@article{9495, abstract = {RNA interference is a conserved process in which double-stranded RNA is processed into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing. In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to silenced RNA is de novo methylated at its cytosine residues. This methylation is not only at canonical CpG sites but also at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly complete loss of asymmetric methylation and a partial loss of CpNpG methylation. The remaining asymmetric and CpNpG methylation was dependent on the activity of CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation. These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of siRNAs. Finally, we demonstrate that DRM activity is required for the initial establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric sites.}, author = {Cao, Xiaofeng and Aufsatz, Werner and Zilberman, Daniel and Mette, M.Florian and Huang, Michael S. and Matzke, Marjori and Jacobsen, Steven E.}, issn = {1879-0445}, journal = {Current Biology}, number = {24}, pages = {2212--2217}, publisher = {Elsevier}, title = {{Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation}}, doi = {10.1016/j.cub.2003.11.052}, volume = {13}, year = {2003}, } @inproceedings{11860, abstract = {Many daily activities present information in the form of a stream of text, and often people can benefit from additional information on the topic discussed. TV broadcast news can be treated as one such stream of text; in this paper we discuss finding news articles on the web that are relevant to news currently being broadcast.We evaluated a variety of algorithms for this problem, looking at the impact of inverse document frequency, stemming, compounds, history, and query length on the relevance and coverage of news articles returned in real time during a broadcast. We also evaluated several postprocessing techniques for improving the precision, including reranking using additional terms, reranking by document similarity, and filtering on document similarity. For the best algorithm, 84%-91% of the articles found were relevant, with at least 64% of the articles being on the exact topic of the broadcast. In addition, a relevant article was found for at least 70% of the topics.}, author = {Henzinger, Monika H and Chang, Bay-Wei and Milch, Brian and Brin, Sergey}, booktitle = {Proceedings of the 12th international conference on World Wide Web}, isbn = {978-158113680-7}, location = {Budapest, Hungary}, publisher = {Association for Computing Machinery}, title = {{Query-free news search}}, doi = {10.1145/775152.775154}, year = {2003}, } @inproceedings{11897, abstract = {This paper addresses the problem of topic distillation on the World Wide Web, namely, given a typical user query to find quality documents related to the query topic. Connectivity analysis has been shown to be useful in identifying high quality pages within a topic specific graph of hyperlinked documents. The essence of our approach is to augment a previous connectivity analysis based algorithm with content analysis. We identify three problems with the existing approach and devise algorithms to tackle them. The results of a user evaluation are reported that show an improvement of precision at 10 documents by at least 45% over pure connectivity analysis. }, author = {Bharat, Krishna and Henzinger, Monika H}, booktitle = {21st annual international ACM SIGIR conference on Research and development in information retrieval}, isbn = {978-1-58113-015-7}, issn = {01635840}, location = {Melbourne, Australia}, pages = {104–111}, publisher = {Association for Computing Machinery}, title = {{Improved algorithms for topic distillation in a hyperlinked environment}}, doi = {10.1145/290941.290972}, year = {2003}, } @inproceedings{11909, abstract = {This article presents a high-level discussion of some problems that are unique to web search engines. The goal is to raise awareness and stimulate research in these areas.}, author = {Henzinger, Monika H and Motwani, Rajeev and Silverstein, Craig}, booktitle = {18th International Joint Conference on Artificial Intelligence}, issn = {1045-0823}, location = {Acapulco, Mexico}, pages = {1573--1579}, publisher = {Association for Computing Machinery}, title = {{Challenges in web search engines}}, year = {2003}, } @inproceedings{3425, author = {Bollenbach, Mark Tobias and Strother, T. and Bauer, Wolfgang}, pages = {277 -- 288}, publisher = {Springer}, title = {{3D supernova collapse calculations}}, doi = {10.1007/978-1-4020-2705-5_21}, volume = {166}, year = {2003}, } @inbook{3458, author = {Peter Jonas and Unsicker, Klaus}, booktitle = {Lehrbuch Vorklinik}, editor = {Schmidt, R. F.