@article{2989, abstract = {In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.}, author = {Friml, Jirí and Benková, Eva and Blilou, Ikram and Wiśniewska, Justyna and Hamann, Thorsten and Ljung, Karin and Woody, Scott and Sandberg, Göran and Scheres, Ben and Jürgens, Gerd and Palme, Klaus}, issn = {0092-8674}, journal = {Cell}, number = {5}, pages = {661 -- 673}, publisher = {Cell Press}, title = {{AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis}}, doi = {10.1016/S0092-8674(02)00656-6}, volume = {108}, year = {2002}, } @article{2991, abstract = {Polar auxin transport controls multiple aspects of plant development including differential growth, embryo and root patterning and vascular tissue differentiation. Identification of proteins involved in this process and availability of new tools enabling `visualization' of auxin and auxin routes in planta largely contributed to the significant progress that has recently been made. New data support classical concepts, but several recent findings are likely to challenge our view on the mechanism of auxin transport. The aim of this review is to provide a comprehensive overview of the polar auxin transport field. It starts with classical models resulting from physiological studies, describes the genetic contributions and discusses the molecular basis of auxin influx and efflux. Finally, selected questions are presented in the context of developmental biology, integrating available data from different fields.}, author = {Friml, Jirí and Palme, Klaus}, journal = {Plant Molecular Biology}, number = {3-4}, pages = {273 -- 284}, publisher = {Springer}, title = {{Polar auxin transport - Old questions and new concepts?}}, doi = {10.1023/A:1015248926412}, volume = {49}, year = {2002}, } @article{3140, abstract = {The maturation of synaptic structures depends on inductive interactions between axons and their prospective targets. One example of such an interaction is the influence of proprioceptive sensory axons on the differentiation of muscle spindles. We have monitored the expression of three transcription factors, Egr3, Pea3, and Erm, that delineate early muscle spindle development in an assay of muscle spindle-inducing signals. We provide genetic evidence that Neuregulin1 (Nrg1) is required for proprioceptive afferent-evoked induction of muscle spindle differentiation in the mouse. Ig-Nrg1 isoforms are preferentially expressed by proprioceptive sensory neurons and are sufficient to induce muscle spindle differentiation in vivo, whereas CRD-Nrg1 isoforms are broadly expressed in sensory and motor neurons but are not required for muscle spindle induction.}, author = {Hippenmeyer, Simon and Shneider, Neil and Birchmeier, Carmen and Burden, Steven and Jessell, Thomas and Arber, Silvia}, issn = {0896-6273}, journal = {Neuron}, number = {6}, pages = {1035 -- 1049}, publisher = {Elsevier}, title = {{A role for Neuregulin1 signaling in muscle spindle differentiation}}, doi = {10.1016/S0896-6273(02)01101-7}, volume = {36}, year = {2002}, } @article{3421, abstract = {Single molecule experiments provide insight into the individuality of biological macromolecules, their unique function, reaction pathways, trajectories and molecular interactions. The exceptional signal-to-noise ratio of the atomic force microscope allows individual proteins to be imaged under physiologically relevant conditions at a lateral resolution of 0.5–1 nm and a vertical resolution of 0.1–0.2 nm. Recently, it has become possible to observe single molecule events using this technique. This capability is reviewed on various water-soluble and membrane proteins. Examples of the observation of function, variability, and assembly of single proteins are discussed. Statistical analysis is important to extend conclusions derived from single molecule experiments to protein species. Such approaches allow the classification of protein conformations and movements. Recent developments of probe microscopy techniques allow simultaneous measurement of multiple signals on individual macromolecules, and greatly extend the range of experiments possible for probing biological systems at the molecular level. Biologists exploring molecular mechanisms will benefit from a burgeoning of scanning probe microscopes and of their future combination with molecular biological experiments.