@inbook{2709, author = {Erdös, László}, booktitle = {13th International Congress of Mathematical Physics}, isbn = {9781571460851}, pages = {273 -- 281}, publisher = { International Press of Boston}, title = {{Long time dynamics of an electron in a weakly coupled phonon field}}, year = {2001}, } @article{2734, abstract = {In this paper we describe an intrinsically geometric way of producing magnetic fields on S3 and R3 for which the corresponding Dirac operators have a non-trivial kernel. In many cases we are able to compute the dimension of the kernel. In particular we can give examples where the kernel has any given dimension. This generalizes the examples of Loss and Yau [1].}, author = {Erdös, László and Solovej, Jan}, issn = {0129-055X}, journal = {Reviews in Mathematical Physics}, number = {10}, pages = {1247 -- 1280}, publisher = {World Scientific Publishing}, title = {{The kernel of Dirac operators on S3 and R3}}, doi = {10.1142/S0129055X01000983}, volume = {13}, year = {2001}, } @article{2735, abstract = {We establish the exact low-energy asymptotics of the integrated density of states (Lifschitz tail) in a homogeneous magnetic field and Poissonian impurities with a repulsive single-site potential of Gaussian decay. It has been known that the Gaussian potential tail discriminates between the so-called “classical” and “quantum” regimes, and precise asymptotics are known in these cases. For the borderline case, the coexistence of the classical and quantum regimes was conjectured. Here we settle this last remaining open case to complete the full picture of the magnetic Lifschitz tails.}, author = {Erdös, László}, issn = {0044-3719}, journal = {Probability Theory and Related Fields}, number = {2}, pages = {219 -- 236}, publisher = {Springer}, title = {{Lifschitz tail in a magnetic field: Coexistence of classical and quantum behavior in the borderline case}}, doi = {10.1007/PL00008803}, volume = {121}, year = {2001}, } @article{2736, abstract = {We consider the time evolution of N bosonic particles interacting via a mean field Coulomb potential. Suppose the initial state is a product wavefunction. We show that at any finite time the correlation functions factorize in the limit N → ∞. Furthermore, the limiting one particle density matrix satisfies the nonlinear Hartree equation. The key ingredients are the uniqueness of the BBGKY hierarchy for the correlation functions and a new apriori estimate for the many-body Schrödinger equations.}, author = {Erdös, László and Yau, Horng}, issn = {1095-0761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {6}, pages = {1169 -- 1205}, publisher = {International Press}, title = {{Derivation of the nonlinear Schrödinger equation from a many body Coulomb system}}, doi = {10.48550/arXiv.math-ph/0111042}, volume = {5}, year = {2001}, } @article{2981, abstract = {Plants contain a novel unique subfamily of Rho GTPases, vital components of cellular signalling networks. Here we report a general role for some members of this family in polarized plant growth processes. We show that Arabidopsis AtRop4 and AtRop6 encode functional GTPases with similar intrinsic GTP hydrolysis rates. We localized AtRop proteins in root meristem cells to the cross-wall and cell plate membranes. Polar localization of AtRops in trichoblasts specifies the growth sites for emerging root hairs. These sites were visible before budding and elongation of the Arabidopsis root hair when AtRops accumulated at their tips. Expression of constitutively active AtRop4 and AtRop6 mutant proteins in root hairs of transgenic Arabidopsis plants abolished polarized growth and delocalized the tip-focused Ca2+ gradient. Polar localization of AtRops was inhibited by brefeldin A, but not by other drugs such as latrunculin B, cytochalasin D or caffeine. Our results demonstrate a general function of AtRop GTPases in tip growth and in polar diffuse growth.}, author = {Molendijk, Arthur and Bischoff, Friedrich and Rajendrakumar, Chadalavada and Friml, Jirí and Braun, Markus and Gilroy, Simon and Palme, Klaus}, issn = {0261-4189}, journal = {EMBO Journal}, number = {11}, pages = {2779 -- 2788}, publisher = {Wiley-Blackwell}, title = {{Arabidopsis thaliana Rop GTPases are localized to tips of root hairs and control polar growth}}, doi = {10.1093/emboj/20.11.2779}, volume = {20}, year = {2001}, } @article{2982, abstract = {Polar auxin transport is crucial for the regulation of auxin action and required for some light-regulated responses during plant development. We have found that two mutants of Arabidopsis - doc1, which displays altered expression of light-regulated genes, and tir3, known for its reduced auxin transport - have similar defects and define mutations in a single gene that we have