}, pages = {3 -- 26}, publisher = {Deutscher Ärzte Verlag}, title = {{Molekulare und zelluläre Grundlagen des Nervensystems.}}, volume = {B}, year = {2003}, } @article{3526, abstract = {Neurons can produce action potentials with high temporal precision(1). A fundamental issue is whether, and how, this capability is used in information processing. According to the `cell assembly' hypothesis, transient synchrony of anatomically distributed groups of neurons underlies processing of both external sensory input and internal cognitive mechanisms(2-4). Accordingly, neuron populations should be arranged into groups whose synchrony exceeds that predicted by common modulation by sensory input. Here we find that the spike times of hippocampal pyramidal cells can be predicted more accurately by using the spike times of simultaneously recorded neurons in addition to the animals location in space. This improvement remained when the spatial prediction was refined with a spatially dependent theta phase modulation(5-8). The time window in which spike times are best predicted from simultaneous peer activity is 10-30 ms, suggesting that cell assemblies are synchronized at this timescale. Because this temporal window matches the membrane time constant of pyramidal neurons(9), the period of the hippocampal gamma oscillation(10) and the time window for synaptic plasticity(11), we propose that cooperative activity at this timescale is optimal for information transmission and storage in cortical circuits.}, author = {Harris, Kenneth D and Jozsef Csicsvari and Hirase, Hajima and Dragoi, George and Buzsáki, György}, journal = {Nature}, number = {6948}, pages = {552 -- 556}, publisher = {Nature Publishing Group}, title = {{Organization of cell assemblies in the hippocampus}}, doi = {0.1038/nature01834}, volume = {424}, year = {2003}, } @article{3528, abstract = {Gamma frequency oscillations (30-100 Hz) have been suggested to underlie various cognitive and motor functions. Here, we examine the generation of gamma oscillation currents in the hippocampus, using two-dimensional, 96-site silicon probes. Two gamma generators were identified, one in the dentate gyrus and another in the CA3-CA1 regions. The coupling strength between the two oscillators varied during both theta and nontheta states. Both pyramidal cells and interneurons were phase-locked to gamma waves. Anatomical connectivity, rather than physical distance, determined the coupling strength of the oscillating neurons. CA3 pyramidal neurons discharged CA3 and CA1 interneurons at latencies indicative of monosynaptic connections. Intrahippocampal gamma oscillation emerges in the CA3 recurrent system, which entrains the CA1 region via its interneurons.}, author = {Jozsef Csicsvari and Jamieson, Brian G and Wise, Kensall D and Buzsáki, György}, journal = {Neuron}, number = {2}, pages = {311 -- 322}, publisher = {Elsevier}, title = {{Mechanisms of gamma oscillations in the hippocampus of the behaving rat}}, doi = {10.1016/S0896-6273(02)01169-8}, volume = {37}, year = {2003}, } @article{3529, abstract = {Parallel recording of neuronal activity in the behaving animal is a prerequisite for our understanding of neuronal representation and storage of information. Here we describe the development of micro-machined silicon microelectrode arrays for unit and local field recordings. The two-dimensional probes with 96 or 64 recording sites provided high-density recording of unit and field activity with minimal tissue displacement or damage. The on-chip active circuit eliminated movement and other artifacts and greatly reduced the weight of the headgear. The precise geometry of the recording tips allowed for the estimation of the spatial location of the recorded neurons and for high-resolution estimation of extracellular current source density. Action potentials could be simultaneously recorded from the soma and dendrites of the same neurons. Silicon technology is a promising approach for high-density, high-resolution sampling of neuronal activity in both basic research and prosthetic devices.