs, such as lateral roots, leaves, and flowers during postembryonic development. Organ primordia develop from founder cell populations into organs by coordinated cell division and differentiation. Here, we show that organ formation in Arabidopsis involves dynamic gradients of the signaling molecule auxin with maxima at the primordia tips. These gradients are mediated by cellular efflux requiring asymmetrically localized PIN proteins, which represent a functionally redundant network for auxin distribution in both aerial and underground organs. PIN1 polar localization undergoes a dynamic rearrangement, which correlates with establishment of auxin gradients and primordium development. Our results suggest that PIN-dependent, local auxin gradients represent a common module for formation of all plant organs, regardless of their mature morphology or developmental origin. }, author = {Eva Benková and Michniewicz, Marta and Sauer, Michael and Teichmann, Thomas and Seifertová, Daniela and Jürgens, Gerd and Jirí Friml}, journal = {Cell}, number = {5}, pages = {591 -- 602}, publisher = {Cell Press}, title = {{Local, efflux-dependent auxin gradients as a common module for plant organ formation}}, doi = {10.1016/S0092-8674(03)00924-3}, volume = {115}, year = {2003}, } @misc{3139, abstract = {Significant advances have been made during the past few years in our understanding of how the spinal monosynaptic reflex develops. Transcription factors in the Neurogenin, Runt, ETS, and LIM families control sequential steps of the specification of various subtypes of dorsal root ganglia sensory neurons. The initiation of muscle spindle differentiation requires neuregulin 1, derived from Ia afferent sensory neurons, and signaling through ErbB receptors in intrafusal muscle fibers. Several retrograde signals from the periphery are important for the establishment of late connectivity in the reflex circuit. Finally, neurotrophin 3 released from muscle spindles regulates the strength of sensory-motor connections within the spinal cord postnatally.}, author = {Chen, Hsiao Huei and Simon Hippenmeyer and Arber, Silvia and Frank, Eric}, booktitle = {Current Opinion in Neurobiology}, number = {1}, pages = {96 -- 102}, publisher = {Elsevier}, title = {{Development of the monosynaptic stretch reflex circuit}}, doi = {10.1016/S0959-4388(03)00006-0}, volume = {13}, year = {2003}, } @article{3150, abstract = {Tripartite G-protein-coupled receptors (GPCRs) represent one of the largest groups of signal transducers, transmitting signals from hormones, neuropeptides, odorants, food and light. Ligand-bound receptors catalyse GDP/GTP exchange on the G-protein α-subunit (Gα), leading to α-GTP separation from the βγ subunits and pathway activation. Activating mutations in the receptors or G proteins underlie many human diseases, including some cancers, dwarfism and premature puberty. Regulators of G-protein signalling (RGS proteins) are known to modulate the level and duration of ligand-induced signalling by accelerating the intrinsic GTPase activity of the Gα subunit, and thus reformation of the inactive GDP-bound Gα. Here we find that even in the absence of receptor, mutation of the RGS family member Sst2 (refs 6-9) permits spontaneous activation of the G-protein-coupled mating pathway in Saccharomyces cerevisiae at levels normally seen only in the presence of ligand. Our work demonstrates the occurence of spontaneous tripartite G-protein signalling in vivo and identifies a requirement for RGS proteins in preventing such receptor-independent activation.}, author = {Daria Siekhaus and Drubin, David G}, journal = {Nature Cell Biology}, number = {3}, pages = {231 -- 235}, publisher = {Nature Publishing Group}, title = {{Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant}}, doi = {10.1038/ncb941}, volume = {5}, year = {2003}, } @article{3151, abstract = {Biosynthesis of most peptide hormones and neuropeptides requires proteolytic excision of the active peptide from inactive proprotein precursors, an activity carried out by subtilisin-like proprotein convertases (SPCs) in constitutive or regulated secretory pathways. The Drosophila amontillado (amon) gene encodes a homolog of the mammalian PC2 protein, an SPC that functions in the regulated secretory pathway in neuroendocrine tissues. We have identified amon mutants by isolating ethylmethanesulfonate (EMS)-induced lethal and visible mutations that define two complementation groups in the amon interval at 97D1 of the third chromosome. DNA sequencing identified the amon complementation group and the DNA sequence change for each of the nine amon alleles isolated. amon mutants display partial embryonic lethality, are defective in larval growth, and arrest during the first to second instar larval molt. Mutant larvae can be rescued by heat-shock-induced expression of the amon protein. Rescued larvae arrest at the subsequent larval molt, suggesting that amon is also required for the second to third instar larval molt. Our data indicate that the amon proprotein convertase is required during embryogenesis and larval development in Drosophila and support the hypothesis that AMON acts to proteolytically process peptide hormones that regulate hatching, larval growth, and larval ecdysis.