renamed BIG. BIG is very similar to the Drosophila gene Calossin/Pushover, a member of a gene family also present in Caenorhabditis elegans and human genomes. The protein encoded by BIG is extraordinary in size, 560 kD, and contains several putative Zn-finger domains. Expression-profiling experiments indicate that altered expression of multiple light-regulated genes in doc1 mutants can be suppressed by elevated levels of auxin caused by overexpression of an auxin biosynthetic gene, suggesting that normal auxin distribution is required to maintain low-level expression of these genes in the dark. Double mutants of tir3 with the auxin mutants pin1, pid, and axr1 display severe defects in auxin-dependent growth of the inflorescence. Chemical inhibitors of auxin transport change the intracellular localization of the auxin efflux carrier PIN1 in doc1/tir3 mutants, supporting the idea that BIG is required for normal auxin efflux.}, author = {Gil, Pedro and Dewey, Elizabeth and Friml, Jirí and Zhao, Yunde and Snowden, Kimberley and Putterill, Jo and Palme, Klaus and Estelle, Mark and Chory, Joanne}, issn = {0890-9369}, journal = {Genes and Development}, number = {15}, pages = {1985 -- 1997}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{BIG: A calossin-like protein required for polar auxin transport in Arabidopsis}}, doi = {10.1101/gad.905201}, volume = {15}, year = {2001}, } @article{2983, abstract = {Polar transport of the phytohormone auxin mediates various processes in plant growth and development, such as apical dominance, tropisms, vascular patterning and axis formation. This view is based largely on the effects of polar auxin transport inhibitors. These compounds disrupt auxin efflux from the cell but their mode of action is unknown. It is thought that polar auxin flux is caused by the asymmetric distribution of efflux carriers acting at the plasma membrane. The polar localization of efflux carrier candidate PIN1 supports this model. Here we show that the seemingly static localization of PIN1 results from rapid actin-dependent cycling between the plasma membrane and endosomal compartments. Auxin transport inhibitors block PIN1 cycling and inhibit trafficking of membrane proteins that are unrelated to auxin transport. Our data suggest that PIN1 cycling is of central importance for auxin transport and that auxin transport inhibitors affect efflux by generally interfering with membrane-trafficking processes. In support of our conclusion, the vesicle-trafficking inhibitor brefeldin A mimics physiological effects of auxin transport inhibitors.}, author = {Geldner, Niko and Friml, Jirí and Stierhof, York and Jürgens, Gerd and Palme, Klaus}, issn = {0028-0836}, journal = {Nature}, number = {6854}, pages = {425 -- 428}, publisher = {Nature Publishing Group}, title = {{Auxin transport inhibitors block PIN1 cycling and vesicle trafficking}}, doi = {10.1038/35096571}, volume = {413}, year = {2001}, } @article{2984, abstract = {Auxins represent an important class of plant hormone that regulate plant development. Plants use specialized carrier proteins to transport the auxin indole-3-acetic acid (IAA) to target tissues. To date, efflux carrier-mediated polar auxin transport has been assumed to represent the sole mode of long distance IAA movement. Localization of the auxin permease AUX1 in the Arabidopsis root apex has revealed a novel phloem-based IAA transport pathway. AUX1, asymmetrically localized to the plasma membrane of root protophloem cells, is proposed to promote the acropetal, post-phloem movement of auxin to the root apex. MS analysis shows that IAA accumulation in aux1 mutant root apices is impaired, consistent with an AUX1 phloem unloading function. AUX1 localization to columella and lateral root cap tissues of the Arabidopsis root apex reveals that the auxin permease regulates a second IAA transport pathway. Expression studies using an auxin-regulated reporter suggest that AUX1 is necessary for root gravitropism by facilitating basipetal auxin transport to distal elongation zone tissues.