}, author = {Mueller, Daniel and Janovjak, Harald L and Lehto, Tiina and Kuerschner, Lars and Anderson, Kurt}, issn = {0079-6107}, journal = {Progress in Biophysics and Molecular Biology}, number = {1-3}, pages = {1 -- 43}, publisher = {Elsevier}, title = {{Observing structure, function and assembly of single proteins by AFM}}, doi = {10.1016/S0079-6107(02)00009-3}, volume = {79}, year = {2002}, } @article{3422, abstract = {Quantitative real-time PCR represents a highly sensitive and powerful technique for the quantitation of nucleic acids. It has a tremendous potential for the high-throughput analysis of gene expression in research and routine diagnostics. However, the major hurdle is not the practical performance of the experiments themselves but rather the efficient evaluation and the mathematical and statistical analysis of the enormous amount of data gained by this technology, as these functions are not included in the software provided by the manufacturers of the detection systems. In this work, we focus on the mathematical evaluation and analysis of the data generated by quantitative real-time PCR, the calculation of the final results, the propagation of experimental variation of the measured values to the final results, and the statistical analysis. We developed a Microsoft Excel-based software application coded in Visual Basic for Applications, called Q-Gene, which addresses these points. Q-Gene manages and expedites the planning, performance, and evaluation of quantitative real-time PCR experiments, as well as the mathematical and statistical analysis, storage, and graphical presentation of the data. The Q-Gene software application is a tool to cope with complex quantitative real-time PCR experiments at a high-throughput scale and considerably expedites and rationalizes the experimental setup, data analysis, and data management while ensuring highest reproducibility.}, author = {Müller, Patrick and Janovjak, Harald L and Miserez, Andre and Dobbie, Zuzana}, issn = {0736-6205}, journal = {Biotechniques}, number = {6}, pages = {1372 -- 1379}, publisher = {Informa Healthcare}, title = {{Processing of gene expression data generated by quantitative real-time RT-PCR}}, volume = {32}, year = {2002}, } @inproceedings{3423, author = {Bauer, Wolfgang and Bollenbach, Mark Tobias and Kleine Berkenbusch, Marko and Harreis, Holger}, booktitle = {Proceedings of the 18th Winter Workshop on Nuclear Dynamics}, location = {Nassau, Bahamas}, pages = {111 -- 118}, publisher = {EP Systema}, title = {{The percolation interpretation of the nuclear fragmentation phase transition}}, year = {2002}, } @inproceedings{3424, abstract = {We give a brief overview of the current understanding of the explosion mechanism of core collapse supernovae. Our main focus is the impact of rotation on the explosion. Recent observations of the polarization of the light emitted by supernova explosions indicate that there are large deviations from spherical symmetry in the very heart of the explosion the origin of which is unknown. We use the new approach of a three dimensional test particle based simulation to simulate the infall phase of a supernova event. The underlying microphysics is simplified to make this computationally possible. A systematic study of the influence of rotation mainly during the infall phase of the collapse of a typical iron core is performed. Indications for significant deviations from spherical symmetry are found in our very rapidly rotating models. © 2002 American Institute of Physics }, author = {Bollenbach, Mark Tobias and Bauer, Wolfgang}, isbn = {9781510832008}, location = {Catania, Italy}, pages = {219 -- 232}, publisher = {American Institute of Physics}, title = {{3d supernovae collapse calculations}}, doi = {10.1063/1.1523196 }, volume = {644}, year = {2002}, } @article{13438, abstract = {ICln is an ion channel identified by expression cloning using a cDNA library from Madin-Darby canine kidney cells. In all organisms tested so far, only one transcript for the ICln protein could be identified. Here we show that two splice variants of the ICln ion channel can be found in Caenorhabditis elegans. Moreover, we show that these two splice variants of the ICln channel protein, which we termed IClnN1 and IClnN2, can be functionally reconstituted and tested in an artificial lipid bilayer. In these experiments, the IClnN1-induced currents showed no voltage-dependent inactivation, whereas the IClnN2-induced currents fully inactivated at positive potentials. The molecular entity responsible for the voltage-dependent inactivation of IClnN2 is a cluster of positively charged amino acids encoded by exon 2a, which is absent in IClnN1. Our experiments suggest a mechanism of channel inactivation that is similar to the “ball and chain” model proposed for the Shaker potassium channel,i.e. a cluster of positively charged amino acids hinders ion permeation through the channel by a molecular and voltage-dependent interaction at the inner vestibulum of the pore. This hypothesis is supported by the finding that synthetic peptides with the same amino acid sequence as the positive cluster can transform the IClnN1-induced current to the current observed after reconstitution of IClnN2. Furthermore, we show that the nematode ICln gene is embedded in an operon harboring two additional genes, which we termed Nx and Ny. Co-reconstitution of Nx and IClnN2 and functional analysis of the related currents revealed a functional interaction between the two proteins, as evidenced by the fact that the IClnN2-induced current in the presence of Nx was no longer voltage-sensitive. The experiments described indicate that the genome organization in nematodes allows an effective approach for the identification of functional partner proteins of ion channels.