}, author = {Jozsef Csicsvari and Henze, Darrell A and Jamieson, Brian G and Harris, Kenneth D and Sirota, Anton M and Bartho, Peter and Wise, Kensall D and Buzsáki, György}, journal = {Journal of Neurophysiology}, number = {2}, pages = {1314 -- 1323}, publisher = {American Physiological Society}, title = {{Massively parallel recording of unit and local field potentials with silicon-based electrodes}}, doi = {10.1152/jn.00116.2003}, volume = {90}, year = {2003}, } @article{3536, abstract = {Genetic engineering of the mouse brain allows investigators to address novel hypotheses in vivo. Because of the paucity of information on the network patterns of the mouse hippocampus, we investigated the electrical patterns in the behaving animal using multisite silicon probes and wire tetrodes. Theta (6-9 Hz) and gamma (40-100 Hz) oscillations were present during exploration and rapid eye movement sleep. Gamma power and theta power were comodulated and gamma power varied as a function of the theta cycle. Pyramidal cells and putative interneurons were phase-locked to theta oscillations. During immobility, consummatory behaviors and slow-wave sleep, sharp waves were present in cornu ammonis region CA1 of the hippocampus stratum radiatum associated with 140-200-Hz “ripples” in the pyramidal cell layer and population burst of CA1 neurons. In the hilus, large-amplitude “dentate spikes” occurred in association with increased discharge of hilar neurons. The amplitude of field patterns was larger in the mouse than in the rat, likely reflecting the higher neuron density in a smaller brain. We suggest that the main hippocampal network patterns are mediated by similar pathways and mechanisms in mouse and rat. }, author = {Buzsáki, György and Buhl, Derek L and Harris, Kenneth D and Jozsef Csicsvari and Czéh, Boldizsár and Morozov, Alexei}, journal = {Neuroscience}, number = {1}, pages = {201 -- 211}, publisher = {Elsevier}, title = {{Hippocampal network patterns of activity in the mouse}}, doi = {10.1016/S0306-4522(02)00669-3}, volume = {116}, year = {2003}, } @article{3543, abstract = {Both neocortical and hippocampal networks organize the firing patterns of their neurons by prominent oscillations during sleep, but the functional role of these rhythms is not well understood. Here, we show a robust correlation of neuronal discharges between the somatosensory cortex and hippocampus on both slow and fine time scales in the mouse and rat. Neuronal bursts in deep cortical layers, associated with sleep spindles and delta waves/slow rhythm, effectively triggered hippocampal discharges related to fast (ripple) oscillations. We hypothesize that oscillation-mediated temporal links coordinate specific information transfer between neocortical and hippocampal cell assemblies. Such a neocortical-hippocampal interplay may be important for memory consolidation.}, author = {Sirota, Anton M and Jozsef Csicsvari and Buhl, Derek L and Buzsáki, György}, journal = {PNAS}, number = {4}, pages = {2065 -- 2069}, publisher = {National Academy of Sciences}, title = {{Communication between neocortex and hippocampus during sleep in rodents}}, doi = {10.1073/pnas.0437938100}, volume = {100}, year = {2003}, } @inproceedings{3556, abstract = {We define the Morse-Smale complex of a Morse function over a 3-manifold as the overlay of the descending and as- cending manifolds of all critical points. In the generic case, its 3-dimensional cells are shaped like crystals and are sepa- rated by quadrangular faces. In this paper, we give a combi- natorial algorithm for constructing such complexes for piece- wise linear data.}, author = {Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio}, pages = {361 -- 370}, publisher = {ACM}, title = {{Morse-Smale complexes for piecewise linear 3-manifolds}}, doi = {10.1145/777792.777846}, year = {2003}, } @inbook{3573, abstract = {Given a finite point set in R, the surface reconstruction problem asks for a surface that passes through many but not necessarily all points. We describe an unambigu- ous definition of such a surface in geometric and topological terms, and sketch a fast algorithm for constructing it. Our solution overcomes past limitations to special point distributions and heuristic design decisions.}, author = {Herbert Edelsbrunner}, booktitle = {Discrete & Computational Geometry}, pages = {379 -- 404}, publisher = {Springer}, title = {{Surface reconstruction by wrapping finite sets in space}}, doi = {10.1007/978-3-642-55566-4_17}, year = {2003}, } @article{3584, abstract = {We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes.}, author = {Edelsbrunner, Herbert and Zomorodian, Afra}, journal = {Homology, Homotopy and Applications}, number = {2}, pages = {19 -- 37}, publisher = {International Press}, title = {{Computing linking numbers of a filtration}}, volume = {5}, year = {2003}, } @article{3593, abstract = {Temporal logics such as Computation Tree Logic (CTL) and Linear Temporal Logic (LTL) have become popular for specifying temporal properties over a wide variety of planning and verification problems. In this paper we work towards building a generalized framework for automated reasoning based on temporal logics. We present a powerful extension of CTL with first-order quantification over the set of reachable states for reasoning about extremal properties of weighted labeled transition systems in general. The proposed logic, which we call Weighted Quantified Computation Tree Logic (WQCTL), captures the essential elements common to the domain of planning and verification problems and can thereby be used as an effective specification language in both domains. We show that in spite of the rich, expressive power of the logic, we are able to evaluate WQCTL formulas in time polynomial in the size of the state space times the length of the formula. Wepresent experimental results on the WQCTL verifier.}, author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P}, journal = {Journal of Automated Reasoning}, number = {2}, pages = {205 -- 232}, publisher = {Springer}, title = {{A branching time temporal framework for quantitative reasoning}}, doi = {10.1023/A:1023217515688}, volume = {30}, year = {2003}, } @article{3618, abstract = {There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals.}, author = {Vines, Timothy H and Nicholas Barton}, journal = {Molecular Ecology}, number = {7}, pages = {1999 -- 2002}, publisher = {Wiley-Blackwell}, title = {{A new approach to detecting mixed families}}, doi = {10.1046/j.1365-294X.2003.01867.x}, volume = {12}, year = {2003}, } @article{3619, abstract = {What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y<1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome.}, author = {Baird, Stuart J and Nicholas Barton and Etheridge, Alison M}, journal = {Theoretical Population Biology}, number = {4}, pages = {451 -- 471}, publisher = {Academic Press}, title = {{The distribution of surviving blocks of an ancestral genome}}, doi = {10.1016/S0040-5809(03)00098-4}, volume = {64}, year = {2003}, } @article{3620, abstract = {Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats.}, author = {Nürnberger, Beate and Hofman, Sebastian and Förg-Brey, Bqruni and Praetzel, Gabriele and Maclean, Alan W and Szymura, Jacek M and Abbott, Catherine M and Nicholas Barton}, journal = {Heredity}, number = {2}, pages = {136 -- 142}, publisher = {Nature Publishing Group}, title = {{A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)}}, doi = {10.1038/sj.hdy.6800291}, volume = {91}, year = {2003}, } @phdthesis{3678, author = {Christoph Lampert}, booktitle = {Bonner Mathematische Schriften}, pages = {1 -- 165}, publisher = {Universität Bonn, Fachbibliothek Mathematik}, title = {{The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric }}, volume = {356}, year = {2003}, } @article{3725, abstract = {The combination of high-resolution atomic force microscopy (AFM) imaging and single-molecule force-spectroscopy was employed to unfold single bacteriorhodopsins (BR) from native purple membrane patches at various physiologically relevant temperatures. The unfolding spectra reveal detailed insight into the stability of individual structural elements of BR against mechanical unfolding. Intermittent states in the unfolding process are associated with the stepwise unfolding of alpha-helices, whereas other states are associated with the unfolding of polypeptide loops connecting the alpha-helices. It was found that the unfolding forces of the secondary structures considerably decreased upon increasing the temperature from 8 to 52°C. Associated with this effect, the probability of individual unfolding pathways of BR was significantly influenced by the temperature. At lower temperatures, transmembrane alpha-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, whereas they predominantly unfolded collectively at elevated temperatures. This suggests that increasing the temperature decreases the mechanical stability of secondary structural elements and changes molecular interactions between secondary structures, thereby forcing them to act as grouped structures.}, author = {Harald Janovjak and Kessler, Max and Oesterhelt, Dieter and Gaub, Hermann and Mueller, Daniel J}, journal = {EMBO Journal}, number = {19}, pages = {5220 -- 5229}, publisher = {Wiley-Blackwell}, title = {{Unfolding pathways of native bacteriorhodopsin depend on temperature}}, doi = {10.1093/emboj/cdg509}, volume = {22}, year = {2003}, }