}, author = {Swarup, Ranjan and Friml, Jirí and Marchant, Alan and Ljung, Karin and Sandberg, Göran and Palme, Klaus and Bennett, Malcolm}, issn = {Genes and Development}, journal = {Genes and Development}, number = {20}, pages = {2648 -- 2653}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Localization of the auxin permease AUX1 suggests two functionally distinct hormone transport pathways operate in the Arabidopsis root apex}}, doi = {10.1101/gad.210501}, volume = {15}, year = {2001}, } @article{2985, abstract = {The elimination voltammetry with linear scan (EVLS) was used to study adenine and cytosine reduction signals at the mercury electrode. In comparison with the linear scan voltammetry (which provides only one unresolved peak), two elimination functions provide good resolution of individual peaks and significant increase of sensitivity. The first elimination function eliminates the kinetic current (Ik) and conserves the diffusion current (Id). The second elimination function eliminates kinetic and charging currents (Ik and Ic) simultaneously and conserves the diffusion current (Id). Both functions give two well-resolved peaks of adenine and cytosine in a wide concentration range, while the linear sweep voltammetry gives badly resolved peaks due to hydrogen evolution. The best resolution of peaks is observed in acetate buffer at pH 3.8 and the detection limit for both substances is 500 nM. The concentration dependence of EVLS peak heights for one substance at the constant concentration of the other substance is linear. The peak potentials differ in these elimination functions. The difference in EVLS peak potentials gives the possibility to evaluate αna. Elimination voltammetry with linear scan contributes to the resolution of cathodic signals of purine and pyrimidine bases at very negative potentials near supporting electrolyte discharge. Copyright © 2001 Elsevier Science B.V.}, author = {Trnková, Libuše and Friml, Jirí and Dračka, Oldřich}, isbn = {1567-5394}, journal = {Bioelectrochemistry}, number = {2}, pages = {131 -- 136}, publisher = {Elsevier}, title = {{Elimination voltammetry of adenine and cytosine mixtures}}, doi = {10.1016/S1567-5394(01)00119-0}, volume = {54}, year = {2001}, } @inproceedings{3169, abstract = {Several new algorithms for visual correspondence based on graph cuts [7, 14, 17] have recently been developed. While these methods give very strong results in practice, they do not handle occlusions properly. Specifically, they treat the two input images asymmetrically, and they do not ensure that a pixel corresponds to at most one pixel in the other image. In this paper, we present a new method which properly addresses occlusions, while preserving the advantages of graph cut algorithms. We give experimental results for stereo as well as motion, which demonstrate that our method performs well both at detecting occlusions and computing disparities.}, author = {Kolmogorov, Vladimir and Zabih, Ramin}, booktitle = {Proceedings of the 8th IEEE International Conference on Computer Vision}, isbn = {0769511430}, location = {Vancouver, Canada}, pages = {508 -- 515}, publisher = {IEEE}, title = {{Computing visual correspondence with occlusions using graph cuts}}, doi = {10.1109/ICCV.2001.937668}, volume = {2}, year = {2001}, } @inbook{3434, abstract = {This chapter contains sections titled: Introduction - History - Developing an Intuition of Likelihood - Method of Maximum Likelihood - Bayesian Inference - Markov Chain Monte Carlo - Assessing Uncertainty of Phylogenies - Hypothesis Testing and Model Choice - Comparative Analysis - Conclusions - References}, author = {Huelsenbeck, John and Bollback, Jonathan P}, booktitle = {Handbook of Statistical Genetics}, editor = {Balding, David and Bishop, Martin and Cannings, Chriss}, isbn = {9781119429142 }, pages = {415 -- 439}, publisher = {Wiley-Blackwell}, title = {{Application of the likelihood function in phylogenetic analysis}}, doi = {10.1002/9780470061619.ch15}, year = {2001}, } @article{3438, abstract = {As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.}, author = {Huelsenbeck, John and Ronquist, Fredrik and Nielsen, Rasmus and Bollback, Jonathan P}, issn = {0036-8075}, journal = {Science}, number = {5550}, pages = {2310 -- 2314}, publisher = {American Association for the Advancement of Science}, title = {{Bayesian inference of phylogeny and its impact on evolutionary biology}}, doi = {10.1126/science.1065889}, volume = {294}, year = {2001}, } @article{3439, abstract = {High molecular weight DNA was extracted from the primary Neotropical malaria vector, Anopheles darlingi from Capanema, Pará, Brazil, to create a small insert genomic library, and then a phagemid library. Enriched sublibraries were constructed from the phagemid library using a microsatellite oligo primed second strand synthesis protocol. The resulting 242 760 individual clones were screened. The mean clone size of the positive clones was 302 bp. Flanking primers were designed for each suitable microsatellite sequence. Eight polymorphic loci were optimized and characterized. The allele size ranges are based on 253 samples of A. darlingi from eastern Amazonian and central Brazil.