}, author = {Fürst, Johannes and Ritter, Markus and Rudzki, Jakob and Danzl, Johann G and Gschwentner, Martin and Scandella, Elke and Jakab, Martin and König, Matthias and Oehl, Bernhard and Lang, Florian and Deetjen, Peter and Paulmichl, Markus}, issn = {0021-9258}, journal = {Journal of Biological Chemistry}, keywords = {Cell Biology, Molecular Biology, Biochemistry}, number = {6}, pages = {4435--4445}, publisher = {Elsevier}, title = {{ICln Ion channel splice variants in Caenorhabditis elegans}}, doi = {10.1074/jbc.m107372200}, volume = {277}, year = {2002}, } @article{1451, abstract = {Extending work of Bielawski-Dancer 3 and Konno 14, we develop a theory of toric hyperkähler varieties, which involves toric geometry, matroid theory and convex polyhedra. The framework is a detailed study of semi-projective toric varieties, meaning GIT quotients of affine spaces by torus actions, and specifically, of Lawrence toric varieties, meaning GIT quotients of even-dimensional affine spaces by symplectic torus actions. A toric hyperkähler variety is a complete intersection in a Lawrence toric variety. Both varieties are non-compact, and they share the same cohomology ring, namely, the Stanley-Reisner ring of a matroid modulo a linear system of parameters. Familiar applications of toric geometry to combinatorics, including the Hard Lefschetz Theorem and the volume polynomials of Khovanskii-Pukhlikov 11, are extended to the hyperkähler setting. When the matroid is graphic, our construction gives the toric quiver varieties, in the sense of Nakajima 17.}, author = {Hausel, Tamas and Sturmfels, Bernd}, issn = {1431-0635}, journal = {Documenta Mathematica}, number = {1}, pages = {495 -- 534}, publisher = {Deutsche Mathematiker Vereinigung}, title = {{Toric hyperkähler varieties}}, doi = {10.4171/DM/130}, volume = {7}, year = {2002}, } @article{18369, author = {Bronstein, Michael M. and Bronstein, Alexander}, issn = {0028-0836}, journal = {Nature}, number = {6917}, pages = {739--739}, publisher = {Springer Nature}, title = {{Biometrics was no match for hair-raising tricks}}, doi = {10.1038/420739a}, volume = {420}, year = {2002}, } @inproceedings{18382, abstract = {Detection of high-energy photons emitted as the result of positron decay is one of the most important low-level stages in PET imaging. In this paper we consider a detector based on the Anger scintillation camera. Incident high-energy gamma quanta, generated due to positron decay, produce scintillation effect in the crystal. As a result, a shower of low energy photons in the visible and UV spectra is emitted. These photons are collected by an array of photo-multipliers (PMTs), optically coupled to the scintillation crystal, and invoke electric impulses in them. The PMT responses are utilized in estimation of the scintillation point coordinates. Our work incorporates side information on the photon incidence angle into the process of position estimation. We use localized, asymptotically optimal, nonlinear estimators, implemented by feedforward and radial basis function (RBF) neural networks. As a byproduct, we get accurate position estimation over the entire area of the detector including the edges. This is difficult to obtain with centroid arithmetic algorithms. We present a comparison of algorithms on a Monte Carlo simulation and discuss the prospects for practical implementation.}, author = {Bronstein, Alexander and Bronstein, M.M. and Zibulevsky, M. and Zeevi, Y.Y.}, booktitle = {The 22nd Convention on Electrical and Electronics Engineers in Israel}, isbn = {0780376935}, location = {Tel-Aviv, Israel}, pages = {341--344}, publisher = {IEEE}, title = {{Optimal non-linear line-of-flight estimation in positron emission tomography}}, doi = {10.1109/eeei.2002.1178493}, volume = {2002-January}, year = {2002}, } @inproceedings{18383, author = {Bronstein, M.M. and Bronstein, Alexander and Zibulevsky, M. and Azhari, H.