}, author = {Rayburn, Lowell Y and Gooding, Holly C and Choksi, Semil P and Maloney, Dhea and Kidd, Ambrose R and Daria Siekhaus and Bender, Michael}, journal = {Genetics}, number = {1}, pages = {227 -- 237}, publisher = {Genetics Society of America}, title = {{Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development}}, volume = {163}, year = {2003}, } @inproceedings{3170, abstract = {Geodesic active contours and graph cuts are two standard image segmentation techniques. We introduce a new segmentation method combining some of their benefits. Our main intuition is that any cut on a graph embedded in some continuous space can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build a grid graph and set its edge weights so that the cost of cuts is arbitrarily close to the length (area) of the corresponding contours (surfaces) for any anisotropic Riemannian metric. There are two interesting consequences of this technical result. First, graph cut algorithms can be used to find globally minimum geodesic contours (minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of boundary conditions. Second, we show how to minimize metrication artifacts in existing graph-cut based methods in vision. Theoretically speaking, our work provides an interesting link between several branches of mathematics -differential geometry, integral geometry, and combinatorial optimization. The main technical problem is solved using Cauchy-Crofton formula from integral geometry.}, author = {Boykov, Yuri and Vladimir Kolmogorov}, pages = {26 -- 33}, publisher = {IEEE}, title = {{Computing geodesics and minimal surfaces via graph cuts}}, doi = {10.1109/ICCV.2003.1238310}, volume = {1}, year = {2003}, } @inproceedings{3171, abstract = {Reconstructing a 3-D scene from more than one camera is a classical problem in computer vision. One of the major sources of difficulty is the fact that not all scene elements are visible from all cameras. In the last few years, two promising approaches have been developed 11,12 that formulate the scene reconstruction problem in terms of energy minimization, and minimize the energy using graph cuts. These energy minimization approaches treat the input images symmetrically, handle visibility constraints correctly, and allow spatial smoothness to be enforced. However, these algorithm propose different problem formulations, and handle a limited class of smoothness terms. One algorithm 11 uses a problem formulation that is restricted to two-camera stereo, and imposes smoothness between a pair of cameras. The other algorithm 12 can handle an arbitrary number of cameras, but imposes smoothness only with respect to a single camera. In this paper we give a more general energy minimization formulation for the problem, which allows a larger class of spatial smoothness constraints. We show that our formulation includes both of the previous approaches as special cases, as well as permitting new energy functions. Experimental results on real data with ground truth are also included. }, author = {Vladimir Kolmogorov and Zabih, Ramin and Gortler, Steven}, pages = {501 -- 516}, publisher = {Springer}, title = {{Generalized multi camera scene reconstruction using graph cuts}}, doi = {10.1007/978-3-540-45063-4_32}, volume = {2683}, year = {2003}, } @inproceedings{3174, abstract = {We address visual correspondence problems without assuming that scene points have similar intensities in different views. This situation is common, usually due to non-lambertian scenes or to differences between cameras. We use maximization of mutual information, a powerful technique for registering images that requires no a priori model of the relationship between scene intensities in different views. However, it has proven difficult to use mutual information to compute dense visual correspondence. Comparing fixed-size windows via mutual information suffers from the well-known problems of fixed windows, namely poor performance at discontinuities and in low-texture regions. In this paper, we show how to compute visual correspondence using mutual information without suffering from these problems. Using 'a simple approximation, mutual information can be incorporated into the standard energy minimization framework used in early vision. The energy can then be efficiently minimized using graph cuts, which preserve discontinuities and handle low-texture regions. The resulting algorithm combines the accurate disparity maps that come from graph cuts with the tolerance for intensity changes that comes from mutual information.