}, author = {Conn, Jan and Bollback, Jonathan P and Onyabe, David and Robinson, Tessa and Wilkerson, Richard and Povoa, Marinete}, issn = {1471-8278}, journal = {Molecular Ecology Notes}, number = {4}, pages = {223 -- 225}, publisher = {Wiley-Blackwell}, title = {{Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi}}, doi = { 10.1046/j.1471-8278.2001.00078.x}, volume = {1}, year = {2001}, } @article{3440, abstract = {Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis. }, author = {Huelsenbeck, John and Bollback, Jonathan P}, issn = {0039-7989}, journal = {Systematic Biology}, number = {3}, pages = {351 -- 366}, publisher = {Oxford University Press}, title = {{Empirical and hierarchical Bayesian estimation of ancestral states}}, doi = {10.1080/10635150119871}, volume = {50}, year = {2001}, } @inproceedings{3447, author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P}, publisher = {Elsevier}, title = {{Weighted quantified computation tree logic}}, year = {2001}, } @article{3493, abstract = {Although agonists and competitive antagonists presumably occupy overlapping binding sites on ligand-gated channels, these interactions cannot be identical because agonists cause channel opening whereas antagonists do not. One explanation is that only agonist binding performs enough work on the receptor to cause the conformational changes that lead to gating. This idea is supported by agonist binding rates at GABAA and nicotinic acetylcholine receptors that are slower than expected for a diffusion-limited process, suggesting that agonist binding involves an energy-requiring event. This hypothesis predicts that competitive antagonist binding should require less activation energy than agonist binding. To test this idea, we developed a novel deconvolution-based method to compare binding and unbinding kinetics of GABAA receptor agonists and antagonists in outside-out patches from rat hippocampal neurons. Agonist and antagonist unbinding rates were steeply correlated with affinity. Unlike the agonists, three of the four antagonists tested had binding rates that were fast, independent of affinity, and could be accounted for by diffusion- and dehydration-limited processes. In contrast, agonist binding involved additional energy-requiring steps, consistent with the idea that channel gating is initiated by agonist-triggered movements within the ligand binding site. Antagonist binding does not appear to produce such movements, and may in fact prevent them.}, author = {Jones, M.V and Jonas, Peter M and Sahara, Y. and Westbrook, G.}, issn = {0006-3495}, journal = {Biophysical Journal}, number = {5}, pages = {2660 -- 2670}, publisher = {Biophysical Society}, title = {{Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists}}, doi = {10.1016/S0006-3495(01)75909-7 }, volume = {81}, year = {2001}, } @article{3494, abstract = {Mutual synaptic interactions between GABAergic interneurons are thought to be of critical importance for the generation of network oscillations and for temporal encoding of information in the hippocampus. However, the functional properties of synaptic transmission between hippocampal interneurons are largely unknown. We have made paired recordings from basket cells (BCs) in the dentate gyrus of rat hippocampal slices, followed by correlated light and electron microscopical analysis. Unitary GABAAreceptor-mediated IPSCs at BC–BC synapses recorded at the soma showed a fast rise and decay, with a mean decay time constant of 2.5 ± 0.2 msec (32°C). Synaptic transmission at BC–BC synapses showed paired-pulse depression (PPD) (32 ± 5% for 10 msec interpulse intervals) and multiple-pulse depression during repetitive stimulation. Detailed passive cable model simulations based on somatodendritic morphology and localization of synaptic contacts further indicated that the conductance change at the postsynaptic site was even faster, decaying with a mean time constant of 1.8 ± 0.6 msec. Sequential triple recordings revealed that the decay time course of IPSCs at BC–BC synapses was approximately twofold faster than that at BC–granule cell synapses, whereas the extent of PPD was comparable. To examine the consequences of the fast postsynaptic conductance change for the generation of oscillatory activity, we developed a computational model of an interneuron network. The model showed robust oscillations at frequencies >60 Hz if the excitatory drive was sufficiently large. Thus the fast conductance change at interneuron–interneuron synapses may promote the generation of high-frequency oscillations observed in the dentate gyrusin vivo. }, author = {Bartos, Marlene and Vida, Imre and Frotscher, Michael and Geiger, Jörg and Jonas, Peter M}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {8}, pages = {2687 -- 2698}, publisher = {Society for Neuroscience}, title = {{Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network.