}, booktitle = {The 22nd Convention on Electrical and Electronics Engineers in Israel}, isbn = {0780376935}, location = {Tel-Aviv, Israel}, pages = {345--347}, publisher = {IEEE}, title = {{Application of the NUFFT for reconstruction problems in diffraction tomography}}, doi = {10.1109/eeei.2002.1178495}, volume = {2002-January}, year = {2002}, } @inproceedings{18404, abstract = {We consider detection of high-energy photons in PET using thick scintillation crystals. Parallax effect and multiple Compton interactions in this type of crystals significantly reduce the accuracy of conventional detection methods. In order to estimate the scintillation point coordinates based on photomultiplier responses, we use asymptotically optimal nonlinear techniques, implemented by feed-forward neural networks, radial basis functions (RBF) networks, and neuro-fuzzy systems. 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.}, author = {Bronstein, Alexander and Bronstein, M. and Zibulevsky, M. and Zeevi, Y.Y.}, booktitle = {Proceedings IEEE International Symposium on Biomedical Imaging}, isbn = {078037584X}, location = {Washington, DC, United States}, pages = {541--544}, publisher = {IEEE}, title = {{Optimal nonlinear estimation of photon coordinates in PET}}, doi = {10.1109/isbi.2002.1029314}, volume = {2002-January}, year = {2002}, } @inproceedings{18405, abstract = {We show an iterative reconstruction framework for diffraction ultrasound tomography. The use of broadband illumination allows the number of projections to be reduced significantly compared to straight ray tomography. The proposed algorithm makes use of fast forward non-uniform Fourier transform (NUFFT) for iterative Fourier inversion. Incorporation of total variation regularization allows noise and Gibbs phenomena to be reduced whilst preserving the edges.}, author = {Bronstein, M. and Bronstein, Alexander and Zibulevsky, M.}, booktitle = {Proceedings IEEE International Symposium on Biomedical Imaging}, isbn = {078037584X}, location = {Washington, DC, United States}, pages = {633--636}, publisher = {IEEE}, title = {{Iterative reconstruction in diffraction tomography using nonuniform fast Fourier transform}}, doi = {10.1109/isbi.2002.1029337}, volume = {2002-January}, year = {2002}, } @article{18409, abstract = {We show an iterative reconstruction framework for diffraction ultrasound tomography. The use of broad-band illumination allows significant reduction of the number of projections compared to straight ray tomography. The proposed algorithm makes use of forward nonuniform fast Fourier transform (NUFFT) for iterative Fourier inversion. Incorporation of total variation regularization allows the reduction of noise and Gibbs phenomena while preserving the edges. The complexity of the NUFFT-based reconstruction is comparable to the frequency-domain interpolation (gridding) algorithm, whereas the reconstruction accuracy (in sense of the L/sup 2/ and the L/sup /spl infin// norm) is better.}, author = {Bronstein, M.M. and Bronstein, Alexander and Zibulevsky, M. and Azhari, H.}, issn = {0278-0062}, journal = {IEEE Transactions on Medical Imaging}, number = {11}, pages = {1395--1401}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Reconstruction in diffraction ultrasound tomography using nonuniform FFT}}, doi = {10.1109/tmi.2002.806423}, volume = {21}, year = {2002}, } @article{12659, abstract = {For many years considerable efforts have been put into investigating and modelling hydrological processes of mountainous catchments. On the one hand, the complexity and intrinsically high variability of the involved processes as well as insufficient knowledge of the underlying physical mechanisms still induce large uncertainties in understanding observed phenomena and predicting the behaviour of the system. On the other hand, the demand for models that are able to simulate mountainous water resource systems is increasing because of the needs related to both water exploitation and water conservation, which clearly call for an integrated vision and modelling of these systems. Accordingly, this paper moves from a brief survey of the most significant achievements in mountain hydrology to discuss what could be future challenging issues related to the broader spectrum of questions, which hydrologic modelling of mountainous river systems may face in the next decades. Firstly, reference is made to existing methodologies for modelling alpine water systems, focussing on some specific aspects that provide a basis for the discussion of the weaknesses and perspectives of present simulation tools. The future is thus discussed, delineating some of the research challenges that may foster a comprehensive and integrated vision of water related issues in mountainous regions.