}, author = {Kim, Junhwan and Vladimir Kolmogorov and Zabih, Ramin}, pages = {1033 -- 1040}, publisher = {IEEE}, title = {{Visual correspondence using energy minimization and mutual information}}, doi = {10.1109/ICCV.2003.1238463}, volume = {2}, year = {2003}, } @article{3209, abstract = {We show that the fixed alphabet shortest common supersequence (SCS) and the fixed alphabet longest common subsequence (LCS) problems parameterized in the number of strings are W[1]-hard. Unless W[1]=FPT, this rules out the existence of algorithms with time complexity of O(f(k)nα) for those problems. Here n is the size of the problem instance, α is constant, k is the number of strings and f is any function of k. The fixed alphabet version of the LCS problem is of particular interest considering the importance of sequence comparison (e.g. multiple sequence alignment) in the fixed length alphabet world of DNA and protein sequences.}, author = {Krzysztof Pietrzak}, journal = {Journal of Computer and System Sciences}, number = {4}, pages = {757 -- 771}, publisher = {Elsevier}, title = {{On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems}}, doi = {10.1016/S0022-0000(03)00078-3}, volume = {67}, year = {2003}, } @inproceedings{3210, abstract = {Luby and Rackoff showed how to construct a (super-)pseudo-random permutation {0,1}2n→ {0,1}2n from some number r of pseudo-random functions {0,1}n → {0,1}n. Their construction, motivated by DES, consists of a cascade of r Feistel permutations. A Feistel permutation 1for a pseudo-random function f is defined as (L, R) → (R,L ⊕ f (R)), where L and R are the left and right part of the input and ⊕ denotes bitwise XOR or, in this paper, any other group operation on {0,1}n. The only non-trivial step of the security proof consists of proving that the cascade of r Feistel permutations with independent uniform random functions {0,1}n → {0,1}n, denoted Ψ2nr is indistinguishable from a uniform random permutation {0,1}2n → {0,1}2n by any computationally unbounded adaptive distinguisher making at most O(2cn) combined chosen plaintext/ciphertext queries for any c < α, where a is a security parameter. Luby and Rackoff proved α = 1/2 for r = 4. A natural problem, proposed by Pieprzyk is to improve on α for larger r. The best known result, α = 3/4 for r = 6, is due to Patarin. In this paper we prove a = 1 -O(1/r), i.e., the trivial upper bound α = 1 can be approached. The proof uses some new techniques that can be of independent interest. }, author = {Maurer, Ueli M and Krzysztof Pietrzak}, pages = {544 -- 561}, publisher = {Springer}, title = {{The security of many round Luby Rackoff pseudo random permutations}}, doi = {10.1007/3-540-39200-9_34}, volume = {2656}, year = {2003}, } @article{13436, abstract = {Cross-metathesis reactions of α,β-unsaturated sulfones and sulfoxides in the presence of molybdenum and ruthenium pre-catalysts were tested. A selective metahesis reaction was achieved between functionalized terminal olefins and vinyl sulfones by using the ‘second generation’ ruthenium catalysts 1c–h while the highly active Schrock catalyst 1b was found to be functional group incompatible with vinyl sulfones. The cross-metathesis products were isolated in good yields with an excellent (E)-selectivity. Both the molybdenum and ruthenium-based complexes were, however, incompatible with α,β- and β,γ-unsaturated sulfoxides.}, author = {Michrowska, Anna and Bieniek, Michał and Kim, Mikhail and Klajn, Rafal and Grela, Karol}, issn = {1464-5416}, journal = {Tetrahedron}, keywords = {Organic Chemistry, Drug Discovery, Biochemistry}, number = {25}, pages = {4525--4531}, publisher = {Elsevier}, title = {{Cross-metathesis reaction of vinyl sulfones and sulfoxides}}, doi = {10.1016/s0040-4020(03)00682-3}, volume = {59}, year = {2003}, } @article{1457, abstract = {Among the major mathematical approaches to mirror symmetry are those of Batyrev-Borisov and Stromdnger-Yau-Zaslow (SYZ). The first is explicit and amenable to computation but is not clearly related to the physical motivation; the second is the opposite. Furthermore, it is far from obvious that mirror partners in one sense will also be mirror partners in the other. This paper concerns a class of examples that can be shown to satisfy the requirements of SYZ, but whose Hodge numbers are also equal. This provides significant evidence in support of SYZ. Moreover, the examples are of great interest in their own right: they are spaces of flat SLr-connections on a smooth curve. The mirror is the corresponding space for the Langlands dual group PGLr. These examples therefore throw a bridge from mirror symmetry to the duality theory of Lie groups and, more broadly, to the geometric Langlands program.