}}, doi = {10.1523/JNEUROSCI.21-08-02687.2001}, volume = {21}, year = {2001}, } @article{3495, abstract = {High Ca2+ permeability and its control by voltage-dependent Mg2+ block are defining features of NMDA receptors. These features are lost if the principal NR1 subunit carries an asparagine (N) to arginine (R) substitution in a critical channel site at NR1 position 598. NR1(R) expression from a single allele in gene-targeted NR1+/R mice is lethal soon after birth, precluding analysis of altered synaptic functions later in life. We therefore employed the forebrain specific αCaMKII promoter to drive tTA-mediated tetracyclin sensitive transcription of transgenes for NR1(R) and for lacZ as reporter. Transgene expression was observed in cortex, striatum, hippocampus, amygdala and olfactory bulb and was mosaic in all these forebrain regions. It was highest in olfactory bulb granule cells, in most of which Ca2+ permeability and voltage-dependent Mg2+ block of NMDA receptors were reduced to different extents. This indicates significant impairment of NMDA receptor function by NR1(R) in presence of the wild-type NR1 complement. Indeed, even though NR1(R) mRNA constituted only 18% of the entire NR1 mRNA population in forebrain, the transgenic mice died during adolescence unless transgene expression was suppressed by doxycycline. Thus, glutamate receptor function can be altered in the mouse by regulated NR1(R) transgene expression.}, author = {Jerecic, Jasna and Schulze, Christian and Jonas, Peter M and Sprengel, Rolf and Seeburg, Peter and Bischofberger, Joseph}, issn = {0169-328X}, journal = {Molecular Brain Research}, number = {1-2}, pages = {96 -- 104}, publisher = {Elsevier}, title = {{Impaired NMDA receptor function in mouse olfactory bulb neurons by tetracycline-sensitive NR1 (N598R) expression}}, doi = {10.1016/S0169-328X(01)00221-2}, volume = {94}, year = {2001}, } @article{3496, abstract = {The mossy fiber-CA3 pyramidal neuron synapse is a main component of the hippocampal trisynaptic circuitry. Recent studies, however, suggested that inhibitory interneurons are the major targets of the mossy fiber system. To study the regulation of mossy fiber-interneuron excitation, we examined unitary and compound excitatory postsynaptic currents in dentate gyrus basket cells, evoked by paired recording between granule and basket cells or extracellular stimulation of mossy fiber collaterals. The application of an associative high-frequency stimulation paradigm induced posttetanic potentiation (PTP) followed by homosynaptic long-term potentiation (LTP). Analysis of numbers of failures, coefficient of variation, and paired-pulse modulation indicated that both PTP and LTP were expressed presynaptically. The Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA) did not affect PTP or LTP at a concentration of 10 mM but attenuated LTP at a concentration of 30 mM. Both forskolin, an adenylyl cyclase activator, and phorbolester diacetate, a protein kinase C stimulator, lead to a long-lasting increase in excitatory postsynaptic current amplitude. H-89, a protein kinase A inhibitor, and bisindolylmaleimide, a protein kinase C antagonist, reduced PTP, whereas only bisindolylmaleimide reduced LTP. These results may suggest a differential contribution of protein kinase A and C pathways to mossy fiber-interneuron plasticity. Interneuron PTP and LTP may provide mechanisms to maintain the balance between synaptic excitation of interneurons and that of principal neurons in the dentate gyrus-CA3 network. }, author = {Alle, Henrik and Jonas, Peter M and Geiger, Jörg}, issn = {0027-8424}, journal = {PNAS}, number = {25}, pages = {14708 -- 14713}, publisher = {National Academy of Sciences}, title = {{PTP and LTP at a hippocampal mossy fiber-interneuron synapse}}, doi = {10.1073/pnas.251610898 }, volume = {98}, year = {2001}, } @misc{3507, abstract = {A molecular classification method is based on a space filling description of a molecule. The three dimensional body corresponding to the space filling molecular structure is divided into Voronoi regions to provide a basis for efficiently processing local structural information. A Delaunay triangulation provides a basis for systematically processing information relating to the Voronoi regions into shape descriptors in the form of topological elements. Preferably, additional shape and/or property descriptors are included in the classification method. The classification methods generally are used to identify similarities between molecules that can be used as property predictors for a variety of applications. Generally, the property predictions are the basis for selection of compounds for incorporation into efficacy evaluations.}, author = {Liang, Jie and Edelsbrunner, Herbert}, title = {{Molecular classification for property prediction}}, year = {2001}, }