}, author = {Burlando, Paolo and Pellicciotti, Francesca and Strasser, Ulrich}, issn = {2224-7955}, journal = {Hydrology Research}, number = {1}, pages = {47--74}, publisher = {IWA Publishing}, title = {{Modelling mountainous water systems between learning and speculating looking for challenges}}, doi = {10.2166/nh.2002.0004}, volume = {33}, year = {2002}, } @article{204, abstract = {Let k⩾5 be an integer, and let x⩾1 be an arbitrary real number. We derive a bound[Formula presented] for the number of positive integers less than or equal to x which can be represented as a sum of two non-negative coprime kth powers, in essentially more than one way.}, author = {Browning, Timothy D}, issn = {0022-314X}, journal = {Journal of Number Theory}, number = {2}, pages = {293 -- 318}, publisher = {Academic Press}, title = {{Equal Sums of Two kth Powers}}, doi = {10.1006/jnth.2002.2800}, volume = {96}, year = {2002}, } @article{11123, abstract = {The small GTPase Ran is a key regulator of nucleocytoplasmic transport during interphase. The asymmetric distribution of the GTP-bound form of Ran across the nuclear envelope — that is, large quantities in the nucleus compared with small quantities in the cytoplasm — determines the directionality of many nuclear transport processes. Recent findings that Ran also functions in spindle formation and nuclear envelope assembly during mitosis suggest that Ran has a general role in chromatin-centred processes. Ran functions in these events as a signal for chromosome position.}, author = {HETZER, Martin W and Gruss, Oliver J. and Mattaj, Iain W.}, issn = {1476-4679}, journal = {Nature Cell Biology}, keywords = {Cell Biology}, number = {7}, pages = {E177--E184}, publisher = {Springer Nature}, title = {{The Ran GTPase as a marker of chromosome position in spindle formation and nuclear envelope assembly}}, doi = {10.1038/ncb0702-e177}, volume = {4}, year = {2002}, } @article{11124, abstract = {Ran GTPase plays important roles in nucleocytoplasmic transport in interphase [1, 2] and in both spindle formation and nuclear envelope (NE) assembly during mitosis [3, 4, 5]. The latter functions rely on the presence of high local concentrations of GTP-bound Ran near mitotic chromatin [3, 4, 5]. RanGTP localization has been proposed to result from the association of Ran's GDP/GTP exchange factor, RCC1, with chromatin [6, 7, 8, 9], but Ran is shown here to bind directly to chromatin in two modes, either dependent or independent of RCC1, and, where bound, to increase the affinity of chromatin for NE membranes. We propose that the Ran binding capacity of chromatin contributes to localized spindle and NE assembly.}, author = {Bilbao-Cortés, Daniel and HETZER, Martin W and Längst, Gernot and Becker, Peter B. and Mattaj, Iain W.}, issn = {0960-9822}, journal = {Current Biology}, keywords = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology}, number = {13}, pages = {1151--1156}, publisher = {Elsevier BV}, title = {{Ran binds to chromatin by two distinct mechanisms}}, doi = {10.1016/s0960-9822(02)00927-2}, volume = {12}, year = {2002}, } @inbook{2338, abstract = {Now that the low temperature properties of quantum-mechanical many-body systems (bosons) at low density, ρ, can be examined experimentally it is appropriate to revisit some of the formulas deduced by many authors 4-5 decades ago. For systems with repulsive (i.e. positive) interaction potentials the experimental low temperature state and the ground state are effectively synonymous -- and this fact is used in all modeling. In such cases, the leading term in the energy/particle is 2πℏ2aρ/m where a is the scattering length of the two-body potential. Owing to the delicate and peculiar nature of bosonic correlations (such as the strange N7/5 law for charged bosons), four decades of research failed to establish this plausible formula rigorously. The only previous lower bound for the energy was found by Dyson in 1957, but it was 14 times too small. The correct asymptotic formula has recently been obtained by us and this work will be presented. The reason behind the mathematical difficulties will be emphasized. A different formula, postulated as late as 1971 by Schick, holds in two-dimensions and this, too, will be shown to be correct. With the aid of the methodology developed to prove the lower bound for the homogeneous gas, two other problems have been successfully addressed. One is the proof by us that the Gross-Pitaevskii equation correctly describes the ground state in the `traps' actually used in the experiments. For this system it is also possible to prove complete Bose condensation, as we have shown. Another topic is a proof that Foldy's 1961 theory of a high density Bose gas of charged particles correctly describes its ground state energy.}, author = {Lieb, Élliott and Solovej, Jan and Seiringer, Robert and Yngvason, Jakob}, booktitle = {Current Developments in Mathematics, 2001}, isbn = {9781571461018}, pages = {131 -- 178}, publisher = {International Press}, title = {{The ground state of the Bose gas}}, doi = {10.48550/arXiv.math-ph/0204027}, year = {2002}, }