}, author = {Tamas Hausel and Thaddeus, Michael}, journal = {Inventiones Mathematicae}, number = {1}, pages = {197 -- 229}, publisher = {Springer}, title = {{Mirror symmetry, langlands duality, and the Hitchin system}}, doi = {10.1007/s00222-003-0286-7}, volume = {153}, year = {2003}, } @article{1458, abstract = {The moduli space of stable bundles of rank $2$ and degree $1$ on a Riemann surface has rational cohomology generated by the so-called universal classes. The work of Baranovsky, King-Newstead, Siebert-Tian and Zagier provided a complete set of relations between these classes, expressed in terms of a recursion in the genus. This paper accomplishes the same thing for the noncompact moduli spaces of Higgs bundles, in the sense of Hitchin and Simpson. There are many more independent relations than for stable bundles, but in a sense the answer is simpler, since the formulas are completely explicit, not recursive. The results of Kirwan on equivariant cohomology for holomorphic circle actions are of key importance.}, author = {Tamas Hausel and Thaddeus, Michael}, journal = {Journal of the American Mathematical Society}, number = {2}, pages = {303 -- 329}, publisher = {American Mathematical Society}, title = {{Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles}}, doi = {10.1090/S0894-0347-02-00417-4}, volume = {16}, year = {2003}, } @article{1459, abstract = {In this paper we explicitly calculate the analogue of the 't Hooft SU (2) Yang-Mills instantons on Gibbons-Hawking multi-centered gravitational instantons, which come in two parallel families: the multi-Eguchi-Hanson, or Ak ALE gravitational instantons and the multi-Taub-NUT spaces, or Ak ALF gravitational instantons. We calculate their energy and find the reducible ones. Following Kronheimer we also exploit the U(1) invariance of our solutions and study the corresponding explicit singular SU (2) magnetic monopole solutions of the Bogomolny equations on flat ℝ3.}, author = {Etesi, Gábor and Tamas Hausel}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {275 -- 288}, publisher = {Springer}, title = {{On Yang-Mills instantons over multi-centered gravitational instantons}}, doi = {10.1007/s00220-003-0806-8}, volume = {235}, year = {2003}, } @inproceedings{18324, abstract = {We present a novel 3D face recognition approach based on geometric invariants introduced by Elad and Kimmel. The key idea of the proposed algorithm is a representation of the facial surface, invariant to isometric deformations, such as those resulting from different expressions and postures of the face. The obtained geometric invariants allow mapping 2D facial texture images into special images that incorporate the 3D geometry of the face. These signature images are then decomposed into their principal components. The result is an efficient and accurate face recognition algorithm that is robust to facial expressions. We demonstrate the results of our method and compare it to existing 2D and 3D face recognition algorithms.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, booktitle = {4th International Conference on Audio- and Video-Based Biometric Person Authentication}, isbn = {9783540403029}, issn = {1611-3349}, location = {Guildford, United Kingdom}, pages = {62--70}, publisher = {Springer Nature}, title = {{Expression-invariant 3D face recognition}}, doi = {10.1007/3-540-44887-x_8}, volume = {2688}, year = {2003}, } @article{18410, abstract = {The authors consider detection of high-energy photons in positron emission tomography using thick scintillation crystals. Parallax effect and multiple Compton interactions in such crystals significantly reduce the accuracy of conventional detection methods. In order to estimate the photon line of flight based on photomultiplier responses, the authors use asymptotically optimal nonlinear techniques, implemented by feedforward and radial basis function neural networks. Incorporation of information about angles of incidence of photons significantly improves accuracy of estimation. The proposed estimators are fast enough to perform detection, using conventional computers. Monte Carlo simulation results show that their approach significantly outperforms the conventional Anger algorithm.}, author = {Bronstein, Alexander and Bronstein, M.M. and Zibulevsky, M. and Zeevi, Y.Y.}, issn = {1558-1578}, journal = {IEEE Transactions on Nuclear Science}, number = {3}, pages = {421--426}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Optimal nonlinear line-of-flight estimation in positron emission tomography}}, doi = {10.1109/tns.2003.812434}, volume = {50}, year = {2003}, }